diff --git a/web/templates/hpai/export.js b/web/templates/hpai/export.js new file mode 100644 index 00000000..592ad2d1 --- /dev/null +++ b/web/templates/hpai/export.js @@ -0,0 +1,2 @@ +// A dictionary of possible export formats +export default {}; diff --git a/web/templates/hpai/schema.json b/web/templates/hpai/schema.json new file mode 100644 index 00000000..ca465096 --- /dev/null +++ b/web/templates/hpai/schema.json @@ -0,0 +1,49098 @@ +{ + "name": "Mpox", + "description": "The HPAI specification was developed by the Public Health Alliance for Genomic Epidemiology (PHA4GE) to better enable harmonization of highly pathogenic avian influenza genomic surveillance contextual data. The specification is intended to support H5N1 monitoring, and provides standardized, ontology-based fields and terms for samples, sequences, and bioinformatics analysis.", + "id": "https://example.com/hpai", + "version": "4.3.3", + "prefixes": { + "linkml": { + "prefix_prefix": "linkml", + "prefix_reference": "https://w3id.org/linkml/" + }, + "GENEPIO": { + "prefix_prefix": "GENEPIO", + "prefix_reference": "http://purl.obolibrary.org/obo/GENEPIO_" + }, + "xsd": { + "prefix_prefix": "xsd", + "prefix_reference": "http://www.w3.org/2001/XMLSchema#" + }, + "shex": { + "prefix_prefix": "shex", + "prefix_reference": "http://www.w3.org/ns/shex#" + }, + "schema": { + "prefix_prefix": "schema", + "prefix_reference": "http://schema.org/" + } + }, + "default_prefix": "https://example.com/hpai/", + "types": { + "WhitespaceMinimizedString": { + "name": "WhitespaceMinimizedString", + "description": "A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).", + "from_schema": "https://example.com/hpai", + "typeof": "string", + "base": "str", + "uri": "xsd:token" + }, + "Provenance": { + "name": "Provenance", + "description": "A field containing a DataHarmonizer versioning marker. It is issued by DataHarmonizer when validation is applied to a given row of data.", + "from_schema": "https://example.com/hpai", + "typeof": "string", + "base": "str", + "uri": "xsd:token" + }, + "string": { + "name": "string", + "description": "A character string", + "notes": [ + "In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"string\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:Text" + ], + "base": "str", + "uri": "xsd:string" + }, + "integer": { + "name": "integer", + "description": "An integer", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"integer\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:Integer" + ], + "base": "int", + "uri": "xsd:integer" + }, + "boolean": { + "name": "boolean", + "description": "A binary (true or false) value", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"boolean\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:Boolean" + ], + "base": "Bool", + "uri": "xsd:boolean", + "repr": "bool" + }, + "float": { + "name": "float", + "description": "A real number that conforms to the xsd:float specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"float\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:Float" + ], + "base": "float", + "uri": "xsd:float" + }, + "double": { + "name": "double", + "description": "A real number that conforms to the xsd:double specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"double\"." + ], + "from_schema": "https://example.com/hpai", + "close_mappings": [ + "schema:Float" + ], + "base": "float", + "uri": "xsd:double" + }, + "decimal": { + "name": "decimal", + "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"decimal\"." + ], + "from_schema": "https://example.com/hpai", + "broad_mappings": [ + "schema:Number" + ], + "base": "Decimal", + "uri": "xsd:decimal" + }, + "time": { + "name": "time", + "description": "A time object represents a (local) time of day, independent of any particular day", + "notes": [ + "URI is dateTime because OWL reasoners do not work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"time\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:Time" + ], + "base": "XSDTime", + "uri": "xsd:time", + "repr": "str" + }, + "date": { + "name": "date", + "description": "a date (year, month and day) in an idealized calendar", + "notes": [ + "URI is dateTime because OWL reasoners don't work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:Date" + ], + "base": "XSDDate", + "uri": "xsd:date", + "repr": "str" + }, + "datetime": { + "name": "datetime", + "description": "The combination of a date and time", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"datetime\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:DateTime" + ], + "base": "XSDDateTime", + "uri": "xsd:dateTime", + "repr": "str" + }, + "date_or_datetime": { + "name": "date_or_datetime", + "description": "Either a date or a datetime", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date_or_datetime\"." + ], + "from_schema": "https://example.com/hpai", + "base": "str", + "uri": "linkml:DateOrDatetime", + "repr": "str" + }, + "uriorcurie": { + "name": "uriorcurie", + "description": "a URI or a CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uriorcurie\"." + ], + "from_schema": "https://example.com/hpai", + "base": "URIorCURIE", + "uri": "xsd:anyURI", + "repr": "str" + }, + "curie": { + "name": "curie", + "conforms_to": "https://www.w3.org/TR/curie/", + "description": "a compact URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"curie\"." + ], + "comments": [ + "in RDF serializations this MUST be expanded to a URI", + "in non-RDF serializations MAY be serialized as the compact representation" + ], + "from_schema": "https://example.com/hpai", + "base": "Curie", + "uri": "xsd:string", + "repr": "str" + }, + "uri": { + "name": "uri", + "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", + "description": "a complete URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uri\"." + ], + "comments": [ + "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" + ], + "from_schema": "https://example.com/hpai", + "close_mappings": [ + "schema:URL" + ], + "base": "URI", + "uri": "xsd:anyURI", + "repr": "str" + }, + "ncname": { + "name": "ncname", + "description": "Prefix part of CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"ncname\"." + ], + "from_schema": "https://example.com/hpai", + "base": "NCName", + "uri": "xsd:string", + "repr": "str" + }, + "objectidentifier": { + "name": "objectidentifier", + "description": "A URI or CURIE that represents an object in the model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"objectidentifier\"." + ], + "comments": [ + "Used for inheritance and type checking" + ], + "from_schema": "https://example.com/hpai", + "base": "ElementIdentifier", + "uri": "shex:iri", + "repr": "str" + }, + "nodeidentifier": { + "name": "nodeidentifier", + "description": "A URI, CURIE or BNODE that represents a node in a model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"nodeidentifier\"." + ], + "from_schema": "https://example.com/hpai", + "base": "NodeIdentifier", + "uri": "shex:nonLiteral", + "repr": "str" + }, + "jsonpointer": { + "name": "jsonpointer", + "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", + "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpointer\"." + ], + "from_schema": "https://example.com/hpai", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "jsonpath": { + "name": "jsonpath", + "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", + "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpath\"." + ], + "from_schema": "https://example.com/hpai", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "sparqlpath": { + "name": "sparqlpath", + "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", + "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"sparqlpath\"." + ], + "from_schema": "https://example.com/hpai", + "base": "str", + "uri": "xsd:string", + "repr": "str" + } + }, + "enums": { + "NullValue": { + "name": "NullValue", + "title": "null value", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Not Applicable [GENEPIO:0001619]": { + "text": "Not Applicable [GENEPIO:0001619]", + "description": "A categorical choice recorded when a datum does not apply to a given context.", + "meaning": "GENEPIO:0001619" + }, + "Missing [GENEPIO:0001618]": { + "text": "Missing [GENEPIO:0001618]", + "description": "A categorical choice recorded when a datum is not included for an unknown reason.", + "meaning": "GENEPIO:0001618" + }, + "Not Collected [GENEPIO:0001620]": { + "text": "Not Collected [GENEPIO:0001620]", + "description": "A categorical choice recorded when a datum was not measured or collected.", + "meaning": "GENEPIO:0001620" + }, + "Not Provided [GENEPIO:0001668]": { + "text": "Not Provided [GENEPIO:0001668]", + "description": "A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage.", + "meaning": "GENEPIO:0001668" + }, + "Restricted Access [GENEPIO:0001810]": { + "text": "Restricted Access [GENEPIO:0001810]", + "description": "A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns.", + "meaning": "GENEPIO:0001810" + } + } + }, + "OrganismMenu": { + "name": "OrganismMenu", + "title": "organism menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Influenza A virus [NCBITaxon:11320]": { + "text": "Influenza A virus [NCBITaxon:11320]", + "meaning": "NCBITaxon:11320" + } + } + }, + "InfluenzaSubtypeMenu": { + "name": "InfluenzaSubtypeMenu", + "title": "influenza_subtype menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "H5N1 subtype (Influenza A virus) [NCBITaxon:102793]": { + "text": "H5N1 subtype (Influenza A virus) [NCBITaxon:102793]", + "meaning": "NCBITaxon:102793" + } + } + }, + "InfluenzaSubtypingSchemeNameMenu": { + "name": "InfluenzaSubtypingSchemeNameMenu", + "title": "influenza_subtyping_scheme_name menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Tripartite Influenza A scheme [GENEPIO:0101121]": { + "text": "Tripartite Influenza A scheme [GENEPIO:0101121]", + "meaning": "GENEPIO:0101121" + }, + "USDA GenoFLU scheme [GENEPIO:0101122]": { + "text": "USDA GenoFLU scheme [GENEPIO:0101122]", + "meaning": "GENEPIO:0101122" + } + } + }, + "TaxonomicIdentificationProcessMenu": { + "name": "TaxonomicIdentificationProcessMenu", + "title": "taxonomic_identification_process menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Whole genome sequencing assay [OBI:0002117]": { + "text": "Whole genome sequencing assay [OBI:0002117]", + "description": "A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.", + "meaning": "OBI:0002117" + }, + "Whole metagenome sequencing assay [OBI:0002623]": { + "text": "Whole metagenome sequencing assay [OBI:0002623]", + "description": "A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.", + "meaning": "OBI:0002623" + }, + "16S ribosomal gene sequencing assay [OBI:0002763]": { + "text": "16S ribosomal gene sequencing assay [OBI:0002763]", + "description": "An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample.", + "meaning": "OBI:0002763" + }, + "PCR assay [OBI:0002740]": { + "text": "PCR assay [OBI:0002740]", + "description": "An organism identification assay that is based on PCR.", + "meaning": "OBI:0002740" + }, + "Comparative phenotypic assessment [OBI:0001546]": { + "text": "Comparative phenotypic assessment [OBI:0001546]", + "description": "Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference", + "meaning": "OBI:0001546" + } + } + }, + "SampleCollectionTimeOfDayMenu": { + "name": "SampleCollectionTimeOfDayMenu", + "title": "sample_collection_time_of_day menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Morning [NCIT:C64934]": { + "text": "Morning [NCIT:C64934]", + "description": "The time period between dawn and noon.", + "meaning": "NCIT:C64934" + }, + "Afternoon [NCIT:C64935]": { + "text": "Afternoon [NCIT:C64935]", + "description": "The time period between noon and sunset.", + "meaning": "NCIT:C64935" + }, + "Evening [NCIT:C64936]": { + "text": "Evening [NCIT:C64936]", + "description": "The time period between late afternoon and bedtime.", + "meaning": "NCIT:C64936" + }, + "Night [NCIT:C65001]": { + "text": "Night [NCIT:C65001]", + "description": "The time in every 24 hour period when it is dark.", + "meaning": "NCIT:C65001" + } + } + }, + "SampleCollectionDurationUnitMenu": { + "name": "SampleCollectionDurationUnitMenu", + "title": "sample_collection_duration_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Second [UO:0000010]": { + "text": "Second [UO:0000010]", + "description": "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.", + "meaning": "UO:0000010" + }, + "Minute [UO:0000031]": { + "text": "Minute [UO:0000031]", + "description": "A time unit which is equal to 60 seconds.", + "meaning": "UO:0000031" + }, + "Hour [UO:0000032]": { + "text": "Hour [UO:0000032]", + "description": "A time unit which is equal to 60 minutes.", + "meaning": "UO:0000032" + }, + "Day [UO:0000033]": { + "text": "Day [UO:0000033]", + "description": "A time unit which is equal to 24 hours.", + "meaning": "UO:0000033" + }, + "Week [UO:0000034]": { + "text": "Week [UO:0000034]", + "description": "A time unit which is equal to 7 days.", + "meaning": "UO:0000034" + }, + "Month [UO:0000035]": { + "text": "Month [UO:0000035]", + "description": "A time unit which is equal to approximately 4-4.5 weeks or 28-31 days.", + "meaning": "UO:0000035" + }, + "Year [UO:0000036]": { + "text": "Year [UO:0000036]", + "description": "A time unit which is equal to 365 days, or 366 days during a leap year.", + "meaning": "UO:0000036" + } + } + }, + "FoodProductMenu": { + "name": "FoodProductMenu", + "title": "food_product menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Animal feed [ENVO:02000047]": { + "text": "Animal feed [ENVO:02000047]", + "description": "Food material which can be used to meet nutritional requirements of animals, particularly livestock such as cattle, goats, sheep, horses, chickens and pigs.", + "meaning": "ENVO:02000047" + }, + "Blood meal [FOODON:00001564]": { + "text": "Blood meal [FOODON:00001564]", + "description": "Blood meal is a dry, inert powder made from blood used as a high-nitrogen organic fertilizer and a high protein animal feed.", + "meaning": "FOODON:00001564", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Bone meal [ENVO:02000054]": { + "text": "Bone meal [ENVO:02000054]", + "description": "A mixture of crushed and coarsely ground bones that is used as an organic fertilizer for plants and formerly in animal feed.", + "meaning": "ENVO:02000054", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Brassica carinata meal [FOODON:00004310]": { + "text": "Brassica carinata meal [FOODON:00004310]", + "description": "A meal that is a co-product produced after the extraction of oil from the seed of the Ethiopian mustard plant (Brassica carinata).", + "meaning": "FOODON:00004310", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Canola meal [FOODON:00002694]": { + "text": "Canola meal [FOODON:00002694]", + "description": "Canola meal is an oilseed meal made from canola grain. Canola meal is a by-product of the oil crushing process.", + "meaning": "FOODON:00002694", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Compound feed premix [FOODON:00004323]": { + "text": "Compound feed premix [FOODON:00004323]", + "description": "A formula mixture of micronutrients that is used as a component in compound feed.", + "meaning": "FOODON:00004323", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Compound feed premix (medicated) [FOODON:00004324]": { + "text": "Compound feed premix (medicated) [FOODON:00004324]", + "description": "A compound feed premix in which medicinal substance has been added.", + "meaning": "FOODON:00004324", + "is_a": "Compound feed premix [FOODON:00004323]" + }, + "Feather meal [FOODON:00003927]": { + "text": "Feather meal [FOODON:00003927]", + "description": "A by product of processing poultry which is made from poultry feathers by partially grinding them under elevated heat and pressure, and then grinding and drying.", + "meaning": "FOODON:00003927", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Fish meal [FOODON:03301620]": { + "text": "Fish meal [FOODON:03301620]", + "description": "Fish meal is primarily used as a protein supplement in compound feed. As of 2010, about 56% of fish meal was used to feed farmed fish, about 20% was used in pig feed, about 12% in poultry feed, and about 12% in other uses, which included fertilizer.", + "meaning": "FOODON:03301620", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Lay ration [FOODON:00004286]": { + "text": "Lay ration [FOODON:00004286]", + "description": "Food formulated for the laying hens to increase egg production and egg shell quality.", + "meaning": "FOODON:00004286", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Meat and bone meal [FOODON:00002738]": { + "text": "Meat and bone meal [FOODON:00002738]", + "description": "Meat and bone meal (MBM) is a product of the rendering industry. It is typically about 48–52% protein, 33–35% ash, 8–12% fat, and 4–7% water. It is primarily used in the formulation of animal feed to improve the amino acid profile of the feed.", + "meaning": "FOODON:00002738", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Meat meal [FOODON:00004282]": { + "text": "Meat meal [FOODON:00004282]", + "description": "A meal that is obtained by cooking, defatting, sterilizing, grinding, and sifting by-products of an animal.", + "meaning": "FOODON:00004282", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Pet food [FOODON:00002682]": { + "text": "Pet food [FOODON:00002682]", + "description": "Pet food is plant or animal material intended for consumption by pets.", + "meaning": "FOODON:00002682", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Soybean meal [FOODON:03302757]": { + "text": "Soybean meal [FOODON:03302757]", + "description": "A type of ground protein-rich residue from the production of soybean oil used chiefly in animal feeds, in adhesives and plastics, in making synthetic protein fibers, and in fermentation media (as for the production of antibiotics).", + "meaning": "FOODON:03302757", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Animal feed ingredient [FOODON:00004322]": { + "text": "Animal feed ingredient [FOODON:00004322]", + "description": "An ingredient that is used in the preparation of animal feed.", + "meaning": "FOODON:00004322" + }, + "Dairy food product [FOODON:00001256]": { + "text": "Dairy food product [FOODON:00001256]", + "description": "A dairy food product has mammilian milk or a milk component as an ingredient.", + "meaning": "FOODON:00001256" + }, + "Cheese block (whole or parts) [FOODON:03000287]": { + "text": "Cheese block (whole or parts) [FOODON:03000287]", + "description": "A whole cheese block or some substance made from a block of processed cheese.", + "meaning": "FOODON:03000287", + "is_a": "Dairy food product [FOODON:00001256]" + }, + "Cow skim milk (powdered) [FOODON:03310016]": { + "text": "Cow skim milk (powdered) [FOODON:03310016]", + "description": "Milk powder that is obtained by removing all of the water from pasteurized skim milk.", + "meaning": "FOODON:03310016", + "is_a": "Dairy food product [FOODON:00001256]" + }, + "Milk [UBERON:0001913]": { + "text": "Milk [UBERON:0001913]", + "description": "An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.", + "meaning": "UBERON:0001913", + "is_a": "Dairy food product [FOODON:00001256]" + }, + "Meat, poultry and fish (organizational term)": { + "text": "Meat, poultry and fish (organizational term)" + }, + "Beef (ground or minced) [FOODON:00001282]": { + "text": "Beef (ground or minced) [FOODON:00001282]", + "description": "A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese.", + "meaning": "FOODON:00001282", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Beef (ground or minced, boneless) [FOODON:03000412]": { + "text": "Beef (ground or minced, boneless) [FOODON:03000412]", + "meaning": "FOODON:03000412", + "is_a": "Beef (ground or minced) [FOODON:00001282]" + }, + "Beef (ground or minced, extra lean) [FOODON:03000398]": { + "text": "Beef (ground or minced, extra lean) [FOODON:03000398]", + "meaning": "FOODON:03000398", + "is_a": "Beef (ground or minced) [FOODON:00001282]" + }, + "Beef (ground or minced, lean) [FOODON:03000394]": { + "text": "Beef (ground or minced, lean) [FOODON:03000394]", + "meaning": "FOODON:03000394", + "is_a": "Beef (ground or minced) [FOODON:00001282]" + }, + "Beef (ground or minced, medium) [FOODON:03000402]": { + "text": "Beef (ground or minced, medium) [FOODON:03000402]", + "meaning": "FOODON:03000402", + "is_a": "Beef (ground or minced) [FOODON:00001282]" + }, + "Beef (ground or minced, regular) [FOODON:03000406]": { + "text": "Beef (ground or minced, regular) [FOODON:03000406]", + "meaning": "FOODON:03000406", + "is_a": "Beef (ground or minced) [FOODON:00001282]" + }, + "Beef (ground or minced, sirloin) [FOODON:03000408]": { + "text": "Beef (ground or minced, sirloin) [FOODON:03000408]", + "meaning": "FOODON:03000408", + "is_a": "Beef (ground or minced) [FOODON:00001282]" + }, + "Beef hamburger (dish) [FOODON:00002737]": { + "text": "Beef hamburger (dish) [FOODON:00002737]", + "description": "A hamburger (short: burger) is a sandwich consisting of one or more cooked patties of ground meat, usually beef, placed inside a sliced bread roll or bun. The patty may be pan fried, grilled, or flame broiled.", + "meaning": "FOODON:00002737", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Beef shoulder [FOODON:03000377]": { + "text": "Beef shoulder [FOODON:03000377]", + "meaning": "FOODON:03000377", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Beef shoulder chop [FOODON:03000387]": { + "text": "Beef shoulder chop [FOODON:03000387]", + "description": "Meat chop from the shoulder region of beef.", + "meaning": "FOODON:03000387", + "is_a": "Beef shoulder [FOODON:03000377]" + }, + "Beef sirloin chop [FOODON:03000389]": { + "text": "Beef sirloin chop [FOODON:03000389]", + "description": "Meat chop from the sirloin region of beef", + "meaning": "FOODON:03000389", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Beef stew chunk [FOODON:00004288]": { + "text": "Beef stew chunk [FOODON:00004288]", + "description": "A chunk of beef used as an ingredient in making stew.", + "meaning": "FOODON:00004288", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Beef tenderloin [FOODON:00003302]": { + "text": "Beef tenderloin [FOODON:00003302]", + "description": "A cut of beef corresponding to the psoas major muscle, which is very tender.", + "meaning": "FOODON:00003302", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Beef (whole cut or parts) [FOODON:03000333]": { + "text": "Beef (whole cut or parts) [FOODON:03000333]", + "meaning": "FOODON:03000333", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Brisket [FOODON:03530020]": { + "text": "Brisket [FOODON:03530020]", + "description": "A cut of meat from the breast or lower chest of beef or veal.", + "meaning": "FOODON:03530020", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Chicken breast [FOODON:00002703]": { + "text": "Chicken breast [FOODON:00002703]", + "description": "Chicken breast consists mainly of the breast meat portion of a chicken, and may or may not include connected bone (boneless versus \"with bone\") and skin.", + "meaning": "FOODON:00002703", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Chicken breast (back off) [FOODON:03000385]": { + "text": "Chicken breast (back off) [FOODON:03000385]", + "description": "A chicken breast with its backbone removed.", + "meaning": "FOODON:03000385", + "is_a": "Chicken breast [FOODON:00002703]" + }, + "Chicken breast (skinless) [FOODON:00003332]": { + "text": "Chicken breast (skinless) [FOODON:00003332]", + "meaning": "FOODON:00003332", + "is_a": "Chicken breast [FOODON:00002703]" + }, + "Chicken breast (with skin) [FOODON:03000374]": { + "text": "Chicken breast (with skin) [FOODON:03000374]", + "meaning": "FOODON:03000374", + "is_a": "Chicken breast [FOODON:00002703]" + }, + "Chicken breast (skinless, boneless) [FOODON:00003364]": { + "text": "Chicken breast (skinless, boneless) [FOODON:00003364]", + "meaning": "FOODON:00003364", + "is_a": "Chicken breast [FOODON:00002703]" + }, + "Chicken breast cutlet [FOODON:00004308]": { + "text": "Chicken breast cutlet [FOODON:00004308]", + "description": "A cutlet made from chicken breast.", + "meaning": "FOODON:00004308", + "is_a": "Chicken breast [FOODON:00002703]" + }, + "Chicken drumstick [FOODON:00002716]": { + "text": "Chicken drumstick [FOODON:00002716]", + "description": "The segment of a chicken's leg between the thigh and tarsus (ankle).", + "meaning": "FOODON:00002716", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Chicken drumstick (skinless) [FOODON:03000366]": { + "text": "Chicken drumstick (skinless) [FOODON:03000366]", + "meaning": "FOODON:03000366", + "is_a": "Chicken drumstick [FOODON:00002716]" + }, + "Chicken drumstick (with skin) [FOODON:03000368]": { + "text": "Chicken drumstick (with skin) [FOODON:03000368]", + "meaning": "FOODON:03000368", + "is_a": "Chicken drumstick [FOODON:00002716]" + }, + "Chicken meat [FOODON:00001040]": { + "text": "Chicken meat [FOODON:00001040]", + "meaning": "FOODON:00001040", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Chicken meat (ground or minced) [FOODON:03311826]": { + "text": "Chicken meat (ground or minced) [FOODON:03311826]", + "description": "A food product made of ground or minced chicken meat.", + "meaning": "FOODON:03311826", + "is_a": "Chicken meat [FOODON:00001040]" + }, + "Chicken meat (ground or minced, lean) [FOODON:03000392]": { + "text": "Chicken meat (ground or minced, lean) [FOODON:03000392]", + "description": "A food product made of lean, ground or minced chicken meat.", + "meaning": "FOODON:03000392", + "is_a": "Chicken meat (ground or minced) [FOODON:03311826]" + }, + "Chicken meat (ground or minced, extra lean) [FOODON:03000396]": { + "text": "Chicken meat (ground or minced, extra lean) [FOODON:03000396]", + "description": "A food product made of extra lean, ground or minced chicken meat.", + "meaning": "FOODON:03000396", + "is_a": "Chicken meat (ground or minced) [FOODON:03311826]" + }, + "Chicken meat (ground or minced, medium) [FOODON:03000400]": { + "text": "Chicken meat (ground or minced, medium) [FOODON:03000400]", + "description": "A food product made of medium, ground or minced chicken meat.", + "meaning": "FOODON:03000400", + "is_a": "Chicken meat (ground or minced) [FOODON:03311826]" + }, + "Chicken meat (ground or minced, regular) [FOODON:03000404]": { + "text": "Chicken meat (ground or minced, regular) [FOODON:03000404]", + "description": "A food product made of regular, ground or minced chicken meat.", + "meaning": "FOODON:03000404", + "is_a": "Chicken meat (ground or minced) [FOODON:03311826]" + }, + "Chicken meat (ground or minced, boneless) [FOODON:03000410]": { + "text": "Chicken meat (ground or minced, boneless) [FOODON:03000410]", + "meaning": "FOODON:03000410", + "is_a": "Chicken meat (ground or minced) [FOODON:03311826]" + }, + "Chicken nugget [FOODON:00002672]": { + "text": "Chicken nugget [FOODON:00002672]", + "description": "A chicken nugget is a chicken product made from chicken meat that is breaded or battered, then deep-fried or baked.", + "meaning": "FOODON:00002672", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Chicken thigh [FOODON:02020219]": { + "text": "Chicken thigh [FOODON:02020219]", + "description": "A whole thigh that derives from a chicken.", + "meaning": "FOODON:02020219", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Chicken thigh (skinless) [FOODON:00003331]": { + "text": "Chicken thigh (skinless) [FOODON:00003331]", + "description": "A chicken thigh after the skin has been removed.", + "meaning": "FOODON:00003331", + "is_a": "Chicken thigh [FOODON:02020219]" + }, + "Chicken thigh (skinless, with bone) [FOODON:02020227]": { + "text": "Chicken thigh (skinless, with bone) [FOODON:02020227]", + "description": "A chicken thigh that is skinless and contains bone element.", + "meaning": "FOODON:02020227", + "is_a": "Chicken thigh [FOODON:02020219]" + }, + "Chicken thigh (skinless, boneless) [FOODON:03000417]": { + "text": "Chicken thigh (skinless, boneless) [FOODON:03000417]", + "meaning": "FOODON:03000417", + "is_a": "Chicken thigh [FOODON:02020219]" + }, + "Chicken upper thigh [FOODON:03000381]": { + "text": "Chicken upper thigh [FOODON:03000381]", + "description": "Meat from the upper thigh of a chicken.", + "meaning": "FOODON:03000381", + "is_a": "Chicken thigh (skinless, boneless) [FOODON:03000417]" + }, + "Chicken thigh (with skin) [FOODON:00003330]": { + "text": "Chicken thigh (with skin) [FOODON:00003330]", + "meaning": "FOODON:00003330", + "is_a": "Chicken thigh [FOODON:02020219]" + }, + "Chicken thigh (with skin, with bone) [FOODON_00003363]": { + "text": "Chicken thigh (with skin, with bone) [FOODON_00003363]", + "description": "A chicken thigh that contains skin and bone material.", + "meaning": "FOODON:00003363", + "is_a": "Chicken thigh [FOODON:02020219]" + }, + "Chicken wing [FOODON:00002674]": { + "text": "Chicken wing [FOODON:00002674]", + "description": "A whole wing that derives from a chicken.", + "meaning": "FOODON:00002674", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Fish food product [FOODON:00001248]": { + "text": "Fish food product [FOODON:00001248]", + "description": "A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins).", + "meaning": "FOODON:00001248", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Fish steak [FOODON:00002986]": { + "text": "Fish steak [FOODON:00002986]", + "description": "A fish steak, alternatively known as a fish cutlet, is a cut of fish which is cut perpendicular to the spine and can either include the bones or be boneless.", + "meaning": "FOODON:00002986", + "is_a": "Fish food product [FOODON:00001248]" + }, + "Ham food product [FOODON:00002502]": { + "text": "Ham food product [FOODON:00002502]", + "description": "Ham is pork from a leg cut that has been preserved by wet or dry curing, with or without smoking. As a processed meat, the term \"ham\" includes both whole cuts of meat and ones that have been mechanically formed.", + "meaning": "FOODON:00002502", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Head cheese [FOODON:03315658]": { + "text": "Head cheese [FOODON:03315658]", + "description": "Head cheese is a cold cut that originated in Europe. Head cheese is not a dairy cheese, but a terrine or meat jelly made with flesh from the head of a calf or pig, or less commonly a sheep or cow, and often set in aspic. A version pickled with vinegar is known as souse.", + "meaning": "FOODON:03315658", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Lamb [FOODON:03411669]": { + "text": "Lamb [FOODON:03411669]", + "description": "A whole lamb or some material processed from a lamb.", + "meaning": "FOODON:03411669", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Meat strip [FOODON:00004285]": { + "text": "Meat strip [FOODON:00004285]", + "description": "A cut of meat which is long, narrow and boneless.", + "meaning": "FOODON:00004285", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Mutton [FOODON:00002912]": { + "text": "Mutton [FOODON:00002912]", + "description": "The meat of an adult sheep is mutton, a term only used for the meat, not the living animals.", + "meaning": "FOODON:00002912", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pork chop [FOODON:00001049]": { + "text": "Pork chop [FOODON:00001049]", + "description": "A cut of meat (a meat chop) cut perpendicularly to the spine of the pig and usually containing a rib or part of a vertebra, served as an individual portion.", + "meaning": "FOODON:00001049", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pork meat (ground or minced) [FOODON:03309969]": { + "text": "Pork meat (ground or minced) [FOODON:03309969]", + "description": "Meat from a pig that has been ground or minced.", + "meaning": "FOODON:03309969", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pork meat (ground or minced, boneless) [FOODON:03000413]": { + "text": "Pork meat (ground or minced, boneless) [FOODON:03000413]", + "meaning": "FOODON:03000413", + "is_a": "Pork meat (ground or minced) [FOODON:03309969]" + }, + "Pork meat (ground or minced, extra lean) [FOODON:03000399]": { + "text": "Pork meat (ground or minced, extra lean) [FOODON:03000399]", + "description": "A food product made of extra-lean, ground or minced pork meat.", + "meaning": "FOODON:03000399", + "is_a": "Pork meat (ground or minced) [FOODON:03309969]" + }, + "Pork meat (ground or minced, lean) [FOODON:03000395]": { + "text": "Pork meat (ground or minced, lean) [FOODON:03000395]", + "description": "A food product made of lean, ground or minced pork meat.", + "meaning": "FOODON:03000395", + "is_a": "Pork meat (ground or minced) [FOODON:03309969]" + }, + "Pork meat (ground or minced, medium) [FOODON:03000403]": { + "text": "Pork meat (ground or minced, medium) [FOODON:03000403]", + "description": "A food product made of medium, ground or minced pork meat.", + "meaning": "FOODON:03000403", + "is_a": "Pork meat (ground or minced) [FOODON:03309969]" + }, + "Pork meat (ground or minced, regular) [FOODON:03000407]": { + "text": "Pork meat (ground or minced, regular) [FOODON:03000407]", + "description": "A food product made of regular, ground or minced pork meat.", + "meaning": "FOODON:03000407", + "is_a": "Pork meat (ground or minced) [FOODON:03309969]" + }, + "Pork meat (ground or minced, Sirloin) [FOODON:03000409]": { + "text": "Pork meat (ground or minced, Sirloin) [FOODON:03000409]", + "description": "Ground or minced pork meat that comes from the sirloin region.", + "meaning": "FOODON:03000409", + "is_a": "Pork meat (ground or minced) [FOODON:03309969]" + }, + "Pork shoulder [FOODON:03000376]": { + "text": "Pork shoulder [FOODON:03000376]", + "meaning": "FOODON:03000376", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pork shoulder chop [FOODON:03000388]": { + "text": "Pork shoulder chop [FOODON:03000388]", + "description": "Meat chop from the blade roast of pork.", + "meaning": "FOODON:03000388", + "is_a": "Pork shoulder [FOODON:03000376]" + }, + "Pork sirloin chop [FOODON:03000390]": { + "text": "Pork sirloin chop [FOODON:03000390]", + "meaning": "FOODON:03000390", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pork steak [FOODON:00003148]": { + "text": "Pork steak [FOODON:00003148]", + "meaning": "FOODON:00003148", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pork tenderloin [FOODON:03000416]": { + "text": "Pork tenderloin [FOODON:03000416]", + "meaning": "FOODON:03000416", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Poultry meat [FOODON:03315883]": { + "text": "Poultry meat [FOODON:03315883]", + "description": "Any meat from one or more poultry birds.", + "meaning": "FOODON:03315883", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Leg (poultry meat cut) [FOODON:03530159]": { + "text": "Leg (poultry meat cut) [FOODON:03530159]", + "description": "The leg cut of a poultry bird.", + "meaning": "FOODON:03530159", + "is_a": "Poultry meat [FOODON:03315883]" + }, + "Poultry drumstick [FOODON:00003469]": { + "text": "Poultry drumstick [FOODON:00003469]", + "description": "The calf part of a poultry hindleg (hindlimb zeugopod)", + "meaning": "FOODON:00003469", + "is_a": "Leg (poultry meat cut) [FOODON:03530159]" + }, + "Neck (poultry meat cut) [FOODON:03530294]": { + "text": "Neck (poultry meat cut) [FOODON:03530294]", + "description": "The neck cut of a poultry bird.", + "meaning": "FOODON:03530294", + "is_a": "Poultry meat [FOODON:03315883]" + }, + "Thigh (poultry meat cut) [FOODON:03530160]": { + "text": "Thigh (poultry meat cut) [FOODON:03530160]", + "description": "The thigh cut of a poultry bird.", + "meaning": "FOODON:03530160", + "is_a": "Poultry meat [FOODON:03315883]" + }, + "Wing (poultry meat cut) [FOODON:03530157]": { + "text": "Wing (poultry meat cut) [FOODON:03530157]", + "description": "The wing cut of a poultry bird.", + "meaning": "FOODON:03530157", + "is_a": "Poultry meat [FOODON:03315883]" + }, + "Sausage (whole) [FOODON:03315904]": { + "text": "Sausage (whole) [FOODON:03315904]", + "description": "A food product that is highly seasoned minced meat and is encased in a skin in the shape of a cylinder.", + "meaning": "FOODON:03315904", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pepperoni [FOODON:03311003]": { + "text": "Pepperoni [FOODON:03311003]", + "description": "A highly seasoned and spicy beef or pork sausage.", + "meaning": "FOODON:03311003", + "is_a": "Sausage (whole) [FOODON:03315904]" + }, + "Salami [FOODON:03312067]": { + "text": "Salami [FOODON:03312067]", + "description": "A cured sausage which consists of fermented and air-dried meat, typically pork.", + "meaning": "FOODON:03312067", + "is_a": "Sausage (whole) [FOODON:03315904]" + }, + "Shellfish [FOODON:03411433]": { + "text": "Shellfish [FOODON:03411433]", + "description": "The term shellfish is used both broadly and specifically. For regulatory purposes it is often narrowly defined as filter-feeding molluscs such as clams, mussels, and oyster to the exclusion of crustaceans and all else. Although their shells may differ, all shellfish are invertebrates.", + "meaning": "FOODON:03411433", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Shrimp [FOODON:03301673]": { + "text": "Shrimp [FOODON:03301673]", + "description": "A whole shrimp or some material processed from a shrimp.", + "meaning": "FOODON:03301673", + "is_a": "Shellfish [FOODON:03411433]" + }, + "Scallop [FOODON:03411489]": { + "text": "Scallop [FOODON:03411489]", + "meaning": "FOODON:03411489", + "is_a": "Shellfish [FOODON:03411433]" + }, + "Turkey breast [FOODON:00002690]": { + "text": "Turkey breast [FOODON:00002690]", + "description": "Turkey breast consists mainly of the breast meat portion of a turkey, and may or may not include connected bone (\"deboned or boneless versus bone-in\") and skin.", + "meaning": "FOODON:00002690", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Turkey breast (back off) [FOODON:03000386]": { + "text": "Turkey breast (back off) [FOODON:03000386]", + "description": "A turkey breast with its backbone removed.", + "meaning": "FOODON:03000386", + "is_a": "Turkey breast [FOODON:00002690]" + }, + "Turkey breast (skinless) [FOODON:03000372]": { + "text": "Turkey breast (skinless) [FOODON:03000372]", + "meaning": "FOODON:03000372", + "is_a": "Turkey breast [FOODON:00002690]" + }, + "Turkey breast (skinless, boneless) [FOODON:03000373]": { + "text": "Turkey breast (skinless, boneless) [FOODON:03000373]", + "meaning": "FOODON:03000373", + "is_a": "Turkey breast [FOODON:00002690]" + }, + "Turkey breast (with skin) [FOODON:03000375]": { + "text": "Turkey breast (with skin) [FOODON:03000375]", + "meaning": "FOODON:03000375", + "is_a": "Turkey breast [FOODON:00002690]" + }, + "Turkey drumstick [FOODON:03000365]": { + "text": "Turkey drumstick [FOODON:03000365]", + "meaning": "FOODON:03000365", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Turkey drumstick (skinless) [FOODON:03000367]": { + "text": "Turkey drumstick (skinless) [FOODON:03000367]", + "meaning": "FOODON:03000367", + "is_a": "Turkey drumstick [FOODON:03000365]" + }, + "Turkey drumstick (with skin) [FOODON:03000369]": { + "text": "Turkey drumstick (with skin) [FOODON:03000369]", + "meaning": "FOODON:03000369", + "is_a": "Turkey drumstick [FOODON:03000365]" + }, + "Turkey meat [FOODON:00001286]": { + "text": "Turkey meat [FOODON:00001286]", + "description": "A turkey meat food product is any food product made predominantly of turkey parts.", + "meaning": "FOODON:00001286", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Turkey meat (ground or minced) [FOODON:00002714]": { + "text": "Turkey meat (ground or minced) [FOODON:00002714]", + "description": "A food product made of ground or minced turkey meat.", + "meaning": "FOODON:00002714", + "is_a": "Turkey meat [FOODON:00001286]" + }, + "Turkey meat (ground or minced, lean) [FOODON:03000393]": { + "text": "Turkey meat (ground or minced, lean) [FOODON:03000393]", + "description": "A food product made of lean, ground or minced turkey meat.", + "meaning": "FOODON:03000393", + "is_a": "Turkey meat [FOODON:00001286]" + }, + "Turkey meat (ground or minced, extra lean) [FOODON:03000397]": { + "text": "Turkey meat (ground or minced, extra lean) [FOODON:03000397]", + "description": "A food product made of extra-lean, ground or minced turkey meat.", + "meaning": "FOODON:03000397", + "is_a": "Turkey meat [FOODON:00001286]" + }, + "Turkey meat (ground or minced, medium) [FOODON:03000401]": { + "text": "Turkey meat (ground or minced, medium) [FOODON:03000401]", + "description": "A food product made of medium, ground or minced turkey meat.", + "meaning": "FOODON:03000401", + "is_a": "Turkey meat [FOODON:00001286]" + }, + "Turkey meat (ground or minced, regular) [FOODON:03000405]": { + "text": "Turkey meat (ground or minced, regular) [FOODON:03000405]", + "description": "A food product made of regular, ground or minced turkey meat.", + "meaning": "FOODON:03000405", + "is_a": "Turkey meat [FOODON:00001286]" + }, + "Turkey meat (ground or minced, boneless) [FOODON:03000411]": { + "text": "Turkey meat (ground or minced, boneless) [FOODON:03000411]", + "meaning": "FOODON:03000411", + "is_a": "Turkey meat [FOODON:00001286]" + }, + "Turkey thigh [FOODON:00003325]": { + "text": "Turkey thigh [FOODON:00003325]", + "description": "A thigh poultry cut of turkey.", + "meaning": "FOODON:00003325", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Turkey thigh (skinless) [FOODON:00003329]": { + "text": "Turkey thigh (skinless) [FOODON:00003329]", + "description": "A turkey thigh after the skin has been removed.", + "meaning": "FOODON:00003329", + "is_a": "Turkey thigh [FOODON:00003325]" + }, + "Turkey thigh (skinless, boneless) [FOODON:03000370]": { + "text": "Turkey thigh (skinless, boneless) [FOODON:03000370]", + "meaning": "FOODON:03000370", + "is_a": "Turkey thigh [FOODON:00003325]" + }, + "Turkey thigh (with skin) [FOODON:00003328]": { + "text": "Turkey thigh (with skin) [FOODON:00003328]", + "description": "A turkey thigh that still contains the skin.", + "meaning": "FOODON:00003328", + "is_a": "Turkey thigh [FOODON:00003325]" + }, + "Turkey upper thigh [FOODON:03000382]": { + "text": "Turkey upper thigh [FOODON:03000382]", + "description": "Meat from the upper thigh of a turkey.", + "meaning": "FOODON:03000382", + "is_a": "Turkey thigh (with skin) [FOODON:00003328]" + }, + "Turkey upper thigh (with skin) [FOODON:03000384]": { + "text": "Turkey upper thigh (with skin) [FOODON:03000384]", + "description": "Turkey's upper thigh that contains the skin.", + "meaning": "FOODON:03000384", + "is_a": "Turkey thigh (with skin) [FOODON:00003328]" + }, + "Turkey wing [FOODON:03000371]": { + "text": "Turkey wing [FOODON:03000371]", + "meaning": "FOODON:03000371", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Veal [FOODON:00003083]": { + "text": "Veal [FOODON:00003083]", + "description": "Veal is the meat of calves, in contrast to the beef from older cattle. Veal can be produced from a calf of either sex and any breed; however, most veal comes from young males of dairy breeds which are not used for breeding.", + "meaning": "FOODON:00003083", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Formula fed veal [FOODON:000039111]": { + "text": "Formula fed veal [FOODON:000039111]", + "meaning": "OODON:000039111", + "is_a": "Veal [FOODON:00003083]" + }, + "Grain-fed veal [FOODON:00004280]": { + "text": "Grain-fed veal [FOODON:00004280]", + "description": "Meat from a calf that is raised on grain, hay, or other solid food, in addition to milk", + "meaning": "FOODON:00004280", + "is_a": "Veal [FOODON:00003083]" + } + } + }, + "FoodProductPropertiesMenu": { + "name": "FoodProductPropertiesMenu", + "title": "food_product_properties menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Organic food claim or use [FOODON:03510128]": { + "text": "Organic food claim or use [FOODON:03510128]", + "description": "USA: The 1990 Farm Act specifies that a food labeled 'organic' must meet four requirements: 1) the food must be raised by specified methods to replenish and maintain the fertility of the soil; 2) the food must be certified as having been produced with a nationally approved list of materials and practices; 3) to be eligible for certification at least three years must have elapsed between the first organic harvest and first use of nationally approved materials on land and crops;and 4) organic foods must meet all local, state and federal regulations governing the quality and safety of the food supply. Europe: Foods produced in accordance with Council Regulation (EC) No 834/2007 of 28 June 2007 on organic production and labelling of organic products and repealing Regulation (EEC) No 2092/91. [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2007:189:0001:0023:EN:PDF]", + "meaning": "FOODON:03510128" + }, + "Food (raw) [FOODON:03311126]": { + "text": "Food (raw) [FOODON:03311126]", + "description": "A food material that has not been cooked.", + "meaning": "FOODON:03311126" + }, + "Food (heat treated) [FOODON:03316043]": { + "text": "Food (heat treated) [FOODON:03316043]", + "meaning": "FOODON:03316043" + }, + "Food (pasteurized) [FOODON:00002654]": { + "text": "Food (pasteurized) [FOODON:00002654]", + "meaning": "FOODON:00002654" + }, + "Dairy product (no fat removed, whole)": { + "text": "Dairy product (no fat removed, whole)" + }, + "Dairy product (skimmed, non-fat)": { + "text": "Dairy product (skimmed, non-fat)" + }, + "Dairy product (semi-skimmed, reduced fat, 1%)": { + "text": "Dairy product (semi-skimmed, reduced fat, 1%)" + }, + "Dairy product (semi-skimmed, reduced fat, 2%)": { + "text": "Dairy product (semi-skimmed, reduced fat, 2%)" + } + } + }, + "FoodPackagingMenu": { + "name": "FoodPackagingMenu", + "title": "food_packaging menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Bottle [FOODON:03490214": { + "text": "Bottle [FOODON:03490214", + "description": "A rigid or semirigid container typically of glass or plastic having a comparatively narrow neck or mouth and usually no handle.", + "meaning": "FOODON:03490214" + }, + "Bag [FOODON:03490197]": { + "text": "Bag [FOODON:03490197]", + "description": "According to FSTA Thesaurus Packaging 3.1 package types, includes boil-in bag, carrier bag, flat bag, inner bag, retort pouch, shipping bag, valve bag, and valve sack", + "meaning": "FOODON:03490197" + }, + "Carton [FOODON:03490213]": { + "text": "Carton [FOODON:03490213]", + "meaning": "FOODON:03490213" + } + } + }, + "EnvironmentalSiteMenu": { + "name": "EnvironmentalSiteMenu", + "title": "environmental_site menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Abattoir [ENVO:01000925]": { + "text": "Abattoir [ENVO:01000925]", + "description": "A facility in which non-human animals are slaughtered and processed for human consumption.", + "meaning": "ENVO:01000925" + }, + "Agricultural Field [ENVO:00000114]": { + "text": "Agricultural Field [ENVO:00000114]", + "description": "A field which is located on land and used for agricultural purposes, such as the grazing of livestock or the cultivation of crops.", + "meaning": "ENVO:00000114" + }, + "Animal cage [ENVO:01000922]": { + "text": "Animal cage [ENVO:01000922]", + "description": "A manufactured cage which may be used to confine, contain, or protect an animal.", + "meaning": "ENVO:01000922" + }, + "Artificial wetland [ENVO:03501406]": { + "text": "Artificial wetland [ENVO:03501406]", + "description": "A wetland ecosystem which is constructed to treat municipal or industrial wastewater, greywater or stormwater runoff.", + "meaning": "ENVO:03501406" + }, + "Breeding ground [ENVO:03501441]": { + "text": "Breeding ground [ENVO:03501441]", + "description": "A place where animals breed.", + "meaning": "ENVO:03501441" + }, + "Building [ENVO:00000073]": { + "text": "Building [ENVO:00000073]", + "description": "A permanent walled and roofed construction.", + "meaning": "ENVO:00000073" + }, + "Barn [ENVO:03501257]": { + "text": "Barn [ENVO:03501257]", + "description": "A farm building used for housing livestock, storing machinery or crops etc", + "meaning": "ENVO:03501257" + }, + "Breeder barn [ENVO:03501383]": { + "text": "Breeder barn [ENVO:03501383]", + "description": "A barn where animals are kept for breeding purposes.", + "meaning": "ENVO:03501383", + "is_a": "Barn [ENVO:03501257]" + }, + "Broiler barn [ENVO:03501386]": { + "text": "Broiler barn [ENVO:03501386]", + "description": "A barn where broiler chickens are reared.", + "meaning": "ENVO:03501386", + "is_a": "Barn [ENVO:03501257]" + }, + "Sheep barn [ENVO:03501385]": { + "text": "Sheep barn [ENVO:03501385]", + "description": "A barn where sheep are kept.", + "meaning": "ENVO:03501385", + "is_a": "Barn [ENVO:03501257]" + }, + "Dairy [ENVO:00003862]": { + "text": "Dairy [ENVO:00003862]", + "description": "A dairy is a building in which animal milk is harvested and, optionally, processed for human consumption.", + "meaning": "ENVO:00003862" + }, + "Farm [ENVO:00000078]": { + "text": "Farm [ENVO:00000078]", + "description": "An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein.", + "meaning": "ENVO:00000078" + }, + "Beef farm [ENVO:03501443]": { + "text": "Beef farm [ENVO:03501443]", + "description": "A farm where cows are kept for the purpose of meat production.", + "meaning": "ENVO:03501443", + "is_a": "Farm [ENVO:00000078]" + }, + "Breeder farm [ENVO:03501384]": { + "text": "Breeder farm [ENVO:03501384]", + "description": "A farm where animals are kept for breeding purposes.", + "meaning": "ENVO:03501384", + "is_a": "Farm [ENVO:00000078]" + }, + "Dairy farm [ENVO:03501416]": { + "text": "Dairy farm [ENVO:03501416]", + "description": "A farm where cows are kept for the purpose of producing milk and other dairy products.", + "meaning": "ENVO:03501416", + "is_a": "Farm [ENVO:00000078]" + }, + "Feedlot [ENVO:01000627]": { + "text": "Feedlot [ENVO:01000627]", + "description": "A feedlot is a plot of land on which livestock are fattened for market [URL:http://www.merriam-webster.com/dictionary/feedlot ].", + "meaning": "ENVO:01000627", + "is_a": "Farm [ENVO:00000078]" + }, + "Beef cattle feedlot [ENVO:03501444]": { + "text": "Beef cattle feedlot [ENVO:03501444]", + "description": "A feedlot where beef cattle are kept with a focus on efficient growth and weight gain of the animals.", + "meaning": "ENVO:03501444", + "is_a": "Feedlot [ENVO:01000627]" + }, + "Fish farm [ENVO:00000294]": { + "text": "Fish farm [ENVO:00000294]", + "description": "A facility in which fish are raised commercially in tanks or enclosures, usually for food.", + "meaning": "ENVO:00000294", + "is_a": "Farm [ENVO:00000078]" + }, + "Research farm [ENVO:03501417]": { + "text": "Research farm [ENVO:03501417]", + "description": "A farm which is used for conducting agricultural research.", + "meaning": "ENVO:03501417", + "is_a": "Farm [ENVO:00000078]" + }, + "Central Experimental Farm [GAZ:00004603]": { + "text": "Central Experimental Farm [GAZ:00004603]", + "description": "An agricultural facility, working farm, and research centre of the Research Branch of Agriculture and Agri-Food Canada. This farm is centrally located in and completely surrounded by the City of Ottawa, Ontario, Canada. The CEF is bordered by the Rideau Canal (a National Historic Site as well) to the east, by Baseline Road to the south, by Merivale and Fisher Roads to the west, and Carling Avenue to the north.", + "meaning": "GAZ:00004603", + "is_a": "Farm [ENVO:00000078]" + }, + "Freshwater environment [ENVO:01000306]": { + "text": "Freshwater environment [ENVO:01000306]", + "description": "An aquatic environment which is determined by freshwater.", + "meaning": "ENVO:01000306" + }, + "Hatchery [ENVO:01001873]": { + "text": "Hatchery [ENVO:01001873]", + "description": "A construction in which eggs are hatched under artificial conditions.", + "meaning": "ENVO:01001873" + }, + "Poultry hatchery [ENVO:01001874]": { + "text": "Poultry hatchery [ENVO:01001874]", + "description": "A hatchery in which the eggs of poultry are hatched under artificial conditions", + "meaning": "ENVO:01001874", + "is_a": "Hatchery [ENVO:01001873]" + }, + "Hospital [ENVO:00002173]": { + "text": "Hospital [ENVO:00002173]", + "description": "A building in which health care services are provided by specialized staff and equipment.", + "meaning": "ENVO:00002173" + }, + "Lake [ENVO:00000020]": { + "text": "Lake [ENVO:00000020]", + "description": "A body of water or other liquid of considerable size contained in a depression on a landmass.", + "meaning": "ENVO:00000020" + }, + "Pond [ENVO:00000033]": { + "text": "Pond [ENVO:00000033]", + "description": "A body of water, usually of smaller size than a lake.", + "meaning": "ENVO:00000033" + }, + "Reservoir [ENVO:00000025]": { + "text": "Reservoir [ENVO:00000025]", + "description": "An artificial body of water, often contained by a dam, constructed for the purpose of water storage.", + "meaning": "ENVO:00000025" + }, + "Irrigation reservoir [ENVO:00000450]": { + "text": "Irrigation reservoir [ENVO:00000450]", + "description": "A reservoir constructed for the purpose of providing water for irrigation.", + "meaning": "ENVO:00000450", + "is_a": "Reservoir [ENVO:00000025]" + }, + "Retail environment [ENVO:01001448]": { + "text": "Retail environment [ENVO:01001448]", + "description": "A planned environmental usage process during which an environment supports the sale of goods to ultimate consumers, usually in small quantities.", + "meaning": "ENVO:01001448" + }, + "Shop [ENVO:00002221]": { + "text": "Shop [ENVO:00002221]", + "description": "A building in which a business presents a selection of goods and offers to trade or sell them to customers for money or other goods.", + "meaning": "ENVO:00002221", + "is_a": "Retail environment [ENVO:01001448]" + }, + "Supermarket [ENVO:01000984]": { + "text": "Supermarket [ENVO:01000984]", + "description": "A food shop in which food products are the primary offer for sale or trade.", + "meaning": "ENVO:01000984", + "is_a": "Shop [ENVO:00002221]" + }, + "River [ENVO:00000022]": { + "text": "River [ENVO:00000022]", + "description": "A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply.", + "meaning": "ENVO:00000022" + }, + "Roost (bird) [ENVO:03501439]": { + "text": "Roost (bird) [ENVO:03501439]", + "description": "A perch on which birds rest.", + "meaning": "ENVO:03501439" + }, + "Wastewater treatment plant [ENVO:00002272]": { + "text": "Wastewater treatment plant [ENVO:00002272]", + "description": "A plant in which wastewater is treated.", + "meaning": "ENVO:00002272" + }, + "Wetland [ENVO:00000043]": { + "text": "Wetland [ENVO:00000043]", + "description": "An area that is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances do support, a prevalence of vegetation typically adapted for life in saturated soil conditions.", + "meaning": "ENVO:00000043" + } + } + }, + "EnvironmentalMaterialMenu": { + "name": "EnvironmentalMaterialMenu", + "title": "environmental_material menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Air [ENVO:00002005]": { + "text": "Air [ENVO:00002005]", + "description": "The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth.", + "meaning": "ENVO:00002005" + }, + "Animal manure [AGRO:00000079]": { + "text": "Animal manure [AGRO:00000079]", + "description": "Organic matter mostly derived from animal feces which can be used as organic fertilizer in agriculture.", + "meaning": "AGRO:00000079" + }, + "Animal feeding equipment [AGRO:00000675]": { + "text": "Animal feeding equipment [AGRO:00000675]", + "description": "An equipment used to feed and water livestock animals.", + "meaning": "AGRO:00000675" + }, + "Animal feeder [AGRO:00000679]": { + "text": "Animal feeder [AGRO:00000679]", + "description": "An animal feeding equipment that has a food storage unit and which enables livestock to obtain their own food.", + "meaning": "AGRO:00000679", + "is_a": "Animal feeding equipment [AGRO:00000675]" + }, + "Animal drinker [AGRO:00000680]": { + "text": "Animal drinker [AGRO:00000680]", + "description": "An animal feeding equipment that has a water storage unit which enables livestock to obtain their own water.", + "meaning": "AGRO:00000680", + "is_a": "Animal feeding equipment [AGRO:00000675]" + }, + "Feed pan [AGRO:00000676]": { + "text": "Feed pan [AGRO:00000676]", + "description": "A bowl or pan which is used to feed livestock.", + "meaning": "AGRO:00000676", + "is_a": "Animal feeding equipment [AGRO:00000675]" + }, + "Watering bowl [AGRO:00000677]": { + "text": "Watering bowl [AGRO:00000677]", + "description": "A bowl from which animals can drink.", + "meaning": "AGRO:00000677", + "is_a": "Animal feeding equipment [AGRO:00000675]" + }, + "Animal transportation equipment [AGRO:00000671]": { + "text": "Animal transportation equipment [AGRO:00000671]", + "description": "An equipment used in the transportation of an animal", + "meaning": "AGRO:00000671" + }, + "Dead haul trailer [GENEPIO:0100896]": { + "text": "Dead haul trailer [GENEPIO:0100896]", + "description": "A trailer used by a dead haul truck to transport dead animal from an abattoir.", + "meaning": "GENEPIO:0100896", + "is_a": "Animal transportation equipment [AGRO:00000671]" + }, + "Dead haul truck [AGRO:00000673]": { + "text": "Dead haul truck [AGRO:00000673]", + "description": "A truck used to haul dead animals from an abattoir.", + "meaning": "AGRO:00000673", + "is_a": "Animal transportation equipment [AGRO:00000671]" + }, + "Live haul trailer [GENEPIO:0100897]": { + "text": "Live haul trailer [GENEPIO:0100897]", + "description": "A trailer used by a live haul truck to transport live animals.", + "meaning": "GENEPIO:0100897", + "is_a": "Animal transportation equipment [AGRO:00000671]" + }, + "Live haul truck [AGRO:00000674]": { + "text": "Live haul truck [AGRO:00000674]", + "description": "A truck used to haul live animals.", + "meaning": "AGRO:00000674", + "is_a": "Animal transportation equipment [AGRO:00000671]" + }, + "Belt [NCIT:C49844]": { + "text": "Belt [NCIT:C49844]", + "description": "A device consisting of a narrow loop of material moving over shafts or pulleys.", + "meaning": "NCIT:C49844" + }, + "Egg belt [AGRO:00000670]": { + "text": "Egg belt [AGRO:00000670]", + "description": "A conveyor belt used to collect eggs in an industrial egg production environment.", + "meaning": "AGRO:00000670", + "is_a": "Belt [NCIT:C49844]" + }, + "Plucking belt [AGRO:00000669]": { + "text": "Plucking belt [AGRO:00000669]", + "description": "A part of the plucking machine that moves the birds through the stages of plucking within the plucking apparatus.", + "meaning": "AGRO:00000669", + "is_a": "Belt [NCIT:C49844]" + }, + "Biosolids [ENVO:00002059]": { + "text": "Biosolids [ENVO:00002059]", + "description": "A treated form of sludge, sometimes used as a fertilizer in agriculture.", + "meaning": "ENVO:00002059" + }, + "Boot [GSSO:012935]": { + "text": "Boot [GSSO:012935]", + "description": "A footwear which covers the foot, the ankle, and sometimes the leg below the knee.", + "meaning": "GSSO:012935" + }, + "Boot cover [OBI:0002806]": { + "text": "Boot cover [OBI:0002806]", + "description": "A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants.", + "meaning": "OBI:0002806", + "is_a": "Boot [GSSO:012935]" + }, + "Broom [ENVO:03501431]": { + "text": "Broom [ENVO:03501431]", + "description": "A cleaning equipment piece which is a bundle of fibres attached to a long handle, and is used for sweeping.", + "meaning": "ENVO:03501431" + }, + "Bulk tank [ENVO:03501379]": { + "text": "Bulk tank [ENVO:03501379]", + "description": "A manufactured product which used to safely store and/or transport solids, liquids, gases and a variety of compounds and mixtures.", + "meaning": "ENVO:03501379" + }, + "Chick box [AGRO:00000678]": { + "text": "Chick box [AGRO:00000678]", + "description": "The box which is used to transport chick (juvenile chicken).", + "meaning": "AGRO:00000678" + }, + "Chick pad [AGRO:00000672]": { + "text": "Chick pad [AGRO:00000672]", + "description": "The lining of a box or crate used to transport chicks (juvenile chickens).", + "meaning": "AGRO:00000672" + }, + "Cleaning equipment [ENVO:03501430]": { + "text": "Cleaning equipment [ENVO:03501430]", + "description": "An equipment piece used for cleaning a built environment or a manufactured product.", + "meaning": "ENVO:03501430" + }, + "Compost [ENVO:00002170]": { + "text": "Compost [ENVO:00002170]", + "description": "The aerobically decomposed remnants of organic materials.", + "meaning": "ENVO:00002170" + }, + "Crate [ENVO:03501372]": { + "text": "Crate [ENVO:03501372]", + "description": "A manufactured product which is a container, traditionally made of wooden slates, designed to protect transported goods from damage.", + "meaning": "ENVO:03501372" + }, + "Dumpster [ENVO:03501400]": { + "text": "Dumpster [ENVO:03501400]", + "description": "A manufactured product which is a reusable container that accumulates waste until it is periodically emptied or replaced.", + "meaning": "ENVO:03501400" + }, + "Dust [ENVO:00002008]": { + "text": "Dust [ENVO:00002008]", + "description": "Minute solid particles with diameters less than 500 micrometers. Occurs in and may be deposited from, the atmosphere.", + "meaning": "ENVO:00002008" + }, + "Fan [NCIT:C49947]": { + "text": "Fan [NCIT:C49947]", + "description": "A device designed to create an air current through the rotation of a planar surface.", + "meaning": "NCIT:C49947" + }, + "Freezer [ENVO:03501415]": { + "text": "Freezer [ENVO:03501415]", + "description": "A manufactured product which is a device used to keep things frozen by maintaining a temperature below the freezing point of water.", + "meaning": "ENVO:03501415" + }, + "Freezer handle [ENVO:03501414]": { + "text": "Freezer handle [ENVO:03501414]", + "description": "A manufactured product which is the handle of a freezer door.", + "meaning": "ENVO:03501414", + "is_a": "Freezer [ENVO:03501415]" + }, + "Manure digester equipment [ENVO:03501424]": { + "text": "Manure digester equipment [ENVO:03501424]", + "description": "An equipment piece which is used in the aerobic or anaerobic microbial digestion of manure.", + "meaning": "ENVO:03501424" + }, + "Nest [ENVO:03501432]": { + "text": "Nest [ENVO:03501432]", + "description": "A structure that is built for certain animals to hold eggs or young.", + "meaning": "ENVO:03501432" + }, + "Bird's nest [ENVO:00005805]": { + "text": "Bird's nest [ENVO:00005805]", + "description": "A bird nest is the spot in which a bird lays and incubates its eggs and raises its young. [ https://en.wikipedia.org/wiki/Bird_nest ]", + "meaning": "ENVO:00005805", + "is_a": "Nest [ENVO:03501432]" + }, + "Permafrost [ENVO:00000134]": { + "text": "Permafrost [ENVO:00000134]", + "description": "Soil or rock and included ice or organic material at or below the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) for two or more years.", + "meaning": "ENVO:00000134" + }, + "Poultry fluff [UBERON:0008291]": { + "text": "Poultry fluff [UBERON:0008291]", + "description": "A feather lacking a vane and having a rudimentary rachis and a tuft of non-interlocked barbs with elongated barbules extending from the calamus.", + "meaning": "UBERON:0008291" + }, + "Poultry litter [AGRO:00000080]": { + "text": "Poultry litter [AGRO:00000080]", + "description": "Manure which is primarily composed of pig feces.", + "meaning": "AGRO:00000080" + }, + "Sediment [ENVO:00002007]": { + "text": "Sediment [ENVO:00002007]", + "description": "Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid.", + "meaning": "ENVO:00002007" + }, + "Soil [ENVO:00001998]": { + "text": "Soil [ENVO:00001998]", + "description": "Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms.", + "meaning": "ENVO:00001998" + }, + "Agricultural soil [ENVO:00002259]": { + "text": "Agricultural soil [ENVO:00002259]", + "description": "A type of soil used for agriculture that supports the physical, chemical, and biological needs of the desired crop during production.", + "meaning": "ENVO:00002259", + "is_a": "Soil [ENVO:00001998]" + }, + "Forest soil [ENVO:00002261]": { + "text": "Forest soil [ENVO:00002261]", + "description": "A portion of soil which is found in a forested area.", + "meaning": "ENVO:00002261", + "is_a": "Soil [ENVO:00001998]" + }, + "Straw [ENVO:00003869]": { + "text": "Straw [ENVO:00003869]", + "description": "An agricultural byproduct, the dry stalk of a cereal plant, after the nutrient grain or seed has been removed.", + "meaning": "ENVO:00003869" + }, + "Water [CHEBI:15377]": { + "text": "Water [CHEBI:15377]", + "description": "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms.", + "meaning": "CHEBI:15377" + }, + "Drinking water [ENVO:00003064]": { + "text": "Drinking water [ENVO:00003064]", + "description": "Water which is suitable for consumption by humans", + "meaning": "ENVO:00003064", + "is_a": "Water [CHEBI:15377]" + }, + "Fecal slurry [ENVO:03501436]": { + "text": "Fecal slurry [ENVO:03501436]", + "description": "A mixture of fecal material mixed, buffer, and other materials, that is homogenized and strained and used in fecal microbiota translpantation.", + "meaning": "ENVO:03501436", + "is_a": "Water [CHEBI:15377]" + }, + "Fluid from meat rinse [GENEPIO:0004323]": { + "text": "Fluid from meat rinse [GENEPIO:0004323]", + "meaning": "GENEPIO:0004323", + "is_a": "Water [CHEBI:15377]" + }, + "Groundwater [ENVO:01001004]": { + "text": "Groundwater [ENVO:01001004]", + "description": "Underground water which is located in pore spaces found in rock or unconsolidated deposits such as soil, clay, or gravel.", + "meaning": "ENVO:01001004", + "is_a": "Water [CHEBI:15377]" + }, + "Poultry plucking water [AGRO_00000693]": { + "text": "Poultry plucking water [AGRO_00000693]", + "description": "A type of water obtained from rinsing poultry carcasses during the feather plucking process.", + "meaning": "AGRO:00000693", + "is_a": "Water [CHEBI:15377]" + }, + "Surface runoff [ENVO:03501408]": { + "text": "Surface runoff [ENVO:03501408]", + "description": "Surface water which is 1) from some rainwater, stormwater, meltwater, or other local source and 2) which can no longer sufficiently rapidly infiltrate into soil, and instead flows along a drainage slope.", + "meaning": "ENVO:03501408", + "is_a": "Water [CHEBI:15377]" + }, + "Surface water [ENVO:00002042]": { + "text": "Surface water [ENVO:00002042]", + "description": "Water that is found on the surface of an astronomical object.", + "meaning": "ENVO:00002042", + "is_a": "Water [CHEBI:15377]" + }, + "Wastewater [ENVO:00002001]": { + "text": "Wastewater [ENVO:00002001]", + "description": "Water that has been adversely affected in quality by anthropogenic influence", + "meaning": "ENVO:00002001", + "is_a": "Water [CHEBI:15377]" + }, + "Sludge [ENVO:00002044]": { + "text": "Sludge [ENVO:00002044]", + "description": "The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes.", + "meaning": "ENVO:00002044", + "is_a": "Wastewater [ENVO:00002001]" + }, + "Primary sludge [ENVO:00002057]": { + "text": "Primary sludge [ENVO:00002057]", + "description": "Sludge generated from the initial processes (i.e., precipitation, sedimentation) of wastewater treatment.", + "meaning": "ENVO:00002057", + "is_a": "Sludge [ENVO:00002044]" + }, + "Secondary sludge [ENVO:00002058]": { + "text": "Secondary sludge [ENVO:00002058]", + "description": "Activated waste biomass generated during wastewater treatment.", + "meaning": "ENVO:00002058", + "is_a": "Sludge [ENVO:00002044]" + }, + "Wastewater effluent [GENEPIO:0100891]": { + "text": "Wastewater effluent [GENEPIO:0100891]", + "meaning": "GENEPIO:0100891", + "is_a": "Wastewater [ENVO:00002001]" + }, + "Primary wastewater effluent [GENEPIO:0100892]": { + "text": "Primary wastewater effluent [GENEPIO:0100892]", + "description": "A wastewater effluent which has been discharged from a primary clarifier after the first stage of sedimentation.", + "meaning": "GENEPIO:0100892", + "is_a": "Wastewater effluent [GENEPIO:0100891]" + }, + "Secondary wastewater effluent [GENEPIO:0100893]": { + "text": "Secondary wastewater effluent [GENEPIO:0100893]", + "description": "A wastewater effluent which has been discharged from a secondary clarifier after the second stage of sedimentation.", + "meaning": "GENEPIO:0100893", + "is_a": "Wastewater effluent [GENEPIO:0100891]" + }, + "Wastewater sediment [GENEPIO:0100890]": { + "text": "Wastewater sediment [GENEPIO:0100890]", + "meaning": "GENEPIO:0100890", + "is_a": "Wastewater [ENVO:00002001]" + }, + "Weep fluid [AGRO:00000692]": { + "text": "Weep fluid [AGRO:00000692]", + "description": "A fluid that leaks from a bag containing an animal carcass, and can include water, chemicals and anatomical fluids.", + "meaning": "AGRO:00000692", + "is_a": "Water [CHEBI:15377]" + } + } + }, + "AnatomicalMaterialMenu": { + "name": "AnatomicalMaterialMenu", + "title": "anatomical_material menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Blood [UBERON:0000178]": { + "text": "Blood [UBERON:0000178]", + "description": "A fluid that is composed of blood plasma and erythrocytes.", + "meaning": "UBERON:0000178" + }, + "Fluid [UBERON:0006314]": { + "text": "Fluid [UBERON:0006314]", + "description": "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.", + "meaning": "UBERON:0006314" + }, + "Fluid (cerebrospinal (CSF)) [UBERON:0001359]": { + "text": "Fluid (cerebrospinal (CSF)) [UBERON:0001359]", + "description": "A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.", + "meaning": "UBERON:0001359", + "is_a": "Fluid [UBERON:0006314]" + }, + "Fluid (amniotic) [UBERON:0000173]": { + "text": "Fluid (amniotic) [UBERON:0000173]", + "description": "Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion.", + "meaning": "UBERON:0000173", + "is_a": "Fluid [UBERON:0006314]" + }, + "Saliva [UBERON:0001836]": { + "text": "Saliva [UBERON:0001836]", + "description": "A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.", + "meaning": "UBERON:0001836", + "is_a": "Fluid [UBERON:0006314]" + }, + "Tissue [UBERON:0000479]": { + "text": "Tissue [UBERON:0000479]", + "description": "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.", + "meaning": "UBERON:0000479" + } + } + }, + "BodyProductMenu": { + "name": "BodyProductMenu", + "title": "body_product menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Digestive tract substance [GENEPIO:0100898]": { + "text": "Digestive tract substance [GENEPIO:0100898]", + "description": "Undigested food material, microbiota, and other materials found in the digestive tract.", + "meaning": "GENEPIO:0100898" + }, + "Caecal content [GENEPIO:0100899]": { + "text": "Caecal content [GENEPIO:0100899]", + "description": "Undigested food material, microbiota, and other materials found in the cecum", + "meaning": "GENEPIO:0100899", + "is_a": "Digestive tract substance [GENEPIO:0100898]" + }, + "Intestinal content [GENEPIO:0100900]": { + "text": "Intestinal content [GENEPIO:0100900]", + "description": "Undigested food material, microbiota, and other materials found in the intestine", + "meaning": "GENEPIO:0100900", + "is_a": "Digestive tract substance [GENEPIO:0100898]" + }, + "Stomach content [GENEPIO:0100901]": { + "text": "Stomach content [GENEPIO:0100901]", + "description": "Undigested food material, microbiota, and other materials found in the stomach", + "meaning": "GENEPIO:0100901", + "is_a": "Digestive tract substance [GENEPIO:0100898]" + }, + "Feces [UBERON:0001988]": { + "text": "Feces [UBERON:0001988]", + "description": "Portion of semisolid bodily waste discharged through the anus.", + "meaning": "UBERON:0001988" + }, + "Fecal composite [GENEPIO:0004512]": { + "text": "Fecal composite [GENEPIO:0004512]", + "description": "A mixture of feces obtained from multiple individuals.", + "meaning": "GENEPIO:0004512", + "is_a": "Feces [UBERON:0001988]" + }, + "Feces (fresh) [GENEPIO:0004513]": { + "text": "Feces (fresh) [GENEPIO:0004513]", + "description": "Feces that was recently excreted.", + "meaning": "GENEPIO:0004513", + "is_a": "Feces [UBERON:0001988]" + }, + "Feces (environmental) [GENEPIO:0004514]": { + "text": "Feces (environmental) [GENEPIO:0004514]", + "description": "Feces which is deposited in the environment.", + "meaning": "GENEPIO:0004514", + "is_a": "Feces [UBERON:0001988]" + }, + "Meconium [UBERON:0007109]": { + "text": "Meconium [UBERON:0007109]", + "description": "A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth.", + "meaning": "UBERON:0007109", + "is_a": "Feces [UBERON:0001988]" + }, + "Milk [UBERON:0001913]": { + "text": "Milk [UBERON:0001913]", + "description": "An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.", + "meaning": "UBERON:0001913" + }, + "Colostrum [UBERON:0001914]": { + "text": "Colostrum [UBERON:0001914]", + "description": "The thin, yellow, serous fluid secreted by the mammary glands during pregnancy and immediately postpartum before lactation begins. It consists of immunologically active substances, white blood cells, water, protein, fat, and carbohydrates. [ MESH : A12.200.194 http://en.wikipedia.org/wiki/Colostrum ]", + "meaning": "UBERON:0001914", + "is_a": "Milk [UBERON:0001913]" + }, + "Mucus [UBERON:0000912]": { + "text": "Mucus [UBERON:0000912]", + "description": "Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.", + "meaning": "UBERON:0000912" + }, + "Urine [UBERON:0001088]": { + "text": "Urine [UBERON:0001088]", + "description": "Excretion that is the output of a kidney.", + "meaning": "UBERON:0001088" + } + } + }, + "AnatomicalPartMenu": { + "name": "AnatomicalPartMenu", + "title": "anatomical_part menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Carcass [UBERON:0008979]": { + "text": "Carcass [UBERON:0008979]", + "description": "A body of a multi-cellular organism that is no longer living.", + "meaning": "UBERON:0008979" + }, + "Digestive system [UBERON:0001007]": { + "text": "Digestive system [UBERON:0001007]", + "description": "Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.", + "meaning": "UBERON:0001007" + }, + "Caecum [UBERON:0001153]": { + "text": "Caecum [UBERON:0001153]", + "description": "pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.", + "meaning": "UBERON:0001153", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Colon [UBERON:0001155]": { + "text": "Colon [UBERON:0001155]", + "description": "A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal.", + "meaning": "UBERON:0001155", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Digestive gland [UBERON:0006925]": { + "text": "Digestive gland [UBERON:0006925]", + "description": "Any gland that is part of the digestive system.", + "meaning": "UBERON:0006925", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Foregut [UBERON:0001041]": { + "text": "Foregut [UBERON:0001041]", + "description": "Anterior subdivision of a digestive tract.", + "meaning": "UBERON:0001041", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Gall bladder [UBERON:0002110]": { + "text": "Gall bladder [UBERON:0002110]", + "description": "An organ that aids digestion and stores bile produced by the liver.", + "meaning": "UBERON:0002110", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Gastrointestinal system mucosa [UBERON:0004786]": { + "text": "Gastrointestinal system mucosa [UBERON:0004786]", + "description": "A mucosa that is part of a gastrointestinal system.", + "meaning": "UBERON:0004786", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Gizzard [UBERON:0005052]": { + "text": "Gizzard [UBERON:0005052]", + "description": "The muscular enlargement of the alimentary canal that has usually thick muscular walls and a tough horny lining for grinding the food and when the crop is present follows it and the proventriculus.", + "meaning": "UBERON:0005052", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Hindgut [UBERON:0001046]": { + "text": "Hindgut [UBERON:0001046]", + "description": "The caudalmost subdivision of a digestive tract.", + "meaning": "UBERON:0001046", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Intestine [UBERON:0000160]": { + "text": "Intestine [UBERON:0000160]", + "description": "Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.", + "meaning": "UBERON:0000160", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Small intestine [UBERON:0002108]": { + "text": "Small intestine [UBERON:0002108]", + "description": "Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum.", + "meaning": "UBERON:0002108", + "is_a": "Intestine [UBERON:0000160]" + }, + "Duodenum [UBERON:0002114]": { + "text": "Duodenum [UBERON:0002114]", + "description": "The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).", + "meaning": "UBERON:0002114", + "is_a": "Small intestine [UBERON:0002108]" + }, + "Ileum [UBERON:0002116]": { + "text": "Ileum [UBERON:0002116]", + "description": "The portion of the small intestine that extends from the jejunum to the colon.", + "meaning": "UBERON:0002116", + "is_a": "Small intestine [UBERON:0002108]" + }, + "Jejunum [UBERON:0002115]": { + "text": "Jejunum [UBERON:0002115]", + "description": "The portion of the small intestine that extends from the duodenum to the ileum.", + "meaning": "UBERON:0002115", + "is_a": "Small intestine [UBERON:0002108]" + }, + "Stomach [UBERON:0000945]": { + "text": "Stomach [UBERON:0000945]", + "description": "An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.", + "meaning": "UBERON:0000945", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Abomasum [UBERON:0007358]": { + "text": "Abomasum [UBERON:0007358]", + "description": "The fourth stomach of ruminating animals, which is an elongated pear-shaped sac lying on the floor of the abdomen, on the right-hand side, and roughly between the seventh and twelfth ribs. It leads to the beginning of the small intestine.", + "meaning": "UBERON:0007358", + "is_a": "Stomach [UBERON:0000945]" + }, + "Rumen [UBERON:0007365]": { + "text": "Rumen [UBERON:0007365]", + "description": "The first compartment of the ruminant stomach. It lies on the left side of the body, occupying the whole of the left side of the abdomen and even stretching across the median plane of the body to the right side. It is capacious, divided into an upper and a lower sac, each of which has a blind sac at its posterior extremity.", + "meaning": "UBERON:0007365", + "is_a": "Stomach [UBERON:0000945]" + }, + "Excretory system (organizational term)": { + "text": "Excretory system (organizational term)" + }, + "Anus [UBERON:0001245]": { + "text": "Anus [UBERON:0001245]", + "description": "Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts.", + "meaning": "UBERON:0001245", + "is_a": "Excretory system (organizational term)" + }, + "Anal gland [UBERON:0011253]": { + "text": "Anal gland [UBERON:0011253]", + "description": "A type of gland occurring as solitary or in pairs or groups, near the anus and sometimes opening into the rectum.", + "meaning": "UBERON:0011253", + "is_a": "Excretory system (organizational term)" + }, + "Cloaca [UBERON:0000162]": { + "text": "Cloaca [UBERON:0000162]", + "description": "Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.", + "meaning": "UBERON:0000162", + "is_a": "Excretory system (organizational term)" + }, + "Liver [UBERON:0002107]": { + "text": "Liver [UBERON:0002107]", + "description": "An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes", + "meaning": "UBERON:0002107", + "is_a": "Excretory system (organizational term)" + }, + "Kidney [UBERON:0002113]": { + "text": "Kidney [UBERON:0002113]", + "description": "A paired organ of the urinary tract which has the production of urine as its primary function.", + "meaning": "UBERON:0002113", + "is_a": "Excretory system (organizational term)" + }, + "Rectum [UBERON:0001052]": { + "text": "Rectum [UBERON:0001052]", + "description": "The terminal portion of the intestinal tube, terminating with the anus.", + "meaning": "UBERON:0001052", + "is_a": "Excretory system (organizational term)" + }, + "Spleen [UBERON:0002106]": { + "text": "Spleen [UBERON:0002106]", + "description": "The organ that functions to filter blood and to store red corpuscles and platelets.", + "meaning": "UBERON:0002106", + "is_a": "Excretory system (organizational term)" + }, + "Urinary bladder [UBERON:0001255]": { + "text": "Urinary bladder [UBERON:0001255]", + "description": "Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion.", + "meaning": "UBERON:0001255", + "is_a": "Excretory system (organizational term)" + }, + "Foot [UBERON:0002387]": { + "text": "Foot [UBERON:0002387]", + "description": "The terminal part of the vertebrate leg upon which an individual stands. 2: An invertebrate organ of locomotion or attachment; especially: a ventral muscular surface or process of a mollusk.", + "meaning": "UBERON:0002387" + }, + "Head [UBERON:0000033]": { + "text": "Head [UBERON:0000033]", + "description": "The head is the anterior-most division of the body.", + "meaning": "UBERON:0000033", + "is_a": "Foot [UBERON:0002387]" + }, + "Brain [UBERON:0000955]": { + "text": "Brain [UBERON:0000955]", + "description": "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell.", + "meaning": "UBERON:0000955", + "is_a": "Foot [UBERON:0002387]" + }, + "Ear [UBERON:0001690]": { + "text": "Ear [UBERON:0001690]", + "description": "Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.", + "meaning": "UBERON:0001690", + "is_a": "Foot [UBERON:0002387]" + }, + "Eye [UBERON:0000970]": { + "text": "Eye [UBERON:0000970]", + "description": "An organ that detects light.", + "meaning": "UBERON:0000970", + "is_a": "Foot [UBERON:0002387]" + }, + "Mouth [UBERON:0000165]": { + "text": "Mouth [UBERON:0000165]", + "description": "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).", + "meaning": "UBERON:0000165", + "is_a": "Foot [UBERON:0002387]" + }, + "Nose [UBERON:0000004]": { + "text": "Nose [UBERON:0000004]", + "description": "The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.", + "meaning": "UBERON:0000004", + "is_a": "Foot [UBERON:0002387]" + }, + "Nasal turbinal [UBERON:0035612]": { + "text": "Nasal turbinal [UBERON:0035612]", + "description": "A skeletal element of the ethmoid region with complex morphology that are lined with mucuous membranes involved in either olfaction or air conditioning.", + "meaning": "UBERON:0035612", + "is_a": "Nose [UBERON:0000004]" + }, + "Nasopharynx (NP) [UBERON:0001728]": { + "text": "Nasopharynx (NP) [UBERON:0001728]", + "description": "The section of the pharynx that lies above the soft palate.", + "meaning": "UBERON:0001728", + "is_a": "Nose [UBERON:0000004]" + }, + "Pair of nares [UBERON:0002109]": { + "text": "Pair of nares [UBERON:0002109]", + "description": "Pair of nostrils.", + "meaning": "UBERON:0002109", + "is_a": "Nose [UBERON:0000004]" + }, + "Paranasal sinus [UBERON:0001825]": { + "text": "Paranasal sinus [UBERON:0001825]", + "description": "The paired air-filled cavities surrounded by the bones of the face that are lined by mucous membranes and are continuous with the nasal cavity.", + "meaning": "UBERON:0001825", + "is_a": "Nose [UBERON:0000004]" + }, + "Snout [UBERON:0006333]": { + "text": "Snout [UBERON:0006333]", + "description": "The projecting nose and mouth of an animal, especially a mammal.", + "meaning": "UBERON:0006333", + "is_a": "Nose [UBERON:0000004]" + }, + "Lymphatic system [UBERON:0006558]": { + "text": "Lymphatic system [UBERON:0006558]", + "description": "An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system.", + "meaning": "UBERON:0006558" + }, + "Lymph node [UBERON:0000029]": { + "text": "Lymph node [UBERON:0000029]", + "description": "Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.", + "meaning": "UBERON:0000029", + "is_a": "Lymphatic system [UBERON:0006558]" + }, + "Mesenteric lymph node [UBERON:0002509]": { + "text": "Mesenteric lymph node [UBERON:0002509]", + "description": "The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group.", + "meaning": "UBERON:0002509", + "is_a": "Lymph node [UBERON:0000029]" + }, + "Mantle (bird) [GENEPIO:0100927]": { + "text": "Mantle (bird) [GENEPIO:0100927]", + "description": "The forward area of a bird's upper side that is sandwiched between the nape and the start of the back.", + "meaning": "GENEPIO:0100927" + }, + "Neck [UBERON:0000974]": { + "text": "Neck [UBERON:0000974]", + "description": "An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.", + "meaning": "UBERON:0000974" + }, + "Esophagus [UBERON:0001043]": { + "text": "Esophagus [UBERON:0001043]", + "description": "Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation.", + "meaning": "UBERON:0001043", + "is_a": "Neck [UBERON:0000974]" + }, + "Trachea [UBERON:0003126]": { + "text": "Trachea [UBERON:0003126]", + "description": "The trachea is the portion of the airway that attaches to the bronchi as it branches.", + "meaning": "UBERON:0003126", + "is_a": "Neck [UBERON:0000974]" + }, + "Nerve [UBERON:0001021]": { + "text": "Nerve [UBERON:0001021]", + "description": "An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.", + "meaning": "UBERON:0001021" + }, + "Spinal cord [UBERON:0002240]": { + "text": "Spinal cord [UBERON:0002240]", + "description": "Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal.", + "meaning": "UBERON:0002240", + "is_a": "Nerve [UBERON:0001021]" + }, + "Organs or organ parts [GENEPIO:0001117]": { + "text": "Organs or organ parts [GENEPIO:0001117]", + "description": "An object aggregate which has as members whole organs or parts of organs, possibly from different organisms.", + "meaning": "GENEPIO:0001117" + }, + "Organ [UBERON:0000062]": { + "text": "Organ [UBERON:0000062]", + "description": "Anatomical structure that performs a specific function or group of functions", + "meaning": "UBERON:0000062", + "is_a": "Organs or organ parts [GENEPIO:0001117]" + }, + "Muscle organ [UBERON:0001630]": { + "text": "Muscle organ [UBERON:0001630]", + "description": "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.", + "meaning": "UBERON:0001630", + "is_a": "Organ [UBERON:0000062]" + }, + "Skin of body [UBERON:0002097]": { + "text": "Skin of body [UBERON:0002097]", + "description": "The organ covering the body that consists of the dermis and epidermis.", + "meaning": "UBERON:0002097", + "is_a": "Organ [UBERON:0000062]" + }, + "Reproductive system [UBERON:0000990]": { + "text": "Reproductive system [UBERON:0000990]", + "description": "Anatomical system that has as its parts the organs concerned with reproduction.", + "meaning": "UBERON:0000990" + }, + "Embryo [UBERON:0000922]": { + "text": "Embryo [UBERON:0000922]", + "description": "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.", + "meaning": "UBERON:0000922", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Fetus [UBERON:0000323]": { + "text": "Fetus [UBERON:0000323]", + "description": "An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching", + "meaning": "UBERON:0000323", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Ovary [UBERON:0000992]": { + "text": "Ovary [UBERON:0000992]", + "description": "The gonad of a female organism which contains germ cells.", + "meaning": "UBERON:0000992", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Oviduct [UBERON:0000993]": { + "text": "Oviduct [UBERON:0000993]", + "description": "A tube or collection of tubes in an animal from the ovaries to the outside of the body.", + "meaning": "UBERON:0000993", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Placenta [UBERON:0001987]": { + "text": "Placenta [UBERON:0001987]", + "description": "Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.", + "meaning": "UBERON:0001987", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Testis [UBERON:0000473]": { + "text": "Testis [UBERON:0000473]", + "description": "A gonad of a male animal. A gonad produces and releases sperm.", + "meaning": "UBERON:0000473", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Udder [UBERON:0013216]": { + "text": "Udder [UBERON:0013216]", + "description": "A large pendulous organ consisting of two or more mammary glands enclosed in a common envelope and each provided with a single nipple.", + "meaning": "UBERON:0013216", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Uterus [UBERON:0000995]": { + "text": "Uterus [UBERON:0000995]", + "description": "The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.", + "meaning": "UBERON:0000995", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Vagina [UBERON:0000996]": { + "text": "Vagina [UBERON:0000996]", + "description": "A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles", + "meaning": "UBERON:0000996", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Yolk sac [UBERON:0001040]": { + "text": "Yolk sac [UBERON:0001040]", + "description": "A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes.", + "meaning": "UBERON:0001040", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Respiratory system [UBERON:0001004]": { + "text": "Respiratory system [UBERON:0001004]", + "description": "Functional system which consists of structures involved in respiration.", + "meaning": "UBERON:0001004" + }, + "Air sac [UBERON:0009060]": { + "text": "Air sac [UBERON:0009060]", + "description": "Any of the membranous air-filled extensions of the lungs of birds, which increase the efficiency of gaseous exchange in the lungs.", + "meaning": "UBERON:0009060", + "is_a": "Respiratory system [UBERON:0001004]" + }, + "Lung [UBERON:0002048]": { + "text": "Lung [UBERON:0002048]", + "description": "Respiration organ that develops as an outpocketing of the esophagus", + "meaning": "UBERON:0002048", + "is_a": "Vascular system [UBERON:0007798]" + }, + "Pleura [UBERON:0000977]": { + "text": "Pleura [UBERON:0000977]", + "description": "The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).", + "meaning": "UBERON:0000977", + "is_a": "Respiratory system [UBERON:0001004]" + }, + "Respiratory system mucosa [UBERON:0004785]": { + "text": "Respiratory system mucosa [UBERON:0004785]", + "description": "The mucous membrane lining the respiratory tract.", + "meaning": "UBERON:0004785", + "is_a": "Respiratory system [UBERON:0001004]" + }, + "Skeletal system [UBERON:0001434]": { + "text": "Skeletal system [UBERON:0001434]", + "description": "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.", + "meaning": "UBERON:0001434" + }, + "Skeletal joint [UBERON:0000982]": { + "text": "Skeletal joint [UBERON:0000982]", + "description": "Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue.", + "meaning": "UBERON:0000982", + "is_a": "Skeletal system [UBERON:0001434]" + }, + "Bone element [UBERON:0001474]": { + "text": "Bone element [UBERON:0001474]", + "description": "Skeletal element that is composed of bone tissue.", + "meaning": "UBERON:0001474", + "is_a": "Skeletal system [UBERON:0001434]" + }, + "Thoracic segment of trunk [UBERON:0000915]": { + "text": "Thoracic segment of trunk [UBERON:0000915]", + "description": "Subdivision of trunk that lies between the head and the abdomen.", + "meaning": "UBERON:0000915" + }, + "Abdomen [UBERON:0000916]": { + "text": "Abdomen [UBERON:0000916]", + "description": "The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.", + "meaning": "UBERON:0000916", + "is_a": "Thoracic segment of trunk [UBERON:0000915]" + }, + "Muscle of abdomen [UBERON:0002378]": { + "text": "Muscle of abdomen [UBERON:0002378]", + "description": "Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis.", + "meaning": "UBERON:0002378", + "is_a": "Abdomen [UBERON:0000916]" + }, + "Peritoneum [UBERON:0002358]": { + "text": "Peritoneum [UBERON:0002358]", + "description": "Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis.", + "meaning": "UBERON:0002358", + "is_a": "Abdomen [UBERON:0000916]" + }, + "Vascular system [UBERON:0007798]": { + "text": "Vascular system [UBERON:0007798]", + "description": "Anatomical system that consists of all blood and lymph vessels.", + "meaning": "UBERON:0007798" + }, + "Blood vessel [UBERON:0001981]": { + "text": "Blood vessel [UBERON:0001981]", + "description": "A vessel through which blood circulates in the body.", + "meaning": "UBERON:0001981", + "is_a": "Vascular system [UBERON:0007798]" + }, + "Bursa of Fabricius [UBERON:0003903]": { + "text": "Bursa of Fabricius [UBERON:0003903]", + "description": "An epithelial and lymphoid organ that develops as a dorsal diverticulum of the proctodeal region of the cloaca in birds. The luminal (interior) surface of the bursa is plicated with as many as 15 primary and 7 secondary plicae or folds. These plicae have hundreds of bursal follicles containing follicle-associated epithelial cells, lymphocytes, macrophages, and plasma cells. Lymphoid stem cells migrate from the fetal liver to the bursa during ontogeny. In the bursa, these stem cells acquire the characteristics of mature, immunocompetent B cells. The bursa is an organ found in birds involved in B cell differentiation.", + "meaning": "UBERON:0003903", + "is_a": "Vascular system [UBERON:0007798]" + }, + "Gill [UBERON:0002535]": { + "text": "Gill [UBERON:0002535]", + "description": "Anatomical surface structure found in many aquatic organisms. It is a respiration organ whose function is the extraction of oxygen from water and the excretion of carbon dioxide. The microscopic structure of a gill is such that it presents a very large surface area to the external environment. Gills usually consist of thin filaments of tissue, branches, or slender tufted processes which have a highly folded surface to increase surface area. A high surface area is crucial to the gas exchange of aquatic organisms as water contains only 1/20 parts dissolved Oxygen compared to air. With the exception of some aquatic insects, the filaments and lamellae (folds) contain blood or coelomic fluid, from which gases are exchanged through the thin walls. Oxygen is carried by the blood to other parts of the body. Carbon dioxide passes from the blood through the thin gill tissue into the water. Gills or gill-like organs, located in different parts of the body, are found in various groups of aquatic animals, including mollusks, crustaceans, insects, fish, and amphibians. [ http://en.wikipedia.org/wiki/Gill ]", + "meaning": "UBERON:0002535", + "is_a": "Vascular system [UBERON:0007798]" + }, + "Heart [UBERON:0000948]": { + "text": "Heart [UBERON:0000948]", + "description": "A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.", + "meaning": "UBERON:0000948", + "is_a": "Vascular system [UBERON:0007798]" + }, + "Pericardium [UBERON:0002407]": { + "text": "Pericardium [UBERON:0002407]", + "description": "The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium.", + "meaning": "UBERON:0002407", + "is_a": "Vascular system [UBERON:0007798]" + }, + "Vent (anatomical) [UBERON:2000298]": { + "text": "Vent (anatomical) [UBERON:2000298]", + "description": "The external opening of the rectum or cloaca.", + "meaning": "UBERON:2000298" + }, + "Bird vent [UBERON:0012464]": { + "text": "Bird vent [UBERON:0012464]", + "description": "The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. [ http://orcid.org/0000-0002-6601-2165 ]", + "meaning": "UBERON:0012464", + "is_a": "Vent (anatomical) [UBERON:2000298]" + }, + "Fish vent [GENEPIO:0100902]": { + "text": "Fish vent [GENEPIO:0100902]", + "description": "The external opening which opens to the reproductive and digestive tracts of the fish. During spawning, the vent serves as an outlet for eggs and sperm. In most fishes, the vent is in front of the anal fin.", + "meaning": "GENEPIO:0100902", + "is_a": "Vent (anatomical) [UBERON:2000298]" + } + } + }, + "CollectionDeviceMenu": { + "name": "CollectionDeviceMenu", + "title": "collection_device menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Air filter [ENVO:00003968]": { + "text": "Air filter [ENVO:00003968]", + "meaning": "ENVO:00003968" + }, + "Auger (earth auger) [AGRO:00000405]": { + "text": "Auger (earth auger) [AGRO:00000405]", + "description": "Manually operated hand tool that consists of cutter head having semicircular blades connected to pipe with the help of clamp and flange. The connecting pipe is further connected to a handle.", + "meaning": "AGRO:00000405" + }, + "Bag [GSSO:008558]": { + "text": "Bag [GSSO:008558]", + "description": "A sac or pouch.", + "meaning": "GSSO:008558" + }, + "Whirlpak sampling bag [GENEPIO:0002122]": { + "text": "Whirlpak sampling bag [GENEPIO:0002122]", + "description": "A sterilized sampling bag that is puncture proof tabs for protection from damage due to wire-end protrusion and leak-proof closures.", + "meaning": "GENEPIO:0002122", + "is_a": "Bag [GSSO:008558]" + }, + "Bottle [FOODON:03490214]": { + "text": "Bottle [FOODON:03490214]", + "description": "A rigid or semirigid container typically of glass or plastic having a comparatively narrow neck or mouth and usually no handle.", + "meaning": "FOODON:03490214" + }, + "Box corer [GENEPIO:0100928]": { + "text": "Box corer [GENEPIO:0100928]", + "description": "A specimen collection device that is used to collect soft sediments in lakes or oceans.", + "meaning": "GENEPIO:0100928" + }, + "Bronchoscope [OBI:0002826]": { + "text": "Bronchoscope [OBI:0002826]", + "description": "A device which is a thin, tube-like instrument which includes a light and a lens used to examine a lung.", + "meaning": "OBI:0002826" + }, + "Collection Container [OBI:0002088]": { + "text": "Collection Container [OBI:0002088]", + "description": "A container with the function of containing a specimen.", + "meaning": "OBI:0002088" + }, + "Collection Cup [GENEPIO:0100026]": { + "text": "Collection Cup [GENEPIO:0100026]", + "description": "A device which is used to collect liquid samples.", + "meaning": "GENEPIO:0100026" + }, + "Culture plate [GENEPIO:0004318]": { + "text": "Culture plate [GENEPIO:0004318]", + "description": "A low flat-bottomed laboratory container for growing a layer of organisms such as bacteria, molds, and cells on a thin layer of nutrient medium.", + "meaning": "GENEPIO:0004318" + }, + "Petri dish [NCIT:C96141]": { + "text": "Petri dish [NCIT:C96141]", + "description": "A shallow dish with a lid used to culture cells.", + "meaning": "NCIT:C96141", + "is_a": "Culture plate [GENEPIO:0004318]" + }, + "Fibrobronchoscope Brush [OBI:0002825]": { + "text": "Fibrobronchoscope Brush [OBI:0002825]", + "meaning": "OBI:0002825" + }, + "Filter [GENEPIO:0100103]": { + "text": "Filter [GENEPIO:0100103]", + "description": "A manufactured product which separates solids from fluids by adding a medium through which only a fluid can pass.", + "meaning": "GENEPIO:0100103" + }, + "Fine Needle [OBI:0002827]": { + "text": "Fine Needle [OBI:0002827]", + "meaning": "OBI:0002827" + }, + "Micropipette [OBI:0001128]": { + "text": "Micropipette [OBI:0001128]", + "meaning": "OBI:0001128" + }, + "Needle [OBI:0000436]": { + "text": "Needle [OBI:0000436]", + "description": "A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.", + "meaning": "OBI:0000436" + }, + "PONAR grab sampler [GENEPIO:0100929]": { + "text": "PONAR grab sampler [GENEPIO:0100929]", + "description": "A specimen collection device that is designed to collect sediment samples from the hard bottoms of a body of water i.e. sand, gravel, consolidated marl or clay.\"", + "meaning": "GENEPIO:0100929" + }, + "Scoop [GENEPIO:0002125]": { + "text": "Scoop [GENEPIO:0002125]", + "description": "A shovel-like utensil that has a deep curved dish and a short handle and is used for digging into a soft substance for lifting out a portion.", + "meaning": "GENEPIO:0002125" + }, + "Soil sample probe [GENEPIO:0100930]": { + "text": "Soil sample probe [GENEPIO:0100930]", + "description": "A specimen collection device designed to penetrate soil with a hollow tube to collect soil sample cores.", + "meaning": "GENEPIO:0100930" + }, + "Spatula [NCIT:C149941]": { + "text": "Spatula [NCIT:C149941]", + "meaning": "CIT:C149941" + }, + "Sponge [OBI:0002819]": { + "text": "Sponge [OBI:0002819]", + "description": "A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter.", + "meaning": "OBI:0002819" + }, + "Suction Catheter [OBI:0002831]": { + "text": "Suction Catheter [OBI:0002831]", + "description": "A catheter which is used to remove mucus and other secretions from the body.", + "meaning": "OBI:0002831" + }, + "Swab [GENEPIO:0100027]": { + "text": "Swab [GENEPIO:0100027]", + "description": "A device which is a soft, absorbent material mounted on one or both ends of a stick.", + "meaning": "GENEPIO:0100027" + }, + "Drag swab [OBI:0002822]": { + "text": "Drag swab [OBI:0002822]", + "description": "A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string", + "meaning": "OBI:0002822", + "is_a": "Swab [GENEPIO:0100027]" + }, + "Surface wipe [OBI:0002824]": { + "text": "Surface wipe [OBI:0002824]", + "description": "A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces.", + "meaning": "OBI:0002824", + "is_a": "Swab [GENEPIO:0100027]" + }, + "Tube [GENEPIO:0101196]": { + "text": "Tube [GENEPIO:0101196]", + "description": "A sample collection device which is cylindrical shape that is open at one end, used to collect material.", + "meaning": "GENEPIO:0101196" + }, + "Blood Collection Tube [OBI:0002859]": { + "text": "Blood Collection Tube [OBI:0002859]", + "description": "A specimen collection tube which is designed for the collection of whole blood. See also: https://en.wikipedia.org/wiki/Blood_culture#Collection", + "meaning": "OBI:0002859", + "is_a": "Tube [GENEPIO:0101196]" + }, + "Microcapillary tube [OBI:0002858]": { + "text": "Microcapillary tube [OBI:0002858]", + "meaning": "OBI:0002858", + "is_a": "Tube [GENEPIO:0101196]" + }, + "Serum Collection Tube [OBI:0002860]": { + "text": "Serum Collection Tube [OBI:0002860]", + "description": "A specimen collection tube which is designed for collecting whole blood and enabling the separation of serum.", + "meaning": "OBI:0002860", + "is_a": "Tube [GENEPIO:0101196]" + }, + "Sputum Collection Tube [OBI:0002861]": { + "text": "Sputum Collection Tube [OBI:0002861]", + "description": "A specimen collection tube which is designed for collecting sputum.", + "meaning": "OBI:0002861", + "is_a": "Tube [GENEPIO:0101196]" + }, + "Urine Collection Tube [OBI:0002862]": { + "text": "Urine Collection Tube [OBI:0002862]", + "description": "A specimen container which is designed for holding urine.", + "meaning": "OBI:0002862", + "is_a": "Tube [GENEPIO:0101196]" + }, + "Vacuum device [GENEPIO:0002127]": { + "text": "Vacuum device [GENEPIO:0002127]", + "description": "A device which generates a vacuum to provide suction of material.", + "meaning": "GENEPIO:0002127" + }, + "Vacutainer [OBIB:0000032]": { + "text": "Vacutainer [OBIB:0000032]", + "description": "A test tube which is either a sterile glass or plastic tube with a closure that is evacuated to create a vacuum inside the tube facilitating the draw of a predetermined volume of liquid. Most commonly used to draw a blood sample directly from the vein, these also are used to collect urine samples. Vacutainer tube may contain additives designed to stabilize and preserve the specimen prior to analytical testing.", + "meaning": "OBIB:0000032", + "is_a": "Vacuum device [GENEPIO:0002127]" + } + } + }, + "CollectionMethodMenu": { + "name": "CollectionMethodMenu", + "title": "collection_method menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Aspiration [HP:0002835]": { + "text": "Aspiration [HP:0002835]", + "description": "Inspiration of a foreign object into the airway.", + "meaning": "HP:0002835" + }, + "Biopsy [OBI:0002650]": { + "text": "Biopsy [OBI:0002650]", + "description": "A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive.", + "meaning": "OBI:0002650" + }, + "Fecal grab [GENEPIO:0004326]": { + "text": "Fecal grab [GENEPIO:0004326]", + "description": "A fecal specimen collection method in which feces is obtained by inserting the collection device into the anus of the host, or the feces is captured as it is excreted.", + "meaning": "GENEPIO:0004326" + }, + "Filtration [OBI:0302885]": { + "text": "Filtration [OBI:0302885]", + "description": "A process which separates components suspended in a fluid based on granularity properties relying on a filter device.", + "meaning": "OBI:0302885" + }, + "Air filtration [GENEPIO:0100031]": { + "text": "Air filtration [GENEPIO:0100031]", + "description": "A filtration process which removes solid particulates from the air via an air filtration device.", + "meaning": "GENEPIO:0100031", + "is_a": "Filtration [OBI:0302885]" + }, + "Water filtration [GENEPIO:0100931]": { + "text": "Water filtration [GENEPIO:0100931]", + "description": "A filtration process which removes or reduces the concentration of particulate matter, including suspended particles, parasites, bacteria, algae, viruses, and fungi, as well as other undesirable chemical and biological contaminants from contaminated water using water filters to produce safe and clean water.", + "meaning": "GENEPIO:0100931", + "is_a": "Filtration [OBI:0302885]" + }, + "Lavage [OBI:0600044]": { + "text": "Lavage [OBI:0600044]", + "description": "A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid", + "meaning": "OBI:0600044" + }, + "Bronchoalveolar lavage [GENEPIO:0100032]": { + "text": "Bronchoalveolar lavage [GENEPIO:0100032]", + "description": "The collection of bronchoalveolar lavage fluid (BAL) from the lungs.", + "meaning": "GENEPIO:0100032", + "is_a": "Lavage [OBI:0600044]" + }, + "Gastric lavage [GENEPIO:0100033]": { + "text": "Gastric lavage [GENEPIO:0100033]", + "description": "The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach.", + "meaning": "GENEPIO:0100033", + "is_a": "Lavage [OBI:0600044]" + }, + "Necropsy [MMO:0000344]": { + "text": "Necropsy [MMO:0000344]", + "description": "A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease.", + "meaning": "MMO:0000344" + }, + "Phlebotomy [NCIT:C28221]": { + "text": "Phlebotomy [NCIT:C28221]", + "description": "The collection of blood from a vein, most commonly via needle venipuncture.", + "meaning": "NCIT:C28221" + }, + "Rinsing for specimen collection [GENEPIO_0002116]": { + "text": "Rinsing for specimen collection [GENEPIO_0002116]", + "description": "The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids.", + "meaning": "GENEPIO:0002116" + }, + "Scooping [GENEPIO:0100932]": { + "text": "Scooping [GENEPIO:0100932]", + "description": "A specimen collection process that is used to dig out an amount of sample using a scoop.", + "meaning": "GENEPIO:0100932" + }, + "Sediment collection [GENEPIO:0100933]": { + "text": "Sediment collection [GENEPIO:0100933]", + "description": "A specimen collection process that is used to collect a sediment sample.", + "meaning": "GENEPIO:0100933" + }, + "Soil coring [GENEPIO:0100934]": { + "text": "Soil coring [GENEPIO:0100934]", + "description": "A specimen collection process that is used to collect soil sample cores.", + "meaning": "GENEPIO:0100934" + }, + "Weep fluid collection (pouring) [GENEPIO:0101003]": { + "text": "Weep fluid collection (pouring) [GENEPIO:0101003]", + "description": "A specimen collection process that is used to collect weep fluid via pouring from the source container into the sample collection device. (e.g. bag or tube)", + "meaning": "GENEPIO:0101003" + } + } + }, + "SampleVolumeMeasurementUnitMenu": { + "name": "SampleVolumeMeasurementUnitMenu", + "title": "sample_volume_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "microliter (uL) [UO:0000101]": { + "text": "microliter (uL) [UO:0000101]", + "description": "A metric unit of volume equivalent to one thousandth of a cubic centimeter or one millionth of a liter.", + "meaning": "UO:0000101" + }, + "milliliter (mL) [UO:0000098]": { + "text": "milliliter (mL) [UO:0000098]", + "description": "A metric unit of volume equivalent to one cubic centimeter or one thousandth of a liter.", + "meaning": "UO:0000098" + }, + "liter (L) [UO:0000099]": { + "text": "liter (L) [UO:0000099]", + "description": "A metric unit of volume equivalent to 1000 cubic centimeters", + "meaning": "UO:0000099" + } + } + }, + "ResidualSampleStatusMenu": { + "name": "ResidualSampleStatusMenu", + "title": "residual_sample_status menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Residual sample remaining (some sample left) [GENEPIO:0101087]": { + "text": "Residual sample remaining (some sample left) [GENEPIO:0101087]", + "meaning": "GENEPIO:0101087" + }, + "No residual sample (sample all used) [GENEPIO:0101088]": { + "text": "No residual sample (sample all used) [GENEPIO:0101088]", + "meaning": "GENEPIO:0101088" + }, + "Residual sample status unkown [GENEPIO:0101089]": { + "text": "Residual sample status unkown [GENEPIO:0101089]", + "meaning": "GENEPIO:0101089" + } + } + }, + "PurposeOfSampling": { + "name": "PurposeOfSampling", + "title": "purpose of sampling", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Cluster/Outbreak investigation [GENEPIO:0100001]": { + "text": "Cluster/Outbreak investigation [GENEPIO:0100001]", + "description": "A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak.", + "meaning": "GENEPIO:0100001" + }, + "Diagnostic testing [GENEPIO:0100002]": { + "text": "Diagnostic testing [GENEPIO:0100002]", + "description": "A sampling strategy in which individuals are sampled in the context of diagnostic testing.", + "meaning": "GENEPIO:0100002" + }, + "Environmental testing [GENEPIO:0100548]": { + "text": "Environmental testing [GENEPIO:0100548]", + "description": "A sampling strategy in which environments are sampled in the context of testing for the presence of, or change in the levels of, chemicals, pathogens or other phenomena.", + "meaning": "GENEPIO:0100548" + }, + "Research [GENEPIO:0100003]": { + "text": "Research [GENEPIO:0100003]", + "description": "A sampling strategy in which samples are collected in order to perform research.", + "meaning": "GENEPIO:0100003" + }, + "Clinical trial [GENEPIO:0100549]": { + "text": "Clinical trial [GENEPIO:0100549]", + "description": "A sampling strategy in which individuals are sampled in the context of experiments or observations performed as part of clinical research.", + "meaning": "GENEPIO:0100549", + "is_a": "Research [GENEPIO:0100003]" + }, + "Field experiment [GENEPIO:0100550]": { + "text": "Field experiment [GENEPIO:0100550]", + "description": "A sampling strategy in which samples are taken during real-life experiments which test directly whether proposed interventions actually work.", + "meaning": "GENEPIO:0100550", + "is_a": "Research [GENEPIO:0100003]" + }, + "Survey study [GENEPIO:0100582]": { + "text": "Survey study [GENEPIO:0100582]", + "description": "A sampling strategy in which individuals and/or materials are sampled for surveillance performed for research purposes.", + "meaning": "GENEPIO:0100582", + "is_a": "Research [GENEPIO:0100003]" + }, + "Surveillance [GENEPIO:0100004]": { + "text": "Surveillance [GENEPIO:0100004]", + "description": "A sampling strategy in which individuals are sampled for surveillance investigations.", + "meaning": "GENEPIO:0100004" + } + } + }, + "PresamplingActivity": { + "name": "PresamplingActivity", + "title": "presampling activity", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Addition of substances to food/water [GENEPIO:0100536]": { + "text": "Addition of substances to food/water [GENEPIO:0100536]", + "description": "The addition of substances to food or water administered to an individual or group of individuals.", + "meaning": "GENEPIO:0100536" + }, + "Antimicrobial pre-treatment [GENEPIO:0100537]": { + "text": "Antimicrobial pre-treatment [GENEPIO:0100537]", + "description": "The administration of an antimicrobial agent to an individual or its addition to a substance prior to some other event or activity.", + "meaning": "GENEPIO:0100537" + }, + "Certified animal husbandry practices [GENEPIO:0100538]": { + "text": "Certified animal husbandry practices [GENEPIO:0100538]", + "description": "The implementation of animal husbandy practices that have been certified by an authorized organization.", + "meaning": "GENEPIO:0100538" + }, + "Certified humane animal husbandry practices [GENEPIO:0100894]": { + "text": "Certified humane animal husbandry practices [GENEPIO:0100894]", + "description": "A certification organization in Washington DC that is dedicated to improving the lives of farm animals in food production from birth through slaughter.", + "meaning": "GENEPIO:0100894", + "is_a": "Certified animal husbandry practices [GENEPIO:0100538]" + }, + "Certified organic farming practices [GENEPIO:0100539]": { + "text": "Certified organic farming practices [GENEPIO:0100539]", + "description": "The implementation of organic farming practices that have been certified by an authorized organization.", + "meaning": "GENEPIO:0100539" + }, + "Conventional farming practices [GENEPIO:0100895]": { + "text": "Conventional farming practices [GENEPIO:0100895]", + "description": "The implementation of farming practices that include man-made inputs such as chemical fertilizers and genetically-modified seeds.", + "meaning": "GENEPIO:0100895" + }, + "Change in storage conditions [GENEPIO:0100540]": { + "text": "Change in storage conditions [GENEPIO:0100540]", + "description": "A change in the storage conditions of a material or a substance.", + "meaning": "GENEPIO:0100540" + }, + "Cleaning/disinfection [GENEPIO:0100541]": { + "text": "Cleaning/disinfection [GENEPIO:0100541]", + "description": "A process of removing unwanted substances, such as dirt, infectious agents, and other impurities, from an object or environment.", + "meaning": "GENEPIO:0100541" + }, + "Extended downtime between activities [GENEPIO:0100542]": { + "text": "Extended downtime between activities [GENEPIO:0100542]", + "description": "A prolonged period of inactivity between processes or events.", + "meaning": "GENEPIO:0100542" + }, + "Microbial pre-treatment [GENEPIO:0100546]": { + "text": "Microbial pre-treatment [GENEPIO:0100546]", + "description": "The deliberate addition of microbes or a mixture of microbes to an individual or substance prior to some other event or activity.", + "meaning": "GENEPIO:0100546" + }, + "Probiotic pre-treatment [GENEPIO:0100547]": { + "text": "Probiotic pre-treatment [GENEPIO:0100547]", + "description": "The addition of a probiotic substance to an individual or material prior to some other event or activity.", + "meaning": "GENEPIO:0100547" + }, + "Vaccination [NCIT:C15346]": { + "text": "Vaccination [NCIT:C15346]", + "description": "Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis or treatment.", + "meaning": "NCIT:C15346" + } + } + }, + "SampleStorageDurationUnit": { + "name": "SampleStorageDurationUnit", + "title": "sample storage duration unit", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Second [UO:0000010]": { + "text": "Second [UO:0000010]", + "description": "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.", + "meaning": "UO:0000010" + }, + "Minute [UO:0000031]": { + "text": "Minute [UO:0000031]", + "description": "A time unit which is equal to 60 seconds.", + "meaning": "UO:0000031" + }, + "Hour [UO:0000032]": { + "text": "Hour [UO:0000032]", + "description": "A time unit which is equal to 60 minutes.", + "meaning": "UO:0000032" + }, + "Day [UO:0000033]": { + "text": "Day [UO:0000033]", + "description": "A time unit which is equal to 24 hours.", + "meaning": "UO:0000033" + }, + "Week [UO:0000034]": { + "text": "Week [UO:0000034]", + "description": "A time unit which is equal to 7 days.", + "meaning": "UO:0000034" + }, + "Month [UO:0000035]": { + "text": "Month [UO:0000035]", + "description": "A time unit which is equal to approximately 4-4.5 weeks or 28-31 days.", + "meaning": "UO:0000035" + }, + "Year [UO:0000036]": { + "text": "Year [UO:0000036]", + "description": "A time unit which is equal to 365 days, or 366 days during a leap year.", + "meaning": "UO:0000036" + } + } + }, + "SpecimenProcessing": { + "name": "SpecimenProcessing", + "title": "specimen processing", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Concentration [OBI:0600041]": { + "text": "Concentration [OBI:0600041]", + "description": "A process used to increase the density of a material of interest by removing other materials in the entity containing the material of interest.", + "meaning": "OBI:0600041" + }, + "Centrifugation [OBI:0302886]": { + "text": "Centrifugation [OBI:0302886]", + "description": "A process separating molecules by size or density using centrifugal forces generated by a spinning rotor.", + "meaning": "OBI:0302886" + }, + "Filtration [OBI:0302885]": { + "text": "Filtration [OBI:0302885]", + "description": "A process which separates components suspended in a fluid based on granularity properties relying on a filter device.", + "meaning": "OBI:0302885" + }, + "Pooling specimens [OBI:0600016]": { + "text": "Pooling specimens [OBI:0600016]", + "description": "Physical combination of several instances of like material.", + "meaning": "OBI:0600016" + } + } + }, + "ExperimentalSpecimenRoleType": { + "name": "ExperimentalSpecimenRoleType", + "title": "experimental specimen role type", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Positive experimental control [GENEPIO:0101018]": { + "text": "Positive experimental control [GENEPIO:0101018]", + "description": "A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment.", + "meaning": "GENEPIO:0101018" + }, + "Validation strain [GENEPIO:0101123]": { + "text": "Validation strain [GENEPIO:0101123]", + "meaning": "GENEPIO:0101123", + "is_a": "Positive experimental control [GENEPIO:0101018]" + }, + "Proficiency test isolate [GENEPIO:0101124]": { + "text": "Proficiency test isolate [GENEPIO:0101124]", + "meaning": "GENEPIO:0101124", + "is_a": "Positive experimental control [GENEPIO:0101018]" + }, + "Negative experimental control [GENEPIO:0101019]": { + "text": "Negative experimental control [GENEPIO:0101019]", + "description": "A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment", + "meaning": "GENEPIO:0101019" + }, + "Technical replicate [EFO:0002090]": { + "text": "Technical replicate [EFO:0002090]", + "description": "A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment.", + "meaning": "EFO:0002090" + }, + "Biological replicate [EFO:0002091]": { + "text": "Biological replicate [EFO:0002091]", + "description": "A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples.", + "meaning": "EFO:0002091" + }, + "Synthetic lab construct [GENEPIO:0101039]": { + "text": "Synthetic lab construct [GENEPIO:0101039]", + "meaning": "GENEPIO:0101039" + }, + "Negative sample [GENEPIO:0101120]": { + "text": "Negative sample [GENEPIO:0101120]", + "meaning": "GENEPIO:0101120" + } + } + }, + "AvailableDataTypesMenu": { + "name": "AvailableDataTypesMenu", + "title": "available_data_types menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Documentation [GENEPIO:0100702]": { + "text": "Documentation [GENEPIO:0100702]", + "description": "A dataset attribute bundle which indicates the presence of documentation data.", + "meaning": "GENEPIO:0100702" + }, + "Experimental parameters documentation [GENEPIO:0100703]": { + "text": "Experimental parameters documentation [GENEPIO:0100703]", + "description": "A documentation data tag which indicates the presence of data that describes experimental parameters.", + "meaning": "GENEPIO:0100703", + "is_a": "Documentation [GENEPIO:0100702]" + }, + "Feed history [GENEPIO:0100704]": { + "text": "Feed history [GENEPIO:0100704]", + "description": "A documentation data tag which indicates the presence of data that describes feed history.", + "meaning": "GENEPIO:0100704", + "is_a": "Documentation [GENEPIO:0100702]" + }, + "Land use information [GENEPIO:0100705]": { + "text": "Land use information [GENEPIO:0100705]", + "description": "A documentation data tag which indicates the presence of data that describes land use information.", + "meaning": "GENEPIO:0100705", + "is_a": "Documentation [GENEPIO:0100702]" + }, + "Therapeutic administration history [GENEPIO:0100706]": { + "text": "Therapeutic administration history [GENEPIO:0100706]", + "description": "A documentation data tag which indicates the presence of data that describes a history of therapeutic administration.", + "meaning": "GENEPIO:0100706", + "is_a": "Documentation [GENEPIO:0100702]" + }, + "Chemical characterization [GENEPIO:0100707]": { + "text": "Chemical characterization [GENEPIO:0100707]", + "description": "A dataset attribute bundle which indicates the presence of chemical characterization data.", + "meaning": "GENEPIO:0100707" + }, + "Microbiological characterization [GENEPIO:0100714]": { + "text": "Microbiological characterization [GENEPIO:0100714]", + "description": "A dataset attribute bundle which indicates the presence of microbiological characterization data.", + "meaning": "GENEPIO:0100714" + }, + "Microbiological identification [GENEPIO:0100715]": { + "text": "Microbiological identification [GENEPIO:0100715]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data.", + "meaning": "GENEPIO:0100715", + "is_a": "Microbiological characterization [GENEPIO:0100714]" + }, + "Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716]": { + "text": "Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Beckson Dickson BBL Crystal identification system.", + "meaning": "GENEPIO:0100716", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Microbiological identification (bioMérieux API) [GENEPIO:0100717]": { + "text": "Microbiological identification (bioMérieux API) [GENEPIO:0100717]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data dervied using the bioMérieux API identification system.", + "meaning": "GENEPIO:0100717", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Microbiological identification (Biolog) [GENEPIO:0100718]": { + "text": "Microbiological identification (Biolog) [GENEPIO:0100718]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Biolog identification system.", + "meaning": "GENEPIO:0100718", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Microbiological identification (FAME) [GENEPIO:0100719]": { + "text": "Microbiological identification (FAME) [GENEPIO:0100719]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Fatty acid methyl esters (FAME) identification system.", + "meaning": "GENEPIO:0100719", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Microbiological identification (Sensititre) [GENEPIO:0100720]": { + "text": "Microbiological identification (Sensititre) [GENEPIO:0100720]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Sensititre identification system.", + "meaning": "GENEPIO:0100720", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Microbiological identification (ViTek) [GENEPIO:0100721]": { + "text": "Microbiological identification (ViTek) [GENEPIO:0100721]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the ViTek identification system.", + "meaning": "GENEPIO:0100721", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Phage type [GENEPIO:0100722]": { + "text": "Phage type [GENEPIO:0100722]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using phage type identification.", + "meaning": "GENEPIO:0100722", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Serotype [GENEPIO:0100723]": { + "text": "Serotype [GENEPIO:0100723]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using serotype identification.", + "meaning": "GENEPIO:0100723", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Phenotypic microbiological characterization [GENEPIO:0100724]": { + "text": "Phenotypic microbiological characterization [GENEPIO:0100724]", + "description": "A microbiological characterization data tag which indicates the presence of phenotypic microbiological characterization data.", + "meaning": "GENEPIO:0100724", + "is_a": "Microbiological characterization [GENEPIO:0100714]" + }, + "AMR phenotypic testing [GENEPIO:0100725]": { + "text": "AMR phenotypic testing [GENEPIO:0100725]", + "description": "A phenotypic microbiological characterization data tag which indicates the presence of antimicrobial resistance (AMR) phenotypic testing characterization data.", + "meaning": "GENEPIO:0100725", + "is_a": "Phenotypic microbiological characterization [GENEPIO:0100724]" + }, + "Biolog phenotype microarray [GENEPIO:0100726]": { + "text": "Biolog phenotype microarray [GENEPIO:0100726]", + "description": "A phenotypic microbiological characterization data tag which indicates the presence of biolog phenotype microarray characterization data.", + "meaning": "GENEPIO:0100726", + "is_a": "Phenotypic microbiological characterization [GENEPIO:0100724]" + }, + "Microbiological quantification [GENEPIO:0100727]": { + "text": "Microbiological quantification [GENEPIO:0100727]", + "description": "A dataset attribute bundle which indicates the presence of microbiological quantification data.", + "meaning": "GENEPIO:0100727" + }, + "Colony count [GENEPIO:0100728]": { + "text": "Colony count [GENEPIO:0100728]", + "description": "A microbiological quantification data tag which indicates the presence of colony count data.", + "meaning": "GENEPIO:0100728", + "is_a": "Microbiological quantification [GENEPIO:0100727]" + }, + "Total coliform count [GENEPIO:0100729]": { + "text": "Total coliform count [GENEPIO:0100729]", + "description": "A colony count microbiological quantification data tag which indicates the presence of data that describes total colony count of coliforms.", + "meaning": "GENEPIO:0100729", + "is_a": "Colony count [GENEPIO:0100728]" + }, + "Total fecal coliform count [GENEPIO:0100730]": { + "text": "Total fecal coliform count [GENEPIO:0100730]", + "description": "A colony count microbiological quantification data tag that indicates the presence of data which describes total colony count of fecal coliforms.", + "meaning": "GENEPIO:0100730", + "is_a": "Colony count [GENEPIO:0100728]" + }, + "Infectivity assay [GENEPIO:0100731]": { + "text": "Infectivity assay [GENEPIO:0100731]", + "description": "A microbiological quantification data tag which indicates the presence of infectivity assay data.", + "meaning": "GENEPIO:0100731", + "is_a": "Microbiological quantification [GENEPIO:0100727]" + }, + "ELISA toxin binding [GENEPIO:0100732]": { + "text": "ELISA toxin binding [GENEPIO:0100732]", + "description": "A microbiological quantification data tag which indicates the presence of data which describes enzyme-linked immunosorbent assay (ELISA) toxin binding.", + "meaning": "GENEPIO:0100732", + "is_a": "Microbiological quantification [GENEPIO:0100727]" + }, + "Molecular characterization [GENEPIO:0100733]": { + "text": "Molecular characterization [GENEPIO:0100733]", + "description": "A dataset attribute bundle which indicates the presence of molecular characterization data.", + "meaning": "GENEPIO:0100733" + }, + "16S rRNA Sanger sequencing [GENEPIO:0100734]": { + "text": "16S rRNA Sanger sequencing [GENEPIO:0100734]", + "description": "A molecular characterization data tag which indicates the presence of 16S rRNA Sanger sequencing characterization data.", + "meaning": "GENEPIO:0100734", + "is_a": "Molecular characterization [GENEPIO:0100733]" + }, + "Metagenomic sequencing [GENEPIO:0101024]": { + "text": "Metagenomic sequencing [GENEPIO:0101024]", + "description": "A molecular characterization data tag which indicates the presence of metagenomic sequencing characterization data.", + "meaning": "GENEPIO:0101024", + "is_a": "Molecular characterization [GENEPIO:0100733]" + }, + "PCR marker detection [GENEPIO:0100735]": { + "text": "PCR marker detection [GENEPIO:0100735]", + "description": "A molecular characterization data tag which indicates the presence of polymerase chain reaction (PCR) marker detection characterization data.", + "meaning": "GENEPIO:0100735", + "is_a": "Molecular characterization [GENEPIO:0100733]" + }, + "BOX PCR fingerprint [GENEPIO:0100736]": { + "text": "BOX PCR fingerprint [GENEPIO:0100736]", + "description": "A PCR marker detection characterization data tag which indicates the presence of BOX-A1R-based repetitive extragenic palindromic (BOX) PCR fingerprint data.", + "meaning": "GENEPIO:0100736", + "is_a": "PCR marker detection [GENEPIO:0100735]" + }, + "ERIC PCR fingerprint [GENEPIO:0100737]": { + "text": "ERIC PCR fingerprint [GENEPIO:0100737]", + "description": "A PCR marker detection characterization data tag which indicates the presence of enterobacterial repetitive intergenic consensus (ERIC) PCR fingerprint data.", + "meaning": "GENEPIO:0100737", + "is_a": "PCR marker detection [GENEPIO:0100735]" + }, + "Plasmid type [GENEPIO:0100738]": { + "text": "Plasmid type [GENEPIO:0100738]", + "description": "A molecular characterization data tag which indicates the presence of plasmid type characterization data.", + "meaning": "GENEPIO:0100738", + "is_a": "Molecular characterization [GENEPIO:0100733]" + }, + "Ribotype [GENEPIO:0100739]": { + "text": "Ribotype [GENEPIO:0100739]", + "description": "A molecular characterization data tag which indicates the presence of ribotype characterization data.", + "meaning": "GENEPIO:0100739", + "is_a": "Molecular characterization [GENEPIO:0100733]" + }, + "Molecular quantification [GENEPIO:0100740]": { + "text": "Molecular quantification [GENEPIO:0100740]", + "description": "A dataset attribute bundle which indicates the presence of molecular quantification data.", + "meaning": "GENEPIO:0100740" + }, + "qPCR marker organism quantification [GENEPIO:0100741]": { + "text": "qPCR marker organism quantification [GENEPIO:0100741]", + "description": "A molecular quantification data tag which indicates the presence of quantitative polymerase chain reaction (qPCR) marker organism quantification data.", + "meaning": "GENEPIO:0100741", + "is_a": "Molecular quantification [GENEPIO:0100740]" + }, + "Physical characterization [GENEPIO:0100742]": { + "text": "Physical characterization [GENEPIO:0100742]", + "description": "A dataset attribute bundle which indicates the presence of physical characterization data.", + "meaning": "GENEPIO:0100742" + }, + "Conductivity measurement [GENEPIO:0100743]": { + "text": "Conductivity measurement [GENEPIO:0100743]", + "description": "A physical characterization data tag which indicates the presence of data that describes conductivity measurement characterization.", + "meaning": "GENEPIO:0100743", + "is_a": "Physical characterization [GENEPIO:0100742]" + }, + "Mollusc shell measurement [GENEPIO:0100744]": { + "text": "Mollusc shell measurement [GENEPIO:0100744]", + "description": "A physical characterization data tag which indicates the presence of data that describes a measurement of a mollusc shell.", + "meaning": "GENEPIO:0100744", + "is_a": "Physical characterization [GENEPIO:0100742]" + }, + "Matter compostion [GENEPIO:0100746]": { + "text": "Matter compostion [GENEPIO:0100746]", + "description": "A physical characterization data tag which indicates the presence of matter compostion characterization data.", + "meaning": "GENEPIO:0100746", + "is_a": "Physical characterization [GENEPIO:0100742]" + }, + "Dry matter composition [GENEPIO:0100747]": { + "text": "Dry matter composition [GENEPIO:0100747]", + "description": "A matter composition characterization data tag which indicates the presence of data that describes dry matter composition.", + "meaning": "GENEPIO:0100747", + "is_a": "Matter compostion [GENEPIO:0100746]" + }, + "Organic matter composition [GENEPIO:0100748]": { + "text": "Organic matter composition [GENEPIO:0100748]", + "description": "A matter composition characterization data tag which indicates the presence of data that describes organic matter composition.", + "meaning": "GENEPIO:0100748", + "is_a": "Matter compostion [GENEPIO:0100746]" + } + } + }, + "HostCommonNameMenu": { + "name": "HostCommonNameMenu", + "title": "host (common name) menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Bird [NCBITaxon:8782]": { + "text": "Bird [NCBITaxon:8782]", + "description": "A group of warm-blooded vertebrates in class Aves, that are characterized by feathers, wings, toothless beaked jaws and the laying of hard-shelled eggs and are usually able to fly.", + "meaning": "NCBITaxon:8782" + }, + "Chicken [NCBITaxon:9031]": { + "text": "Chicken [NCBITaxon:9031]", + "description": "A domesticated junglefowl of the species Gallus gallus.", + "meaning": "NCBITaxon:9031", + "is_a": "Bird [NCBITaxon:8782]" + }, + "Seabird [FOODON:00004504]": { + "text": "Seabird [FOODON:00004504]", + "description": "A bird that is adapted to live within the marine environment.", + "meaning": "FOODON:00004504", + "is_a": "Bird [NCBITaxon:8782]" + }, + "Cormorant [NCBITaxon:9206]": { + "text": "Cormorant [NCBITaxon:9206]", + "description": "A family of aquatic birds (Phalacrocoracidae).", + "meaning": "NCBITaxon:9206", + "is_a": "Seabird [FOODON:00004504]" + }, + "Double Crested Cormorant [NCBITaxon:56069]": { + "text": "Double Crested Cormorant [NCBITaxon:56069]", + "description": "A species of the cormorant family of water birds (Phalacrocorax auritus).", + "meaning": "NCBITaxon:56069", + "is_a": "Cormorant [NCBITaxon:9206]" + }, + "Crane [NCBITaxon:9109]": { + "text": "Crane [NCBITaxon:9109]", + "description": "A family of large, long-legged, and long-necked birds (Gruidae).", + "meaning": "NCBITaxon:9109", + "is_a": "Seabird [FOODON:00004504]" + }, + "Whooping Crane [NCBITaxon:9117]": { + "text": "Whooping Crane [NCBITaxon:9117]", + "description": "An endangered crane species that is native to North America and is named for its whooping sound.", + "meaning": "NCBITaxon:9117", + "is_a": "Crane [NCBITaxon:9109]" + }, + "Gull (Seagull) [NCBITaxon:8911]": { + "text": "Gull (Seagull) [NCBITaxon:8911]", + "description": "A large genus of gulls within the family Laridae.", + "meaning": "NCBITaxon:8911", + "is_a": "Seabird [FOODON:00004504]" + }, + "Glaucous-winged Gull [NCBITaxon:119606]": { + "text": "Glaucous-winged Gull [NCBITaxon:119606]", + "description": "A species of large, white-headed gull (Larus glaucescens).", + "meaning": "NCBITaxon:119606", + "is_a": "Gull (Seagull) [NCBITaxon:8911]" + }, + "Great Black-backed Gull [NCBITaxon:8912]": { + "text": "Great Black-backed Gull [NCBITaxon:8912]", + "description": "A species of white gull that has a black back and wings (Larus marinus).", + "meaning": "NCBITaxon:8912", + "is_a": "Gull (Seagull) [NCBITaxon:8911]" + }, + "Herring Gull [NCBITaxon:35669]": { + "text": "Herring Gull [NCBITaxon:35669]", + "description": "A species of large gull, that is up to 66 cm (26 in) long (Larus argentatus).", + "meaning": "NCBITaxon:35669", + "is_a": "Gull (Seagull) [NCBITaxon:8911]" + }, + "Ring-billed Gull [NCBITaxon:126683]": { + "text": "Ring-billed Gull [NCBITaxon:126683]", + "description": "A species of ring-billed gull that has a black ring around its bill (Larus delawarensis).", + "meaning": "NCBITaxon:126683", + "is_a": "Gull (Seagull) [NCBITaxon:8911]" + }, + "Eider [NCBITaxon:50366]": { + "text": "Eider [NCBITaxon:50366]", + "description": "A genus of large seaducks (Somateria).", + "meaning": "NCBITaxon:50366", + "is_a": "Seabird [FOODON:00004504]" + }, + "Common Eider [NCBITaxon:76058]": { + "text": "Common Eider [NCBITaxon:76058]", + "description": "A species of a large sea-duck that is distributed over the northern coasts of Europe, North America and eastern Siberia (Somateria mollissima).", + "meaning": "NCBITaxon:76058", + "is_a": "Eider [NCBITaxon:50366]" + }, + "Turkey [NCBITaxon:9103]": { + "text": "Turkey [NCBITaxon:9103]", + "description": "A large, mainly domesticated game bird characterized by a bald head and wattles (in the male) of the species Meleagris gallopavo.", + "meaning": "NCBITaxon:9103", + "is_a": "Bird [NCBITaxon:8782]" + }, + "Fish [FOODON:03411222]": { + "text": "Fish [FOODON:03411222]", + "description": "Fish are the gill-bearing aquatic craniate animals that lack limbs with digits. Most fish are ectothermic (\"cold-blooded\"), allowing their body temperatures to vary as ambient temperatures change, though some of the large active swimmers like white shark and tuna can hold a higher core temperature.", + "meaning": "FOODON:03411222" + }, + "Mammal [FOODON:03411134]": { + "text": "Mammal [FOODON:03411134]", + "description": "Mammals (from Latin mamma \"breast\") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones.", + "meaning": "FOODON:03411134" + }, + "Companion animal [FOODON:03000300]": { + "text": "Companion animal [FOODON:03000300]", + "description": "An animal that is kept as a companion.", + "meaning": "FOODON:03000300", + "is_a": "Mammal [FOODON:03411134]" + }, + "Cow [NCBITaxon:9913]": { + "text": "Cow [NCBITaxon:9913]", + "description": "A group of large, domesticated, cloven-hooved herbivores.", + "meaning": "NCBITaxon:9913", + "is_a": "Mammal [FOODON:03411134]" + }, + "Deer [NCBITaxon:9850]": { + "text": "Deer [NCBITaxon:9850]", + "meaning": "NCBITaxon:9850", + "is_a": "Mammal [FOODON:03411134]" + }, + "Human [NCBITaxon:9606]": { + "text": "Human [NCBITaxon:9606]", + "description": "A bipedal primate mammal of the species Homo sapiens.", + "meaning": "NCBITaxon:9606", + "is_a": "Mammal [FOODON:03411134]" + }, + "Pig [NCBITaxon:9823]": { + "text": "Pig [NCBITaxon:9823]", + "description": "A stout-bodied, hooved and short-legged, omnivorous mammal from the species Sus scofus, with thick skin usually sparsely coated with short bristles.", + "meaning": "NCBITaxon:9823", + "is_a": "Mammal [FOODON:03411134]" + }, + "Sheep [NCBITaxon:9940]": { + "text": "Sheep [NCBITaxon:9940]", + "description": "A domesticated, even-toed, ungluate, ruminant mammal typically kept as livestock for its wool and meat, usually of the species Ovis aries.", + "meaning": "NCBITaxon:9940", + "is_a": "Mammal [FOODON:03411134]" + }, + "Shellfish [FOODON:03411433]": { + "text": "Shellfish [FOODON:03411433]", + "description": "The term shellfish is used both broadly and specifically. For regulatory purposes it is often narrowly defined as filter-feeding molluscs such as clams, mussels, and oyster to the exclusion of crustaceans and all else. Although their shells may differ, all shellfish are invertebrates.", + "meaning": "FOODON:03411433" + } + } + }, + "HostScientificNameMenu": { + "name": "HostScientificNameMenu", + "title": "host (scientific name) menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Anoplopoma fimbria [NCBITaxon:229290]": { + "text": "Anoplopoma fimbria [NCBITaxon:229290]", + "description": "One of two members of the fish family Anoplopomatidae and the only species in the genus Anoplopoma.", + "meaning": "NCBITaxon:229290" + }, + "Bos taurus [NCBITaxon:9913]": { + "text": "Bos taurus [NCBITaxon:9913]", + "description": "A group of large, domesticated, cloven-hooved herbivores.", + "meaning": "NCBITaxon:9913" + }, + "Crassostrea virginica [NCBITaxon:6565]": { + "text": "Crassostrea virginica [NCBITaxon:6565]", + "description": "A species of true oyster (Crassostrea virginica).", + "meaning": "NCBITaxon:6565" + }, + "Gallus gallus [NCBITaxon:9031]": { + "text": "Gallus gallus [NCBITaxon:9031]", + "description": "A domesticated junglefowl of the species Gallus gallus.", + "meaning": "NCBITaxon:9031" + }, + "Grus americana [NCBITaxon:9117]": { + "text": "Grus americana [NCBITaxon:9117]", + "description": "An endangered crane species that is native to North America and is named for its whooping sound.", + "meaning": "NCBITaxon:9117" + }, + "Homarus americanus [NCBITaxon:6706]": { + "text": "Homarus americanus [NCBITaxon:6706]", + "description": "A species of lobster that is found on the Atlantic coast of North America (Homarus americanus).", + "meaning": "NCBITaxon:6706" + }, + "Homo sapiens [NCBITaxon:9606]": { + "text": "Homo sapiens [NCBITaxon:9606]", + "description": "A bipedal primate mammal of the species Homo sapiens.", + "meaning": "NCBITaxon:9606" + }, + "Larus argentatus [NCBITaxon:35669]": { + "text": "Larus argentatus [NCBITaxon:35669]", + "description": "A species of large gull, that is up to 66 cm (26 in) long (Larus argentatus).", + "meaning": "NCBITaxon:35669" + }, + "Larus delawarensis [NCBITaxon:126683]": { + "text": "Larus delawarensis [NCBITaxon:126683]", + "description": "A species of ring-billed gull that has a black ring around its bill (Larus delawarensis).", + "meaning": "NCBITaxon:126683" + }, + "Larus glaucescens [NCBITaxon:119606]": { + "text": "Larus glaucescens [NCBITaxon:119606]", + "description": "A species of large, white-headed gull (Larus glaucescens).", + "meaning": "NCBITaxon:119606" + }, + "Larus marinus [NCBITaxon:8912]": { + "text": "Larus marinus [NCBITaxon:8912]", + "description": "A species of white gull that has a black back and wings (Larus marinus).", + "meaning": "NCBITaxon:8912" + }, + "Meleagris gallopavo [NCBITaxon:9103]": { + "text": "Meleagris gallopavo [NCBITaxon:9103]", + "description": "A large, mainly domesticated game bird characterized by a bald head and wattles (in the male) of the species Meleagris gallopavo.", + "meaning": "NCBITaxon:9103" + }, + "Mytilus edulis [NCBITaxon:6550]": { + "text": "Mytilus edulis [NCBITaxon:6550]", + "description": "A medium-sized edible marine bivalve mollusc in the family Mytilidae, the mussels.", + "meaning": "NCBITaxon:6550" + }, + "Oncorhynchus kisutch [NCBITaxon:8019]": { + "text": "Oncorhynchus kisutch [NCBITaxon:8019]", + "description": "A species of pacific salmon in North America, that is commonly called as coho salmon.", + "meaning": "NCBITaxon:8019" + }, + "Oncorhynchus mykiss [NCBITaxon:8022]": { + "text": "Oncorhynchus mykiss [NCBITaxon:8022]", + "description": "A species of trout native to cold-water tributaries of the Pacific Ocean in Asia and North America (Oncorhynchus mykiss).", + "meaning": "NCBITaxon:8022" + }, + "Oncorhynchus tshawytscha [NCBITaxon:74940]": { + "text": "Oncorhynchus tshawytscha [NCBITaxon:74940]", + "description": "The largest species of pacific salmon in North America (Oncorhynchus tshawytscha).", + "meaning": "NCBITaxon:74940" + }, + "Ovis aries [NCBITaxon:9940]": { + "text": "Ovis aries [NCBITaxon:9940]", + "description": "A domesticated, even-toed, ungluate, ruminant mammal typically kept as livestock for its wool and meat, usually of the species Ovis aries.", + "meaning": "NCBITaxon:9940" + }, + "Phalacrocorax auritus [NCBITaxon:56069]": { + "text": "Phalacrocorax auritus [NCBITaxon:56069]", + "description": "A species of the cormorant family of water birds (Phalacrocorax auritus).", + "meaning": "NCBITaxon:56069" + }, + "Salmo salar [NCBITaxon:8030]": { + "text": "Salmo salar [NCBITaxon:8030]", + "description": "A species of ray-finned fish in the family Salmonidae (Salmo salar).", + "meaning": "NCBITaxon:8030" + }, + "Somateria mollissima [NCBITaxon:76058]": { + "text": "Somateria mollissima [NCBITaxon:76058]", + "description": "A species of a large sea-duck that is distributed over the northern coasts of Europe, North America and eastern Siberia (Somateria mollissima).", + "meaning": "NCBITaxon:76058" + }, + "Sus scrofa domesticus [NCBITaxon:9825]": { + "text": "Sus scrofa domesticus [NCBITaxon:9825]", + "description": "A stout-bodied, hooved and short-legged, omnivorous mammal, with thick skin usually sparsely coated with short bristles raised for its meat.", + "meaning": "NCBITaxon:9825" + } + } + }, + "HostFoodProductionNameMenu": { + "name": "HostFoodProductionNameMenu", + "title": "host (food production name) menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Cow (by age/production stage) (organizational term)": { + "text": "Cow (by age/production stage) (organizational term)" + }, + "Calf [FOODON:03411349]": { + "text": "Calf [FOODON:03411349]", + "description": "Calves are the young of domestic cattle. Calves are reared to become adult cattle, or are slaughtered for their meat, called veal.", + "meaning": "FOODON:03411349", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Dry cow [FOODON:00004411]": { + "text": "Dry cow [FOODON:00004411]", + "description": "A cow that is in a stage of its lactation cycle where milk production ceases prior to calving.", + "meaning": "FOODON:00004411", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Feeder cow [FOODON:00004292]": { + "text": "Feeder cow [FOODON:00004292]", + "description": "A young cow mature enough either to undergo backgrounding or to be fattened in preparation for slaughter.", + "meaning": "FOODON:00004292", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Finisher cow [FOODON:00004293]": { + "text": "Finisher cow [FOODON:00004293]", + "meaning": "FOODON:00004293", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Milker cow [FOODON:03411201]": { + "text": "Milker cow [FOODON:03411201]", + "description": "A cow that is bred specifically for milk production.", + "meaning": "FOODON:03411201", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Stocker cow [FOODON:00004294]": { + "text": "Stocker cow [FOODON:00004294]", + "description": "A type of cow that has been weaned and is being fed in a way to add physical bulk to its body.", + "meaning": "FOODON:00004294", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Weanling cow [FOODON:00004295]": { + "text": "Weanling cow [FOODON:00004295]", + "description": "A type of young cow that has been weaned and consumes solid food.", + "meaning": "FOODON:00004295", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Cow (by sex/reproductive stage) (organizational term)": { + "text": "Cow (by sex/reproductive stage) (organizational term)" + }, + "Bull [FOODON:00000015]": { + "text": "Bull [FOODON:00000015]", + "description": "A cattle bull is an adult \"intact\" (i.e. not castrated) male of a cattle species.", + "meaning": "FOODON:00000015", + "is_a": "Cow (by sex/reproductive stage) (organizational term)" + }, + "Cow [NCBITaxon:9913]": { + "text": "Cow [NCBITaxon:9913]", + "description": "A group of large, domesticated, cloven-hooved herbivores.", + "meaning": "NCBITaxon:9913", + "is_a": "Cow (by sex/reproductive stage) (organizational term)" + }, + "Freemartin [FOODON:00004296]": { + "text": "Freemartin [FOODON:00004296]", + "description": "A cow that is genetically female, but has many characteristics of a male and is usually infertile.", + "meaning": "FOODON:00004296", + "is_a": "Cow (by sex/reproductive stage) (organizational term)" + }, + "Heifer [FOODON:00002518]": { + "text": "Heifer [FOODON:00002518]", + "description": "A heifer is a young female, under three years of age, of a cattle species before she has had a calf of her own.", + "meaning": "FOODON:00002518", + "is_a": "Cow (by sex/reproductive stage) (organizational term)" + }, + "Steer [FOODON:00002531]": { + "text": "Steer [FOODON:00002531]", + "description": "A cattle steer is an adult castrated male of a cattle species.", + "meaning": "FOODON:00002531", + "is_a": "Cow (by sex/reproductive stage) (organizational term)" + }, + "Pig (by age/production stage) (organizational term)": { + "text": "Pig (by age/production stage) (organizational term)" + }, + "Finisher pig [FOODON:00003371]": { + "text": "Finisher pig [FOODON:00003371]", + "description": "A grower pig over 70 kg (150 lb) liveweight.", + "meaning": "FOODON:00003371", + "is_a": "Pig (by age/production stage) (organizational term)" + }, + "Grower pig [FOODON:00003370]": { + "text": "Grower pig [FOODON:00003370]", + "description": "A pig between weaning and sale or transfer to the breeding herd, sold for slaughter or killed for rations.", + "meaning": "FOODON:00003370", + "is_a": "Pig (by age/production stage) (organizational term)" + }, + "Nursing pig [FOODON:00004297 ]": { + "text": "Nursing pig [FOODON:00004297 ]", + "meaning": "OODON:00004297", + "is_a": "Pig (by age/production stage) (organizational term)" + }, + "Pig [NCBITaxon:9823]": { + "text": "Pig [NCBITaxon:9823]", + "description": "A stout-bodied, hooved and short-legged, omnivorous mammal from the species Sus scofus, with thick skin usually sparsely coated with short bristles.", + "meaning": "NCBITaxon:9823", + "is_a": "Pig (by age/production stage) (organizational term)" + }, + "Piglet [FOODON:00003952]": { + "text": "Piglet [FOODON:00003952]", + "description": "An unweaned or immature pig.", + "meaning": "FOODON:00003952", + "is_a": "Pig (by age/production stage) (organizational term)" + }, + "Weanling (weaner) pig [FOODON:00003373]": { + "text": "Weanling (weaner) pig [FOODON:00003373]", + "description": "A young pig recently separated from the sow", + "meaning": "FOODON:00003373", + "is_a": "Pig (by age/production stage) (organizational term)" + }, + "Pig (by sex/reproductive stage) (organizational term)": { + "text": "Pig (by sex/reproductive stage) (organizational term)" + }, + "Barrow [FOODON:03411280]": { + "text": "Barrow [FOODON:03411280]", + "description": "A male swine castrated before sexual maturity.", + "meaning": "FOODON:03411280", + "is_a": "Pig (by sex/reproductive stage) (organizational term)" + }, + "Boar [FOODON:03412248]": { + "text": "Boar [FOODON:03412248]", + "description": "An adult male swine.", + "meaning": "FOODON:03412248", + "is_a": "Pig (by sex/reproductive stage) (organizational term)" + }, + "Gilt [FOODON:00003369]": { + "text": "Gilt [FOODON:00003369]", + "description": "A female pig under the age of 1 year. The term is also often used to refer to a pig who has not farrowed, or given birth to a litter.", + "meaning": "FOODON:00003369", + "is_a": "Pig (by sex/reproductive stage) (organizational term)" + }, + "Sow [FOODON:00003333]": { + "text": "Sow [FOODON:00003333]", + "description": "An adult female swine.", + "meaning": "FOODON:00003333", + "is_a": "Pig (by sex/reproductive stage) (organizational term)" + }, + "Poultry or game bird [FOODON:03411563]": { + "text": "Poultry or game bird [FOODON:03411563]", + "description": "Domesticated birds kept by humans for their eggs, their meat or their feathers.", + "meaning": "FOODON:03411563" + }, + "Broiler or fryer chicken [FOODON:03411198]": { + "text": "Broiler or fryer chicken [FOODON:03411198]", + "description": "A chicken younger than 10 weeks old (previously younger than 13 weeks), of either sex, that is tender-meated with soft, pliable, smooth-textured skin and flexible breastbone cartilage.", + "meaning": "FOODON:03411198", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Capon [FOODON:03411711]": { + "text": "Capon [FOODON:03411711]", + "description": "A surgically neutered male chicken younger than four months old (previously younger than eight months) that is tender-meated with soft, pliable, smooth-textured skin.", + "meaning": "FOODON:03411711", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Chick [FOODON:00004299]": { + "text": "Chick [FOODON:00004299]", + "description": "A young offspring of any bird.", + "meaning": "FOODON:00004299", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Chicken [NCBITaxon:9031]": { + "text": "Chicken [NCBITaxon:9031]", + "description": "A domesticated junglefowl of the species Gallus gallus.", + "meaning": "NCBITaxon:9031", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Egg [UBERON:0007379]": { + "text": "Egg [UBERON:0007379]", + "description": "The hard-shelled reproductive body produced by a bird (especially by the common domestic chicken) or a reptile; also: its contents used as food.", + "meaning": "UBERON:0007379", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Hatchling [FOODON:00004300]": { + "text": "Hatchling [FOODON:00004300]", + "description": "A young animal that has recently emerged from its egg.", + "meaning": "FOODON:00004300", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Hen [FOODON:00003282]": { + "text": "Hen [FOODON:00003282]", + "description": "An adult female chicken.", + "meaning": "FOODON:00003282", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Layer chicken [FOODON:00004301]": { + "text": "Layer chicken [FOODON:00004301]", + "description": "A type of chicken kept for laying eggs.", + "meaning": "FOODON:00004301", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Layer turkey [FOODON:00004302]": { + "text": "Layer turkey [FOODON:00004302]", + "description": "A type of turkey kept for laying eggs.", + "meaning": "FOODON:00004302", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Poult [FOODON:00002962]": { + "text": "Poult [FOODON:00002962]", + "description": "A poult is a young domestic chicken, turkey, pheasant, or other fowl being raised for food.", + "meaning": "FOODON:00002962", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Pullet [FOODON:00004303]": { + "text": "Pullet [FOODON:00004303]", + "description": "A young hen, especially one less than one year old.", + "meaning": "FOODON:00004303", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Rooster [FOODON:03411714]": { + "text": "Rooster [FOODON:03411714]", + "description": "A mature male chicken with coarse skin, toughened and darkened meat, and hardened breastbone tip.", + "meaning": "FOODON:03411714", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Tom (Gobbler) [FOODON:00004304 ]": { + "text": "Tom (Gobbler) [FOODON:00004304 ]", + "meaning": "OODON:00004304", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Turkey [NCBITaxon:9103]": { + "text": "Turkey [NCBITaxon:9103]", + "description": "A large, mainly domesticated game bird characterized by a bald head and wattles (in the male) of the species Meleagris gallopavo.", + "meaning": "NCBITaxon:9103", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Sheep [NCBITaxon:9940]": { + "text": "Sheep [NCBITaxon:9940]", + "description": "A domesticated, even-toed, ungluate, ruminant mammal typically kept as livestock for its wool and meat, usually of the species Ovis aries.", + "meaning": "NCBITaxon:9940" + }, + "Ram [FOODON:00004305]": { + "text": "Ram [FOODON:00004305]", + "description": "An adult male sheep kept for breeding and for wool production.", + "meaning": "FOODON:00004305", + "is_a": "Sheep [NCBITaxon:9940]" + }, + "Wether sheep [FOODON:00004306]": { + "text": "Wether sheep [FOODON:00004306]", + "description": "A castrated male sheep.", + "meaning": "FOODON:00004306", + "is_a": "Sheep [NCBITaxon:9940]" + }, + "Ewe [FOODON:03412610]": { + "text": "Ewe [FOODON:03412610]", + "description": "A ewe is a female sheep.", + "meaning": "FOODON:03412610", + "is_a": "Sheep [NCBITaxon:9940]" + }, + "Lamb [FOODON:03411669]": { + "text": "Lamb [FOODON:03411669]", + "description": "A whole lamb or some material processed from a lamb.", + "meaning": "FOODON:03411669", + "is_a": "Sheep [NCBITaxon:9940]" + }, + "Fish [FOODON:03411222]": { + "text": "Fish [FOODON:03411222]", + "description": "Fish are the gill-bearing aquatic craniate animals that lack limbs with digits. Most fish are ectothermic (\"cold-blooded\"), allowing their body temperatures to vary as ambient temperatures change, though some of the large active swimmers like white shark and tuna can hold a higher core temperature.", + "meaning": "FOODON:03411222" + }, + "Fish egg [FOODON_00004319]": { + "text": "Fish egg [FOODON_00004319]", + "description": "An egg or spawn of a fish that is contained within or separated from the ovary.", + "meaning": "FOODON:00004319", + "is_a": "Fish [FOODON:03411222]" + }, + "Fry (fish) [FOODON_00004318]": { + "text": "Fry (fish) [FOODON_00004318]", + "description": "A fish that is recently hatched and has reached the stage where its yolk-sac has almost disappeared and its swim bladder is operational to the point where the fish can actively feed for itself.", + "meaning": "FOODON:00004318", + "is_a": "Fish [FOODON:03411222]" + }, + "Juvenile fish [FOODON_00004317]": { + "text": "Juvenile fish [FOODON_00004317]", + "description": "A fish that has not reached to sexual maturity.", + "meaning": "FOODON:00004317", + "is_a": "Fish [FOODON:03411222]" + } + } + }, + "HostAgeUnitMenu": { + "name": "HostAgeUnitMenu", + "title": "host_age_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "month [UO:0000035]": { + "text": "month [UO:0000035]", + "description": "A time unit which is equal to approximately 4-4.5 weeks or 28-31 days.", + "meaning": "UO:0000035" + }, + "year [UO:0000036]": { + "text": "year [UO:0000036]", + "description": "A time unit which is equal to 365 days, or 366 days during a leap year.", + "meaning": "UO:0000036" + } + } + }, + "HostAgeBinMenu": { + "name": "HostAgeBinMenu", + "title": "host_age_bin menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "First winter [GENEPIO:0100684]": { + "text": "First winter [GENEPIO:0100684]", + "description": "An age group used to classify birds identified by their first winter nonbreeding plumage, generally indicating a juvenile bird.", + "meaning": "GENEPIO:0100684" + }, + "First summer [GENEPIO:0100685]": { + "text": "First summer [GENEPIO:0100685]", + "description": "An age group used to classify birds identified by their first summer nonbreeding plumage, generally indicating a juvenile bird.", + "meaning": "GENEPIO:0100685" + }, + "Second winter [GENEPIO:0100686]": { + "text": "Second winter [GENEPIO:0100686]", + "description": "An age group used to classify birds identified by their second winter plumage (many types of birds molt several times during the same season).", + "meaning": "GENEPIO:0100686" + }, + "Second summer [GENEPIO:0100687]": { + "text": "Second summer [GENEPIO:0100687]", + "description": "An age group used to classify birds identified by their second summer plumage (many types of birds molt several times during the same season).", + "meaning": "GENEPIO:0100687" + }, + "Third winter [GENEPIO:0100688]": { + "text": "Third winter [GENEPIO:0100688]", + "description": "An age group used to classify birds identified by their third winter plumage (many types of birds molt several times during the same season).", + "meaning": "GENEPIO:0100688" + }, + "Third summer [GENEPIO:0100689]": { + "text": "Third summer [GENEPIO:0100689]", + "description": "An age group used to classify birds identified by their third summer plumage (many types of birds molt several times during the same season).", + "meaning": "GENEPIO:0100689" + }, + "0 - 9 [GENEPIO:0100049]]": { + "text": "0 - 9 [GENEPIO:0100049]]", + "meaning": "ENEPIO:0100049" + }, + "10 - 19 [GENEPIO:0100050]": { + "text": "10 - 19 [GENEPIO:0100050]", + "description": "An age group that stratifies the age of a case to be between 10 to 19 years old (inclusive).", + "meaning": "GENEPIO:0100050" + }, + "20 - 29 [GENEPIO:0100051]": { + "text": "20 - 29 [GENEPIO:0100051]", + "description": "An age group that stratifies the age of a case to be between 20 to 29 years old (inclusive).", + "meaning": "GENEPIO:0100051" + }, + "30 - 39 [GENEPIO:0100052]": { + "text": "30 - 39 [GENEPIO:0100052]", + "description": "An age group that stratifies the age of a case to be between 30 to 39 years old (inclusive).", + "meaning": "GENEPIO:0100052" + }, + "40 - 49 [GENEPIO:0100053]": { + "text": "40 - 49 [GENEPIO:0100053]", + "description": "An age group that stratifies the age of a case to be between 40 to 49 years old (inclusive).", + "meaning": "GENEPIO:0100053" + }, + "50 - 59 [GENEPIO:0100054]": { + "text": "50 - 59 [GENEPIO:0100054]", + "description": "An age group that stratifies the age of a case to be between 50 to 59 years old (inclusive).", + "meaning": "GENEPIO:0100054" + }, + "60 - 69 [GENEPIO:0100055]": { + "text": "60 - 69 [GENEPIO:0100055]", + "description": "An age group that stratifies the age of a case to be between 60 to 69 years old (inclusive).", + "meaning": "GENEPIO:0100055" + }, + "70 - 79 [GENEPIO:0100056]": { + "text": "70 - 79 [GENEPIO:0100056]", + "description": "An age group that stratifies the age of a case to be between 70 to 79 years old (inclusive).", + "meaning": "GENEPIO:0100056" + }, + "80 - 89 [GENEPIO:0100057]": { + "text": "80 - 89 [GENEPIO:0100057]", + "description": "An age group that stratifies the age of a case to be between 80 to 89 years old (inclusive).", + "meaning": "GENEPIO:0100057" + }, + "90 - 99 [GENEPIO:0100058]": { + "text": "90 - 99 [GENEPIO:0100058]", + "description": "An age group that stratifies the age of a case to be between 90 to 99 years old (inclusive).", + "meaning": "GENEPIO:0100058" + }, + "100+ [GENEPIO:0100059]": { + "text": "100+ [GENEPIO:0100059]", + "description": "An age group that stratifies the age of a case to be greater than or equal to 100 years old.", + "meaning": "GENEPIO:0100059" + } + } + }, + "HostGender": { + "name": "HostGender", + "title": "host_gender", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Female [NCIT:C46110]": { + "text": "Female [NCIT:C46110]", + "description": "An individual who reports belonging to the cultural gender role distinction of female.", + "meaning": "NCIT:C46110" + }, + "Male [NCIT:C46109]": { + "text": "Male [NCIT:C46109]", + "description": "An individual who reports belonging to the cultural gender role distinction of male.", + "meaning": "NCIT:C46109" + }, + "Non-binary gender [GSSO:000132]": { + "text": "Non-binary gender [GSSO:000132]", + "description": "Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female.", + "meaning": "GSSO:000132" + }, + "Transgender (assigned male at birth) [GSSO:004004]": { + "text": "Transgender (assigned male at birth) [GSSO:004004]", + "description": "Having a feminine gender (identity) which is different from the sex one was assigned at birth.", + "meaning": "GSSO:004004" + }, + "Transgender (assigned female at birth) [GSSO:004005]": { + "text": "Transgender (assigned female at birth) [GSSO:004005]", + "description": "Having a masculine gender (identity) which is different from the sex one was assigned at birth.", + "meaning": "GSSO:004005" + }, + "Undeclared [NCIT:C110959]": { + "text": "Undeclared [NCIT:C110959]", + "meaning": "CIT:C110959" + } + } + }, + "HostDiseaseMenu": { + "name": "HostDiseaseMenu", + "title": "host_disease menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Highly pathogenic avian influenza A (HPAI)": { + "text": "Highly pathogenic avian influenza A (HPAI)" + } + } + }, + "HostHealthStateMenu": { + "name": "HostHealthStateMenu", + "title": "host_health_state menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Asymptomatic [NCIT:C3833]": { + "text": "Asymptomatic [NCIT:C3833]", + "description": "Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction.", + "meaning": "NCIT:C3833" + }, + "Deceased [NCIT:C28554]": { + "text": "Deceased [NCIT:C28554]", + "description": "The cessation of life.", + "meaning": "NCIT:C28554" + }, + "Healthy [NCIT:C115935]": { + "text": "Healthy [NCIT:C115935]", + "meaning": "CIT:C115935" + }, + "Recovered [NCIT:C49498]": { + "text": "Recovered [NCIT:C49498]", + "description": "One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated.", + "meaning": "NCIT:C49498" + }, + "Symptomatic [NCIT:C25269]": { + "text": "Symptomatic [NCIT:C25269]", + "description": "Exhibiting the symptoms of a particular disease.", + "meaning": "NCIT:C25269" + } + } + }, + "HostHealthStatusDetailsMenu": { + "name": "HostHealthStatusDetailsMenu", + "title": "host_health_status_details menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Hospitalized [NCIT:C25179]": { + "text": "Hospitalized [NCIT:C25179]", + "description": "The condition of being treated as a patient in a hospital.", + "meaning": "NCIT:C25179" + }, + "Hospitalized (Non-ICU) [GENEPIO:0100045]": { + "text": "Hospitalized (Non-ICU) [GENEPIO:0100045]", + "description": "The condition of being treated as a patient in a hospital without admission to an intensive care unit (ICU).", + "meaning": "GENEPIO:0100045", + "is_a": "Hospitalized [NCIT:C25179]" + }, + "Hospitalized (ICU) [GENEPIO:0100046]": { + "text": "Hospitalized (ICU) [GENEPIO:0100046]", + "description": "The condition of being treated as a patient in a hospital intensive care unit (ICU).", + "meaning": "GENEPIO:0100046", + "is_a": "Hospitalized [NCIT:C25179]" + }, + "Mechanical Ventilation [NCIT:C70909]": { + "text": "Mechanical Ventilation [NCIT:C70909]", + "meaning": "NCIT:C70909" + }, + "Medically Isolated [GENEPIO:0100047]": { + "text": "Medically Isolated [GENEPIO:0100047]", + "description": "Separation of people with a contagious disease from population to reduce the spread of the disease.", + "meaning": "GENEPIO:0100047" + }, + "Medically Isolated (Negative Pressure) [GENEPIO:0100048]": { + "text": "Medically Isolated (Negative Pressure) [GENEPIO:0100048]", + "description": "Medical isolation in a negative pressure environment: 6 to 12 air exchanges per hour, and direct exhaust to the outside or through a high efficiency particulate air filter.", + "meaning": "GENEPIO:0100048", + "is_a": "Medically Isolated [GENEPIO:0100047]" + }, + "Self-quarantining [NCIT:C173768]": { + "text": "Self-quarantining [NCIT:C173768]", + "meaning": "CIT:C173768" + } + } + }, + "HostHealthOutcomeMenu": { + "name": "HostHealthOutcomeMenu", + "title": "host_health_outcome menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Deceased [NCIT:C28554]": { + "text": "Deceased [NCIT:C28554]", + "description": "The cessation of life.", + "meaning": "NCIT:C28554" + }, + "Deteriorating [NCIT:C25254]": { + "text": "Deteriorating [NCIT:C25254]", + "description": "Advancing in extent or severity.", + "meaning": "NCIT:C25254" + }, + "Recovered [NCIT:C49498]": { + "text": "Recovered [NCIT:C49498]", + "description": "One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated.", + "meaning": "NCIT:C49498" + }, + "Stable [NCIT:C30103]": { + "text": "Stable [NCIT:C30103]", + "description": "Subject to little fluctuation; showing little if any change.", + "meaning": "NCIT:C30103" + } + } + }, + "SignsAndSymptomsMenu": { + "name": "SignsAndSymptomsMenu", + "title": "signs_and_symptoms menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Abnormal lung auscultation [HP:0030829]": { + "text": "Abnormal lung auscultation [HP:0030829]", + "meaning": "HP:0030829" + }, + "Acute Respiratory Distress Syndrome [HP:0033677]": { + "text": "Acute Respiratory Distress Syndrome [HP:0033677]", + "meaning": "HP:0033677" + }, + "Altered mental status [HP:0011446]": { + "text": "Altered mental status [HP:0011446]", + "meaning": "HP:0011446" + }, + "Cognitive impairment [HP:0100543]": { + "text": "Cognitive impairment [HP:0100543]", + "meaning": "HP:0100543", + "is_a": "Altered mental status [HP:0011446]" + }, + "Coma [HP:0001259]": { + "text": "Coma [HP:0001259]", + "meaning": "HP:0001259", + "is_a": "Altered mental status [HP:0011446]" + }, + "Confusion [HP:0001289]": { + "text": "Confusion [HP:0001289]", + "meaning": "HP:0001289", + "is_a": "Altered mental status [HP:0011446]" + }, + "Delirium (sudden severe confusion) [HP:0031258]": { + "text": "Delirium (sudden severe confusion) [HP:0031258]", + "meaning": "HP:0031258", + "is_a": "Confusion [HP:0001289]" + }, + "Arrhythmia [HP:0011675]": { + "text": "Arrhythmia [HP:0011675]", + "meaning": "HP:0011675" + }, + "Asthenia (generalized weakness) [HP:0025406]": { + "text": "Asthenia (generalized weakness) [HP:0025406]", + "meaning": "HP:0025406" + }, + "Bleeding gums [GENEPIO:0101182]": { + "text": "Bleeding gums [GENEPIO:0101182]", + "meaning": "GENEPIO:0101182" + }, + "Chest tightness or pressure [HP:0031352]": { + "text": "Chest tightness or pressure [HP:0031352]", + "meaning": "HP:0031352" + }, + "Rigors (fever shakes) [HP:0025145]": { + "text": "Rigors (fever shakes) [HP:0025145]", + "meaning": "HP:0025145", + "is_a": "Chest tightness or pressure [HP:0031352]" + }, + "Chills (sudden cold sensation) [HP:0025143]": { + "text": "Chills (sudden cold sensation) [HP:0025143]", + "description": "A sudden sensation of feeling cold.", + "meaning": "HP:0025143" + }, + "Conjunctivitis (pink eye) [HP:0000509]": { + "text": "Conjunctivitis (pink eye) [HP:0000509]", + "description": "Inflammation of the conjunctiva.", + "meaning": "HP:0000509" + }, + "Coryza (rhinitis) [MP:0001867]": { + "text": "Coryza (rhinitis) [MP:0001867]", + "meaning": "MP:0001867" + }, + "Cough [HP:0012735]": { + "text": "Cough [HP:0012735]", + "description": "A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation.", + "meaning": "HP:0012735" + }, + "Nonproductive cough (dry cough) [HP:0031246]": { + "text": "Nonproductive cough (dry cough) [HP:0031246]", + "meaning": "HP:0031246", + "is_a": "Cough [HP:0012735]" + }, + "Productive cough (wet cough) [HP:0031245]": { + "text": "Productive cough (wet cough) [HP:0031245]", + "meaning": "HP:0031245", + "is_a": "Cough [HP:0012735]" + }, + "Diarrhea [DOID:13250]": { + "text": "Diarrhea [DOID:13250]", + "meaning": "DOID:13250" + }, + "Dyspnea (breathing difficulty) [HP:0002094]": { + "text": "Dyspnea (breathing difficulty) [HP:0002094]", + "meaning": "HP:0002094" + }, + "Fatigue (tiredness) [HP:0012378]": { + "text": "Fatigue (tiredness) [HP:0012378]", + "description": "A subjective feeling of tiredness characterized by a lack of energy and motivation.", + "meaning": "HP:0012378" + }, + "Fever [HP:0001945]": { + "text": "Fever [HP:0001945]", + "description": "Body temperature elevated above the normal range.", + "meaning": "HP:0001945" + }, + "Fever (>=38°C) [GENEPIO:0100066]": { + "text": "Fever (>=38°C) [GENEPIO:0100066]", + "meaning": "GENEPIO:0100066", + "is_a": "Fever [HP:0001945]" + }, + "Headache [HP:0002315]": { + "text": "Headache [HP:0002315]", + "description": "Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve.", + "meaning": "HP:0002315" + }, + "Hypoxemia (low blood oxygen) [HP:0012418]": { + "text": "Hypoxemia (low blood oxygen) [HP:0012418]", + "meaning": "HP:0012418" + }, + "Silent hypoxemia [GENEPIO:0100068]": { + "text": "Silent hypoxemia [GENEPIO:0100068]", + "meaning": "GENEPIO:0100068", + "is_a": "Hypoxemia (low blood oxygen) [HP:0012418]" + }, + "Malaise (general discomfort/unease) [HP:0033834]": { + "text": "Malaise (general discomfort/unease) [HP:0033834]", + "meaning": "HP:0033834" + }, + "Muscle weakness [HP:0001324]": { + "text": "Muscle weakness [HP:0001324]", + "meaning": "HP:0001324" + }, + "Nasal obstruction (stuffy nose) [HP:0001742]": { + "text": "Nasal obstruction (stuffy nose) [HP:0001742]", + "meaning": "HP:0001742" + }, + "Nausea [HP:0002018]": { + "text": "Nausea [HP:0002018]", + "description": "A sensation of unease in the stomach together with an urge to vomit.", + "meaning": "HP:0002018" + }, + "Pain [HP:0012531]": { + "text": "Pain [HP:0012531]", + "meaning": "HP:0012531" + }, + "Arthralgia (painful joints) [HP:0002829]": { + "text": "Arthralgia (painful joints) [HP:0002829]", + "meaning": "HP:0002829", + "is_a": "Pain [HP:0012531]" + }, + "Myalgia (muscle pain) [HP:0003326]": { + "text": "Myalgia (muscle pain) [HP:0003326]", + "description": "Pain in muscle.", + "meaning": "HP:0003326", + "is_a": "Pain [HP:0012531]" + }, + "Pharyngitis (sore throat) [HP:0025439]": { + "text": "Pharyngitis (sore throat) [HP:0025439]", + "meaning": "HP:0025439" + }, + "Rhinorrhea (runny nose) [HP:0031417]": { + "text": "Rhinorrhea (runny nose) [HP:0031417]", + "meaning": "HP:0031417" + }, + "Shivering (involuntary muscle twitching) [HP:0025144]": { + "text": "Shivering (involuntary muscle twitching) [HP:0025144]", + "meaning": "HP:0025144" + }, + "Sneezing [HP:0025095]": { + "text": "Sneezing [HP:0025095]", + "meaning": "HP:0025095" + }, + "Sputum Production [HP:0033709]": { + "text": "Sputum Production [HP:0033709]", + "meaning": "HP:0033709" + }, + "Swollen Lymph Nodes [HP:0002716]": { + "text": "Swollen Lymph Nodes [HP:0002716]", + "description": "Enlargment (swelling) of a lymph node.", + "meaning": "HP:0002716" + }, + "Tachypnea (accelerated respiratory rate) [HP:0002789]": { + "text": "Tachypnea (accelerated respiratory rate) [HP:0002789]", + "meaning": "HP:0002789" + }, + "Vomiting (throwing up) [HP:0002013]": { + "text": "Vomiting (throwing up) [HP:0002013]", + "description": "Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions.", + "meaning": "HP:0002013" + } + } + }, + "PreExistingConditionsAndRiskFactorsMenu": { + "name": "PreExistingConditionsAndRiskFactorsMenu", + "title": "pre-existing_conditions_and_risk_factors menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Age 60+ [VO:0004925]": { + "text": "Age 60+ [VO:0004925]", + "meaning": "VO:0004925" + }, + "Anemia [DOID:2355]": { + "text": "Anemia [DOID:2355]", + "meaning": "DOID:2355" + }, + "Hemoglobinopathy [DOID:2860]": { + "text": "Hemoglobinopathy [DOID:2860]", + "meaning": "DOID:2860", + "is_a": "Anemia [DOID:2355]" + }, + "Anorexia [HP:0002039]": { + "text": "Anorexia [HP:0002039]", + "meaning": "HP:0002039" + }, + "Birthing labor [NCIT:C92743]": { + "text": "Birthing labor [NCIT:C92743]", + "meaning": "NCIT:C92743" + }, + "Bone marrow failure [NCIT:C80693]": { + "text": "Bone marrow failure [NCIT:C80693]", + "meaning": "NCIT:C80693" + }, + "Cancer [MONDO:0004992]": { + "text": "Cancer [MONDO:0004992]", + "description": "A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas.", + "meaning": "MONDO:0004992" + }, + "Breast cancer [MONDO:0007254]": { + "text": "Breast cancer [MONDO:0007254]", + "meaning": "MONDO:0007254", + "is_a": "Cancer [MONDO:0004992]" + }, + "Colorectal cancer [MONDO:0005575]": { + "text": "Colorectal cancer [MONDO:0005575]", + "meaning": "MONDO:0005575", + "is_a": "Cancer [MONDO:0004992]" + }, + "Hematologic malignancy (cancer of the blood) [DOID:2531]": { + "text": "Hematologic malignancy (cancer of the blood) [DOID:2531]", + "meaning": "DOID:2531", + "is_a": "Cancer [MONDO:0004992]" + }, + "Lung cancer [MONDO:0008903]": { + "text": "Lung cancer [MONDO:0008903]", + "meaning": "MONDO:0008903", + "is_a": "Cancer [MONDO:0004992]" + }, + "Metastatic disease [MONDO:0024880]": { + "text": "Metastatic disease [MONDO:0024880]", + "meaning": "MONDO:0024880", + "is_a": "Cancer [MONDO:0004992]" + }, + "Cancer treatment [NCIT:C16212]": { + "text": "Cancer treatment [NCIT:C16212]", + "description": "Any intervention for management of a malignant neoplasm.", + "meaning": "NCIT:C16212" + }, + "Cancer surgery [NCIT:C157740]": { + "text": "Cancer surgery [NCIT:C157740]", + "meaning": "NCIT:C157740", + "is_a": "Cancer treatment [NCIT:C16212]" + }, + "Chemotherapy [NCIT:C15632]": { + "text": "Chemotherapy [NCIT:C15632]", + "description": "The use of synthetic or naturally-occurring chemicals for the treatment of diseases.", + "meaning": "NCIT:C15632", + "is_a": "Cancer treatment [NCIT:C16212]" + }, + "Adjuvant chemotherapy [NCIT:C15360]": { + "text": "Adjuvant chemotherapy [NCIT:C15360]", + "meaning": "NCIT:C15360", + "is_a": "Chemotherapy [NCIT:C15632]" + }, + "Cardiac disorder [NCIT:C3079]": { + "text": "Cardiac disorder [NCIT:C3079]", + "meaning": "NCIT:C3079" + }, + "Arrhythmia [HP:0011675]": { + "text": "Arrhythmia [HP:0011675]", + "meaning": "HP:0011675", + "is_a": "Cardiac disorder [NCIT:C3079]" + }, + "Cardiac disease [MONDO:0005267]": { + "text": "Cardiac disease [MONDO:0005267]", + "meaning": "MONDO:0005267", + "is_a": "Cardiac disorder [NCIT:C3079]" + }, + "Cardiomyopathy [HP:0001638]": { + "text": "Cardiomyopathy [HP:0001638]", + "meaning": "HP:0001638", + "is_a": "Cardiac disorder [NCIT:C3079]" + }, + "Cardiac injury [GENEPIO:0100074]": { + "text": "Cardiac injury [GENEPIO:0100074]", + "meaning": "GENEPIO:0100074", + "is_a": "Cardiac disorder [NCIT:C3079]" + }, + "Hypertension (high blood pressure) [HP:0000822]": { + "text": "Hypertension (high blood pressure) [HP:0000822]", + "meaning": "HP:0000822", + "is_a": "Cardiac disorder [NCIT:C3079]" + }, + "Hypotension (low blood pressure) [HP:0002615]": { + "text": "Hypotension (low blood pressure) [HP:0002615]", + "meaning": "HP:0002615", + "is_a": "Cardiac disorder [NCIT:C3079]" + }, + "Cesarean section [HP:0011410]": { + "text": "Cesarean section [HP:0011410]", + "meaning": "HP:0011410" + }, + "Chronic cough [GENEPIO:0100075]": { + "text": "Chronic cough [GENEPIO:0100075]", + "meaning": "GENEPIO:0100075" + }, + "Chronic gastrointestinal disease [GENEPIO:0100076]": { + "text": "Chronic gastrointestinal disease [GENEPIO:0100076]", + "meaning": "GENEPIO:0100076" + }, + "Corticosteroids [NCIT:C211]": { + "text": "Corticosteroids [NCIT:C211]", + "meaning": "NCIT:C211" + }, + "Diabetes mellitus (diabetes) [HP:0000819]": { + "text": "Diabetes mellitus (diabetes) [HP:0000819]", + "description": "A group of abnormalities characterized by hyperglycemia and glucose intolerance.", + "meaning": "HP:0000819" + }, + "Type I diabetes mellitus (T1D) [HP:0100651]": { + "text": "Type I diabetes mellitus (T1D) [HP:0100651]", + "description": "A chronic condition in which the pancreas produces little or no insulin. Type I diabetes mellitus is manifested by the sudden onset of severe hyperglycemia with rapid progression to diabetic ketoacidosis unless treated with insulin.", + "meaning": "HP:0100651", + "is_a": "Diabetes mellitus (diabetes) [HP:0000819]" + }, + "Type II diabetes mellitus (T2D) [HP:0005978]": { + "text": "Type II diabetes mellitus (T2D) [HP:0005978]", + "description": "A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia.", + "meaning": "HP:0005978", + "is_a": "Diabetes mellitus (diabetes) [HP:0000819]" + }, + "Eczema [HP:0000964]": { + "text": "Eczema [HP:0000964]", + "meaning": "HP:0000964" + }, + "Electrolyte disturbance [HP:0003111]": { + "text": "Electrolyte disturbance [HP:0003111]", + "meaning": "HP:0003111" + }, + "Hypocalcemia [HP:0002901]": { + "text": "Hypocalcemia [HP:0002901]", + "meaning": "HP:0002901", + "is_a": "Electrolyte disturbance [HP:0003111]" + }, + "Hypokalemia [HP:0002900]": { + "text": "Hypokalemia [HP:0002900]", + "meaning": "HP:0002900", + "is_a": "Electrolyte disturbance [HP:0003111]" + }, + "Hypomagnesemia [HP:0002917]": { + "text": "Hypomagnesemia [HP:0002917]", + "meaning": "HP:0002917", + "is_a": "Electrolyte disturbance [HP:0003111]" + }, + "Encephalitis (brain inflammation) [HP:0002383]": { + "text": "Encephalitis (brain inflammation) [HP:0002383]", + "meaning": "HP:0002383" + }, + "Epilepsy [MONDO:0005027]": { + "text": "Epilepsy [MONDO:0005027]", + "meaning": "MONDO:0005027" + }, + "Hemodialysis [NCIT:C15248]": { + "text": "Hemodialysis [NCIT:C15248]", + "meaning": "NCIT:C15248" + }, + "Hemoglobinopathy [MONDO:0044348]": { + "text": "Hemoglobinopathy [MONDO:0044348]", + "meaning": "MONDO:0044348" + }, + "Human immunodeficiency virus (HIV) [MONDO:0005109]": { + "text": "Human immunodeficiency virus (HIV) [MONDO:0005109]", + "description": "An infection caused by the human immunodeficiency virus.", + "meaning": "MONDO:0005109" + }, + "Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]": { + "text": "Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]", + "description": "A syndrome resulting from the acquired deficiency of cellular immunity caused by the human immunodeficiency virus (HIV). It is characterized by the reduction of the Helper T-lymphocytes in the peripheral blood and the lymph nodes.", + "meaning": "MONDO:0012268", + "is_a": "Human immunodeficiency virus (HIV) [MONDO:0005109]" + }, + "HIV and antiretroviral therapy (ART) [NCIT:C16118]": { + "text": "HIV and antiretroviral therapy (ART) [NCIT:C16118]", + "description": "Treatment of human immunodeficiency virus (HIV) infections with medications that target the virus directly, limiting the ability of infected cells to produce new HIV particles.", + "meaning": "NCIT:C16118", + "is_a": "Human immunodeficiency virus (HIV) [MONDO:0005109]" + }, + "Immunocompromised [NCIT:C14139]": { + "text": "Immunocompromised [NCIT:C14139]", + "description": "A loss of any arm of immune functions, resulting in potential or actual increase in infections. This state may be reached secondary to specific genetic lesions, syndromes with unidentified or polygenic causes, acquired deficits from other disease states, or as result of therapy for other diseases or conditions.", + "meaning": "NCIT:C14139" + }, + "Lupus [MONDO:0004670]": { + "text": "Lupus [MONDO:0004670]", + "description": "An autoimmune, connective tissue chronic inflammatory disorder affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood cells. It is more commonly seen in women than men. Variants include discoid and systemic lupus erythematosus.", + "meaning": "MONDO:0004670", + "is_a": "Immunocompromised [NCIT:C14139]" + }, + "Inflammatory bowel disease (IBD) [MONDO:0005265]": { + "text": "Inflammatory bowel disease (IBD) [MONDO:0005265]", + "meaning": "MONDO:0005265" + }, + "Colitis [HP:0002583]": { + "text": "Colitis [HP:0002583]", + "meaning": "HP:0002583", + "is_a": "Inflammatory bowel disease (IBD) [MONDO:0005265]" + }, + "Ulcerative colitis [HP:0100279]": { + "text": "Ulcerative colitis [HP:0100279]", + "meaning": "HP:0100279", + "is_a": "Colitis [HP:0002583]" + }, + "Crohn's disease [HP:0100280]": { + "text": "Crohn's disease [HP:0100280]", + "meaning": "HP:0100280", + "is_a": "Inflammatory bowel disease (IBD) [MONDO:0005265]" + }, + "Renal disorder [NCIT:C3149]": { + "text": "Renal disorder [NCIT:C3149]", + "meaning": "NCIT:C3149" + }, + "Renal disease [MONDO:0005240]": { + "text": "Renal disease [MONDO:0005240]", + "meaning": "MONDO:0005240", + "is_a": "Renal disorder [NCIT:C3149]" + }, + "Chronic renal disease [HP:0012622]": { + "text": "Chronic renal disease [HP:0012622]", + "meaning": "HP:0012622", + "is_a": "Renal disease [MONDO:0005240]" + }, + "Renal failure [HP:0000083]": { + "text": "Renal failure [HP:0000083]", + "meaning": "HP:0000083", + "is_a": "Renal disorder [NCIT:C3149]" + }, + "Liver disease [MONDO:0005154]": { + "text": "Liver disease [MONDO:0005154]", + "meaning": "MONDO:0005154" + }, + "Chronic liver disease [NCIT:C113609]": { + "text": "Chronic liver disease [NCIT:C113609]", + "meaning": "NCIT:C113609", + "is_a": "Liver disease [MONDO:0005154]" + }, + "Fatty liver disease (FLD) [HP:0001397]": { + "text": "Fatty liver disease (FLD) [HP:0001397]", + "meaning": "HP:0001397", + "is_a": "Chronic liver disease [NCIT:C113609]" + }, + "Myalgia (muscle pain) [HP:0003326]": { + "text": "Myalgia (muscle pain) [HP:0003326]", + "description": "Pain in muscle.", + "meaning": "HP:0003326" + }, + "Myalgic encephalomyelitis (ME) [MONDO:0005404]": { + "text": "Myalgic encephalomyelitis (ME) [MONDO:0005404]", + "meaning": "MONDO:0005404" + }, + "Neurological disorder [MONDO:0005071]": { + "text": "Neurological disorder [MONDO:0005071]", + "meaning": "MONDO:0005071" + }, + "Neuromuscular disorder [MONDO:0019056]": { + "text": "Neuromuscular disorder [MONDO:0019056]", + "meaning": "MONDO:0019056", + "is_a": "Neurological disorder [MONDO:0005071]" + }, + "Obesity [HP:0001513]": { + "text": "Obesity [HP:0001513]", + "meaning": "HP:0001513" + }, + "Severe obesity [MONDO:0005139]": { + "text": "Severe obesity [MONDO:0005139]", + "meaning": "MONDO:0005139", + "is_a": "Obesity [HP:0001513]" + }, + "Respiratory disorder [MONDO:0005087]": { + "text": "Respiratory disorder [MONDO:0005087]", + "meaning": "MONDO:0005087" + }, + "Asthma [HP:0002099]": { + "text": "Asthma [HP:0002099]", + "meaning": "HP:0002099", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Chronic bronchitis [HP:0004469]": { + "text": "Chronic bronchitis [HP:0004469]", + "meaning": "HP:0004469", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Chronic obstructive pulmonary disease [HP:0006510]": { + "text": "Chronic obstructive pulmonary disease [HP:0006510]", + "meaning": "HP:0006510", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Emphysema [HP:0002097]": { + "text": "Emphysema [HP:0002097]", + "meaning": "HP:0002097", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Lung disease [MONDO:0005275]": { + "text": "Lung disease [MONDO:0005275]", + "meaning": "MONDO:0005275", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Chronic lung disease [HP:0006528]": { + "text": "Chronic lung disease [HP:0006528]", + "meaning": "HP:0006528", + "is_a": "Lung disease [MONDO:0005275]" + }, + "Pulmonary fibrosis [HP:0002206]": { + "text": "Pulmonary fibrosis [HP:0002206]", + "meaning": "HP:0002206", + "is_a": "Lung disease [MONDO:0005275]" + }, + "Pneumonia [HP:0002090]": { + "text": "Pneumonia [HP:0002090]", + "meaning": "HP:0002090", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Respiratory failure [HP:0002878]": { + "text": "Respiratory failure [HP:0002878]", + "meaning": "HP:0002878", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Adult respiratory distress syndrome [HP:0033677]": { + "text": "Adult respiratory distress syndrome [HP:0033677]", + "meaning": "HP:0033677", + "is_a": "Respiratory failure [HP:0002878]" + }, + "Newborn respiratory distress syndrome [MONDO:0009971]": { + "text": "Newborn respiratory distress syndrome [MONDO:0009971]", + "meaning": "MONDO:0009971", + "is_a": "Respiratory failure [HP:0002878]" + }, + "Tuberculosis [MONDO:0018076]": { + "text": "Tuberculosis [MONDO:0018076]", + "meaning": "MONDO:0018076", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Postpartum (≤6 weeks) [GENEPIO:0100077]": { + "text": "Postpartum (≤6 weeks) [GENEPIO:0100077]", + "meaning": "GENEPIO:0100077" + }, + "Pregnancy [NCIT:C25742]": { + "text": "Pregnancy [NCIT:C25742]", + "description": "The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth.", + "meaning": "NCIT:C25742" + }, + "Reye syndrome [DOID:14525]": { + "text": "Reye syndrome [DOID:14525]", + "meaning": "DOID:14525" + }, + "Rheumatic disease [MONDO:0005554]": { + "text": "Rheumatic disease [MONDO:0005554]", + "meaning": "MONDO:0005554" + }, + "Sickle cell disease [MONDO:0011382]": { + "text": "Sickle cell disease [MONDO:0011382]", + "meaning": "MONDO:0011382" + }, + "Substance use [NBO:0001845]": { + "text": "Substance use [NBO:0001845]", + "meaning": "NBO:0001845" + }, + "Alcohol abuse [MONDO:0002046]": { + "text": "Alcohol abuse [MONDO:0002046]", + "meaning": "MONDO:0002046", + "is_a": "Substance use [NBO:0001845]" + }, + "Drug abuse [GENEPIO:0100078]": { + "text": "Drug abuse [GENEPIO:0100078]", + "meaning": "GENEPIO:0100078", + "is_a": "Substance use [NBO:0001845]" + }, + "Injection drug abuse [GENEPIO:0100079]": { + "text": "Injection drug abuse [GENEPIO:0100079]", + "meaning": "GENEPIO:0100079", + "is_a": "Drug abuse [GENEPIO:0100078]" + }, + "Smoking [NBO:0015005]": { + "text": "Smoking [NBO:0015005]", + "meaning": "NBO:0015005", + "is_a": "Substance use [NBO:0001845]" + }, + "Vaping [NCIT:C173621]": { + "text": "Vaping [NCIT:C173621]", + "meaning": "NCIT:C173621", + "is_a": "Substance use [NBO:0001845]" + }, + "Tachypnea (accelerated respiratory rate) [HP:0002789]": { + "text": "Tachypnea (accelerated respiratory rate) [HP:0002789]", + "meaning": "HP:0002789" + }, + "Transplant [NCIT:C159659]": { + "text": "Transplant [NCIT:C159659]", + "meaning": "CIT:C159659" + }, + "Cardiac transplant [NCIT:C131759]": { + "text": "Cardiac transplant [NCIT:C131759]", + "meaning": "NCIT:C131759", + "is_a": "Transplant [NCIT:C159659]" + }, + "Hematopoietic stem cell transplant (bone marrow transplant) [GENEPIO:0100080]": { + "text": "Hematopoietic stem cell transplant (bone marrow transplant) [GENEPIO:0100080]", + "meaning": "GENEPIO:0100080", + "is_a": "Transplant [NCIT:C159659]" + }, + "Kidney transplant [NCIT:C157332]": { + "text": "Kidney transplant [NCIT:C157332]", + "meaning": "NCIT:C157332", + "is_a": "Transplant [NCIT:C159659]" + }, + "Liver transplant [GENEPIO:0100081]": { + "text": "Liver transplant [GENEPIO:0100081]", + "meaning": "GENEPIO:0100081", + "is_a": "Transplant [NCIT:C159659]" + } + } + }, + "ComplicationsMenu": { + "name": "ComplicationsMenu", + "title": "complications menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Abnormal blood oxygen level [HP:0500165]": { + "text": "Abnormal blood oxygen level [HP:0500165]", + "meaning": "HP:0500165" + }, + "Acute lung injury [MONDO:0015796]": { + "text": "Acute lung injury [MONDO:0015796]", + "meaning": "MONDO:0015796" + }, + "Ventilation induced lung injury (VILI) [GENEPIO:0100092]": { + "text": "Ventilation induced lung injury (VILI) [GENEPIO:0100092]", + "meaning": "GENEPIO:0100092", + "is_a": "Acute lung injury [MONDO:0015796]" + }, + "Acute respiratory failure [MONDO:0001208]": { + "text": "Acute respiratory failure [MONDO:0001208]", + "meaning": "MONDO:0001208" + }, + "Arrhythmia (complication) [HP:0011675]": { + "text": "Arrhythmia (complication) [HP:0011675]", + "meaning": "HP:0011675" + }, + "Tachycardia [HP:0001649]": { + "text": "Tachycardia [HP:0001649]", + "meaning": "HP:0001649", + "is_a": "Arrhythmia (complication) [HP:0011675]" + }, + "Cardiac injury [GENEPIO:0100074]": { + "text": "Cardiac injury [GENEPIO:0100074]", + "meaning": "GENEPIO:0100074" + }, + "Cardiac arrest [HP:0001695]": { + "text": "Cardiac arrest [HP:0001695]", + "meaning": "HP:0001695" + }, + "Blood clot [HP:0001977]": { + "text": "Blood clot [HP:0001977]", + "meaning": "HP:0001977" + }, + "Arterial clot [HP:0004420]": { + "text": "Arterial clot [HP:0004420]", + "meaning": "HP:0004420", + "is_a": "Blood clot [HP:0001977]" + }, + "Deep vein thrombosis (DVT) [HP:0002625]": { + "text": "Deep vein thrombosis (DVT) [HP:0002625]", + "meaning": "HP:0002625", + "is_a": "Blood clot [HP:0001977]" + }, + "Pulmonary embolism (PE) [HP:0002204]": { + "text": "Pulmonary embolism (PE) [HP:0002204]", + "meaning": "HP:0002204", + "is_a": "Blood clot [HP:0001977]" + }, + "Cardiomyopathy [HP:0001638]": { + "text": "Cardiomyopathy [HP:0001638]", + "meaning": "HP:0001638" + }, + "Central nervous system invasion [MONDO:0024619]": { + "text": "Central nervous system invasion [MONDO:0024619]", + "meaning": "MONDO:0024619" + }, + "Stroke (complication) [HP:0001297]": { + "text": "Stroke (complication) [HP:0001297]", + "meaning": "HP:0001297" + }, + "Central Nervous System Vasculitis [MONDO:0003346]": { + "text": "Central Nervous System Vasculitis [MONDO:0003346]", + "meaning": "MONDO:0003346", + "is_a": "Stroke (complication) [HP:0001297]" + }, + "Acute ischemic stroke [HP:0002140]": { + "text": "Acute ischemic stroke [HP:0002140]", + "meaning": "HP:0002140", + "is_a": "Stroke (complication) [HP:0001297]" + }, + "Coma [HP:0001259]": { + "text": "Coma [HP:0001259]", + "meaning": "HP:0001259" + }, + "Convulsions [HP:0011097]": { + "text": "Convulsions [HP:0011097]", + "meaning": "HP:0011097" + }, + "Cystic fibrosis [MONDO:0009061]": { + "text": "Cystic fibrosis [MONDO:0009061]", + "meaning": "MONDO:0009061" + }, + "Cytokine release syndrome [MONDO:0600008]": { + "text": "Cytokine release syndrome [MONDO:0600008]", + "meaning": "MONDO:0600008" + }, + "Disseminated intravascular coagulation (DIC) [MPATH:108]": { + "text": "Disseminated intravascular coagulation (DIC) [MPATH:108]", + "meaning": "MPATH:108" + }, + "Encephalopathy [HP:0001298]": { + "text": "Encephalopathy [HP:0001298]", + "meaning": "HP:0001298" + }, + "Fulminant myocarditis [GENEPIO:0100088]": { + "text": "Fulminant myocarditis [GENEPIO:0100088]", + "meaning": "GENEPIO:0100088" + }, + "Guillain-Barré syndrome [MONDO:0016218]": { + "text": "Guillain-Barré syndrome [MONDO:0016218]", + "meaning": "MONDO:0016218" + }, + "Internal hemorrhage (complication; internal bleeding) [HP:0011029]": { + "text": "Internal hemorrhage (complication; internal bleeding) [HP:0011029]", + "meaning": "HP:0011029" + }, + "Intracerebral haemorrhage [MONDO:0013792]": { + "text": "Intracerebral haemorrhage [MONDO:0013792]", + "meaning": "MONDO:0013792", + "is_a": "Internal hemorrhage (complication; internal bleeding) [HP:0011029]" + }, + "Kawasaki disease [MONDO:0012727]": { + "text": "Kawasaki disease [MONDO:0012727]", + "meaning": "MONDO:0012727" + }, + "Complete Kawasaki disease [GENEPIO:0100089]": { + "text": "Complete Kawasaki disease [GENEPIO:0100089]", + "meaning": "GENEPIO:0100089", + "is_a": "Kawasaki disease [MONDO:0012727]" + }, + "Incomplete Kawasaki disease [GENEPIO:0100090]": { + "text": "Incomplete Kawasaki disease [GENEPIO:0100090]", + "meaning": "GENEPIO:0100090", + "is_a": "Kawasaki disease [MONDO:0012727]" + }, + "Liver dysfunction [HP:0001410]": { + "text": "Liver dysfunction [HP:0001410]", + "meaning": "HP:0001410" + }, + "Acute liver injury [GENEPIO:0100091]": { + "text": "Acute liver injury [GENEPIO:0100091]", + "meaning": "GENEPIO:0100091", + "is_a": "Liver dysfunction [HP:0001410]" + }, + "Long COVID-19 [MONDO:0100233]": { + "text": "Long COVID-19 [MONDO:0100233]", + "meaning": "MONDO:0100233" + }, + "Meningitis [HP:0001287]": { + "text": "Meningitis [HP:0001287]", + "meaning": "HP:0001287" + }, + "Migraine [HP:0002076]": { + "text": "Migraine [HP:0002076]", + "meaning": "HP:0002076" + }, + "Miscarriage [HP:0005268]": { + "text": "Miscarriage [HP:0005268]", + "meaning": "HP:0005268" + }, + "Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163]": { + "text": "Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163]", + "meaning": "MONDO:0100163" + }, + "Multisystem inflammatory syndrome in adults (MIS-A) [MONDO:0100319]": { + "text": "Multisystem inflammatory syndrome in adults (MIS-A) [MONDO:0100319]", + "meaning": "MONDO:0100319" + }, + "Muscle injury [GENEPIO:0100093]": { + "text": "Muscle injury [GENEPIO:0100093]", + "meaning": "GENEPIO:0100093" + }, + "Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404]": { + "text": "Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404]", + "meaning": "MONDO:0005404" + }, + "Myocardial infarction (heart attack) [MONDO:0005068]": { + "text": "Myocardial infarction (heart attack) [MONDO:0005068]", + "meaning": "MONDO:0005068" + }, + "Myocardial injury [HP:0001700]": { + "text": "Myocardial injury [HP:0001700]", + "meaning": "HP:0001700" + }, + "Neonatal complications [NCIT:C168498]": { + "text": "Neonatal complications [NCIT:C168498]", + "meaning": "CIT:C168498" + }, + "Noncardiogenic pulmonary edema [GENEPIO:0100085]": { + "text": "Noncardiogenic pulmonary edema [GENEPIO:0100085]", + "meaning": "GENEPIO:0100085" + }, + "Acute respiratory distress syndrome (ARDS) [HP:0033677]": { + "text": "Acute respiratory distress syndrome (ARDS) [HP:0033677]", + "meaning": "HP:0033677", + "is_a": "Noncardiogenic pulmonary edema [GENEPIO:0100085]" + }, + "Organ failure [GENEPIO:0100094]": { + "text": "Organ failure [GENEPIO:0100094]", + "meaning": "GENEPIO:0100094" + }, + "Paralysis [HP:0003470]": { + "text": "Paralysis [HP:0003470]", + "meaning": "HP:0003470" + }, + "Pneumothorax (collapsed lung) [HP:0002107]": { + "text": "Pneumothorax (collapsed lung) [HP:0002107]", + "meaning": "HP:0002107" + }, + "Pneumonia (complication) [HP:0002090]": { + "text": "Pneumonia (complication) [HP:0002090]", + "meaning": "HP:0002090" + }, + "Pregancy complications [HP:0001197]": { + "text": "Pregancy complications [HP:0001197]", + "meaning": "HP:0001197" + }, + "Rhabdomyolysis [HP:0003201]": { + "text": "Rhabdomyolysis [HP:0003201]", + "meaning": "HP:0003201" + }, + "Secondary infection [IDO:0000567]": { + "text": "Secondary infection [IDO:0000567]", + "description": "An infection bearing the secondary infection role.", + "meaning": "IDO:0000567" + }, + "Seizure (complication) [HP:0001250]": { + "text": "Seizure (complication) [HP:0001250]", + "meaning": "HP:0001250" + }, + "Sepsis/Septicemia [HP:0100806]": { + "text": "Sepsis/Septicemia [HP:0100806]", + "description": "Systemic inflammatory response to infection.", + "meaning": "HP:0100806" + }, + "Sepsis (systemic inflammatory response to infection) [IDO:0000636]": { + "text": "Sepsis (systemic inflammatory response to infection) [IDO:0000636]", + "meaning": "IDO:0000636", + "is_a": "Sepsis/Septicemia [HP:0100806]" + }, + "Septicemia (bloodstream infection) [NCIT:C3364]": { + "text": "Septicemia (bloodstream infection) [NCIT:C3364]", + "meaning": "NCIT:C3364", + "is_a": "Sepsis/Septicemia [HP:0100806]" + }, + "Shock [HP:0031273]": { + "text": "Shock [HP:0031273]", + "meaning": "HP:0031273" + }, + "Hyperinflammatory shock [GENEPIO:0100097]": { + "text": "Hyperinflammatory shock [GENEPIO:0100097]", + "meaning": "GENEPIO:0100097", + "is_a": "Shock [HP:0031273]" + }, + "Septic shock [NCIT:C35018]": { + "text": "Septic shock [NCIT:C35018]", + "meaning": "NCIT:C35018", + "is_a": "Shock [HP:0031273]" + }, + "Vasculitis [HP:0002633]": { + "text": "Vasculitis [HP:0002633]", + "meaning": "HP:0002633" + } + } + }, + "ExposureEventMenu": { + "name": "ExposureEventMenu", + "title": "exposure_event menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Mass Gathering [GENEPIO:0100237]": { + "text": "Mass Gathering [GENEPIO:0100237]", + "description": "A gathering or event attended by a sufficient number of people to strain the planning and response resources of the host community, state/province, nation, or region where it is being held.", + "meaning": "GENEPIO:0100237" + }, + "Convention [GENEPIO:0100238]": { + "text": "Convention [GENEPIO:0100238]", + "description": "A gathering of individuals who meet at an arranged place and time in order to discuss or engage in some common interest. The most common conventions are based upon industry, profession, and fandom.", + "meaning": "GENEPIO:0100238", + "is_a": "Mass Gathering [GENEPIO:0100237]" + }, + "Convocation [GENEPIO:0100239]": { + "text": "Convocation [GENEPIO:0100239]", + "meaning": "GENEPIO:0100239", + "is_a": "Mass Gathering [GENEPIO:0100237]" + }, + "Agricultural Event [GENEPIO:0100240]": { + "text": "Agricultural Event [GENEPIO:0100240]", + "description": "A gathering exhibiting the equipment, animals, sports and recreation associated with agriculture and animal husbandry.", + "meaning": "GENEPIO:0100240", + "is_a": "Mass Gathering [GENEPIO:0100237]" + }, + "Religious Gathering [GENEPIO:0100241]": { + "text": "Religious Gathering [GENEPIO:0100241]", + "meaning": "GENEPIO:0100241" + }, + "Mass [GENEPIO:0100242]": { + "text": "Mass [GENEPIO:0100242]", + "meaning": "GENEPIO:0100242", + "is_a": "Religious Gathering [GENEPIO:0100241]" + }, + "Social Gathering [PCO:0000033]": { + "text": "Social Gathering [PCO:0000033]", + "description": "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially.", + "meaning": "PCO:0000033" + }, + "Baby Shower [PCO:0000039]": { + "text": "Baby Shower [PCO:0000039]", + "meaning": "PCO:0000039", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Community Event [PCO:0000034]": { + "text": "Community Event [PCO:0000034]", + "meaning": "PCO:0000034", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Family Gathering [GENEPIO:0100243]": { + "text": "Family Gathering [GENEPIO:0100243]", + "meaning": "GENEPIO:0100243", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Family Reunion [GENEPIO:0100244]": { + "text": "Family Reunion [GENEPIO:0100244]", + "meaning": "GENEPIO:0100244", + "is_a": "Family Gathering [GENEPIO:0100243]" + }, + "Funeral [GENEPIO:0100245]": { + "text": "Funeral [GENEPIO:0100245]", + "meaning": "GENEPIO:0100245", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Party [PCO:0000035]": { + "text": "Party [PCO:0000035]", + "meaning": "PCO:0000035", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Potluck [PCO:0000037]": { + "text": "Potluck [PCO:0000037]", + "meaning": "PCO:0000037", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Wedding [PCO:0000038]": { + "text": "Wedding [PCO:0000038]", + "meaning": "PCO:0000038", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Animal contact event [GENEPIO:0101183]": { + "text": "Animal contact event [GENEPIO:0101183]", + "meaning": "GENEPIO:0101183" + }, + "Trip to a live animal market [GENEPIO:0101185]": { + "text": "Trip to a live animal market [GENEPIO:0101185]", + "meaning": "GENEPIO:0101185", + "is_a": "Animal contact event [GENEPIO:0101183]" + }, + "Trip to a farm [GENEPIO:0101186]": { + "text": "Trip to a farm [GENEPIO:0101186]", + "meaning": "GENEPIO:0101186", + "is_a": "Animal contact event [GENEPIO:0101183]" + }, + "Wildlife encounter [GENEPIO:0101188]": { + "text": "Wildlife encounter [GENEPIO:0101188]", + "meaning": "GENEPIO:0101188", + "is_a": "Animal contact event [GENEPIO:0101183]" + }, + "Hunting trip [GENEPIO:0101184]": { + "text": "Hunting trip [GENEPIO:0101184]", + "meaning": "GENEPIO:0101184", + "is_a": "Wildlife encounter [GENEPIO:0101188]" + }, + "Animal transportation event [GENEPIO:0101187]": { + "text": "Animal transportation event [GENEPIO:0101187]", + "meaning": "GENEPIO:0101187" + }, + "Other exposure event": { + "text": "Other exposure event" + } + } + }, + "ExposureContactLevelMenu": { + "name": "ExposureContactLevelMenu", + "title": "exposure_contact_level menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Contact with infected animal [GENEPIO:0101189]": { + "text": "Contact with infected animal [GENEPIO:0101189]", + "meaning": "GENEPIO:0101189" + }, + "Direct (host-to-animal contact) [GENEPIO:0101190]": { + "text": "Direct (host-to-animal contact) [GENEPIO:0101190]", + "meaning": "GENEPIO:0101190", + "is_a": "Contact with infected animal [GENEPIO:0101189]" + }, + "Indirect contact (host-to-animal) [GENEPIO:0101191]": { + "text": "Indirect contact (host-to-animal) [GENEPIO:0101191]", + "meaning": "GENEPIO:0101191", + "is_a": "Contact with infected animal [GENEPIO:0101189]" + }, + "Close animal contact (face-to-face contact) [GENEPIO:0101192]": { + "text": "Close animal contact (face-to-face contact) [GENEPIO:0101192]", + "meaning": "GENEPIO:0101192", + "is_a": "Indirect contact (host-to-animal) [GENEPIO:0101191]" + }, + "Casual animal contact [GENEPIO:0101193]": { + "text": "Casual animal contact [GENEPIO:0101193]", + "meaning": "GENEPIO:0101193", + "is_a": "Indirect contact (host-to-animal) [GENEPIO:0101191]" + }, + "Contact with infected individual": { + "text": "Contact with infected individual" + }, + "Direct (human-to-human contact) [TRANS:0000001]": { + "text": "Direct (human-to-human contact) [TRANS:0000001]", + "description": "Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission.", + "meaning": "TRANS:0000001", + "is_a": "Contact with infected individual" + }, + "Indirect contact [GENEPIO:0100246]": { + "text": "Indirect contact [GENEPIO:0100246]", + "description": "A type of contact in which an individual does not come in direct contact with a source of infection e.g. through airborne transmission, contact with contaminated surfaces.", + "meaning": "GENEPIO:0100246", + "is_a": "Contact with infected individual" + }, + "Close contact (face-to-face contact) [GENEPIO:0100247]": { + "text": "Close contact (face-to-face contact) [GENEPIO:0100247]", + "description": "A type of indirect contact where an individual sustains unprotected exposure by being within 6 feet of an infected individual over a sustained period of time.", + "meaning": "GENEPIO:0100247", + "is_a": "Indirect contact [GENEPIO:0100246]" + }, + "Casual contact [GENEPIO:0100248]": { + "text": "Casual contact [GENEPIO:0100248]", + "description": "A type of indirect contact where an individual may at the same location at the same time as a positive case; however, they may have been there only briefly, or it may have been a location that carries a lower risk of transmission.", + "meaning": "GENEPIO:0100248", + "is_a": "Indirect contact [GENEPIO:0100246]" + } + } + }, + "HostRoleMenu": { + "name": "HostRoleMenu", + "title": "host_role menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Attendee [GENEPIO:0100249]": { + "text": "Attendee [GENEPIO:0100249]", + "description": "A role inhering in a person that is realized when the bearer is present on a given occasion or at a given place.", + "meaning": "GENEPIO:0100249" + }, + "Student [OMRSE:00000058]": { + "text": "Student [OMRSE:00000058]", + "description": "A human social role that, if realized, is realized by the process of formal education that the bearer undergoes.", + "meaning": "OMRSE:00000058", + "is_a": "Attendee [GENEPIO:0100249]" + }, + "Patient [OMRSE:00000030]": { + "text": "Patient [OMRSE:00000030]", + "description": "A patient role that inheres in a human being.", + "meaning": "OMRSE:00000030" + }, + "Inpatient [NCIT:C25182]": { + "text": "Inpatient [NCIT:C25182]", + "description": "A patient who is residing in the hospital where he is being treated.", + "meaning": "NCIT:C25182", + "is_a": "Patient [OMRSE:00000030]" + }, + "Outpatient [NCIT:C28293]": { + "text": "Outpatient [NCIT:C28293]", + "description": "A patient who comes to a healthcare facility for diagnosis or treatment but is not admitted for an overnight stay.", + "meaning": "NCIT:C28293", + "is_a": "Patient [OMRSE:00000030]" + }, + "Passenger [GENEPIO:0100250]": { + "text": "Passenger [GENEPIO:0100250]", + "description": "A role inhering in a person that is realized when the bearer travels in a vehicle but bears little to no responsibility for vehicle operation nor arrival at its destination.", + "meaning": "GENEPIO:0100250" + }, + "Resident [GENEPIO:0100251]": { + "text": "Resident [GENEPIO:0100251]", + "description": "A role inhering in a person that is realized when the bearer maintains residency in a given place.", + "meaning": "GENEPIO:0100251" + }, + "Visitor [GENEPIO:0100252]": { + "text": "Visitor [GENEPIO:0100252]", + "description": "A role inhering in a person that is realized when the bearer pays a visit to a specific place or event.", + "meaning": "GENEPIO:0100252" + }, + "Volunteer [GENEPIO:0100253]": { + "text": "Volunteer [GENEPIO:0100253]", + "description": "A role inhering in a person that is realized when the bearer enters into any service of their own free will.", + "meaning": "GENEPIO:0100253" + }, + "Work [GENEPIO:0100254]": { + "text": "Work [GENEPIO:0100254]", + "description": "A role inhering in a person that is realized when the bearer performs labor for a living.", + "meaning": "GENEPIO:0100254" + }, + "Administrator [GENEPIO:0100255]": { + "text": "Administrator [GENEPIO:0100255]", + "description": "A role inhering in a person that is realized when the bearer is engaged in administration or administrative work.", + "meaning": "GENEPIO:0100255", + "is_a": "Work [GENEPIO:0100254]" + }, + "First Responder [GENEPIO:0100256]": { + "text": "First Responder [GENEPIO:0100256]", + "description": "A role inhering in a person that is realized when the bearer is among the first to arrive at the scene of an emergency and has specialized training to provide assistance.", + "meaning": "GENEPIO:0100256", + "is_a": "Work [GENEPIO:0100254]" + }, + "Firefighter [GENEPIO:0100257]": { + "text": "Firefighter [GENEPIO:0100257]", + "meaning": "GENEPIO:0100257", + "is_a": "First Responder [GENEPIO:0100256]" + }, + "Paramedic [GENEPIO:0100258]": { + "text": "Paramedic [GENEPIO:0100258]", + "meaning": "GENEPIO:0100258", + "is_a": "First Responder [GENEPIO:0100256]" + }, + "Police Officer [GENEPIO:0100259]": { + "text": "Police Officer [GENEPIO:0100259]", + "meaning": "GENEPIO:0100259", + "is_a": "First Responder [GENEPIO:0100256]" + }, + "Housekeeper [GENEPIO:0100260]": { + "text": "Housekeeper [GENEPIO:0100260]", + "description": "A role inhering in a person that is realized when the bearer is an individual who performs cleaning duties and/or is responsible for the supervision of cleaning staff.", + "meaning": "GENEPIO:0100260", + "is_a": "Work [GENEPIO:0100254]" + }, + "Kitchen Worker [GENEPIO:0100261]": { + "text": "Kitchen Worker [GENEPIO:0100261]", + "description": "A role inhering in a person that is realized when the bearer is an employee that performs labor in a kitchen.", + "meaning": "GENEPIO:0100261", + "is_a": "Work [GENEPIO:0100254]" + }, + "Healthcare Worker [GENEPIO:0100334]": { + "text": "Healthcare Worker [GENEPIO:0100334]", + "description": "A role inhering in a person that is realized when the bearer is an employee that performs labor in a healthcare setting.", + "meaning": "GENEPIO:0100334", + "is_a": "Work [GENEPIO:0100254]" + }, + "Community Healthcare Worker [GENEPIO:0100420]": { + "text": "Community Healthcare Worker [GENEPIO:0100420]", + "description": "A role inhering in a person that is realized when the bearer a professional caregiver that provides health care or supportive care in the individual home where the patient or client is living, as opposed to care provided in group accommodations like clinics or nursing home.", + "meaning": "GENEPIO:0100420", + "is_a": "Healthcare Worker [GENEPIO:0100334]" + }, + "Laboratory Worker [GENEPIO:0100262]": { + "text": "Laboratory Worker [GENEPIO:0100262]", + "description": "A role inhering in a person that is realized when the bearer is an employee that performs labor in a laboratory.", + "meaning": "GENEPIO:0100262", + "is_a": "Healthcare Worker [GENEPIO:0100334]" + }, + "Nurse [OMRSE:00000014]": { + "text": "Nurse [OMRSE:00000014]", + "description": "A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.", + "meaning": "OMRSE:00000014", + "is_a": "Healthcare Worker [GENEPIO:0100334]" + }, + "Personal Care Aid [GENEPIO:0100263]": { + "text": "Personal Care Aid [GENEPIO:0100263]", + "description": "A role inhering in a person that is realized when the bearer works to help another person complete their daily activities.", + "meaning": "GENEPIO:0100263", + "is_a": "Healthcare Worker [GENEPIO:0100334]" + }, + "Pharmacist [GENEPIO:0100264]": { + "text": "Pharmacist [GENEPIO:0100264]", + "description": "A role inhering in a person that is realized when the bearer is a health professional who specializes in dispensing prescription drugs at a healthcare facility.", + "meaning": "GENEPIO:0100264", + "is_a": "Healthcare Worker [GENEPIO:0100334]" + }, + "Physician [OMRSE:00000013]": { + "text": "Physician [OMRSE:00000013]", + "description": "A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.", + "meaning": "OMRSE:00000013", + "is_a": "Healthcare Worker [GENEPIO:0100334]" + }, + "Rotational Worker [GENEPIO:0100354]": { + "text": "Rotational Worker [GENEPIO:0100354]", + "description": "A role inhering in a person that is realized when the bearer performs labor on a regular schedule, often requiring travel to geographic locations other than where they live.", + "meaning": "GENEPIO:0100354", + "is_a": "Work [GENEPIO:0100254]" + }, + "Seasonal Worker [GENEPIO:0100355]": { + "text": "Seasonal Worker [GENEPIO:0100355]", + "description": "A role inhering in a person that is realized when the bearer performs labor for a particular period of the year, such as harvest, or Christmas.", + "meaning": "GENEPIO:0100355", + "is_a": "Work [GENEPIO:0100254]" + }, + "Veterinarian [GENEPIO:0100265]": { + "text": "Veterinarian [GENEPIO:0100265]", + "description": "A role inhering in a person that is realized when the bearer is a professional who practices veterinary medicine.", + "meaning": "GENEPIO:0100265", + "is_a": "Work [GENEPIO:0100254]" + }, + "Social role [OMRSE:00000001]": { + "text": "Social role [OMRSE:00000001]", + "description": "A social role inhering in a human being.", + "meaning": "OMRSE:00000001" + }, + "Acquaintance of case [GENEPIO:0100266]": { + "text": "Acquaintance of case [GENEPIO:0100266]", + "description": "A role inhering in a person that is realized when the bearer is in a state of being acquainted with a person.", + "meaning": "GENEPIO:0100266", + "is_a": "Social role [OMRSE:00000001]" + }, + "Relative of case [GENEPIO:0100267]": { + "text": "Relative of case [GENEPIO:0100267]", + "description": "A role inhering in a person that is realized when the bearer is a relative of the case.", + "meaning": "GENEPIO:0100267", + "is_a": "Social role [OMRSE:00000001]" + }, + "Child of case [GENEPIO:0100268]": { + "text": "Child of case [GENEPIO:0100268]", + "description": "A role inhering in a person that is realized when the bearer is a person younger than the age of majority.", + "meaning": "GENEPIO:0100268", + "is_a": "Relative of case [GENEPIO:0100267]" + }, + "Parent of case [GENEPIO:0100269]": { + "text": "Parent of case [GENEPIO:0100269]", + "description": "A role inhering in a person that is realized when the bearer is a caregiver of the offspring of their own species.", + "meaning": "GENEPIO:0100269", + "is_a": "Relative of case [GENEPIO:0100267]" + }, + "Father of case [GENEPIO:0100270]": { + "text": "Father of case [GENEPIO:0100270]", + "description": "A role inhering in a person that is realized when the bearer is the male parent of a child.", + "meaning": "GENEPIO:0100270", + "is_a": "Parent of case [GENEPIO:0100269]" + }, + "Mother of case [GENEPIO:0100271]": { + "text": "Mother of case [GENEPIO:0100271]", + "description": "A role inhering in a person that is realized when the bearer is the female parent of a child.", + "meaning": "GENEPIO:0100271", + "is_a": "Parent of case [GENEPIO:0100269]" + }, + "Spouse of case [GENEPIO:0100272]": { + "text": "Spouse of case [GENEPIO:0100272]", + "description": "A role inhering in a person that is realized when the bearer is a significant other in a marriage, civil union, or common-law marriage.", + "meaning": "GENEPIO:0100272", + "is_a": "Social role [OMRSE:00000001]" + }, + "Other Host Role": { + "text": "Other Host Role" + } + } + }, + "ExposureSettingMenu": { + "name": "ExposureSettingMenu", + "title": "exposure_setting menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Human Exposure [ECTO:3000005]": { + "text": "Human Exposure [ECTO:3000005]", + "description": "A history of exposure to Homo sapiens.", + "meaning": "ECTO:3000005" + }, + "Contact with Patient [GENEPIO:0100185]": { + "text": "Contact with Patient [GENEPIO:0100185]", + "description": "A process occuring within or in the vicinity of a human patient that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100185", + "is_a": "Human Exposure [ECTO:3000005]" + }, + "Contact with Person with Acute Respiratory Illness [GENEPIO:0100187]": { + "text": "Contact with Person with Acute Respiratory Illness [GENEPIO:0100187]", + "meaning": "GENEPIO:0100187", + "is_a": "Human Exposure [ECTO:3000005]" + }, + "Contact with Person with Fever and/or Cough [GENEPIO:0100188]": { + "text": "Contact with Person with Fever and/or Cough [GENEPIO:0100188]", + "meaning": "GENEPIO:0100188", + "is_a": "Human Exposure [ECTO:3000005]" + }, + "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]": { + "text": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]", + "description": "A process occuring within or in the vicinity of a human residential environment that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100190" + }, + "Abbatoir [ECTO:1000033]": { + "text": "Abbatoir [ECTO:1000033]", + "description": "A exposure event involving the interaction of an exposure receptor to abattoir.", + "meaning": "ECTO:1000033", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Animal Rescue [GENEPIO:0100191]": { + "text": "Animal Rescue [GENEPIO:0100191]", + "description": "A process occuring within or in the vicinity of an animal rescue facility that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100191", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Childcare [GENEPIO:0100192]": { + "text": "Childcare [GENEPIO:0100192]", + "description": "A process occuring within or in the vicinity of a human childcare environment that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100192", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Daycare [GENEPIO:0100193]": { + "text": "Daycare [GENEPIO:0100193]", + "description": "A process occuring within or in the vicinity of a human daycare environment that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100193", + "is_a": "Childcare [GENEPIO:0100192]" + }, + "Nursery [GENEPIO:0100194]": { + "text": "Nursery [GENEPIO:0100194]", + "description": "A process occuring within or in the vicinity of a human nursery that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100194", + "is_a": "Childcare [GENEPIO:0100192]" + }, + "Community Service Centre [GENEPIO:0100195]": { + "text": "Community Service Centre [GENEPIO:0100195]", + "description": "A process occuring within or in the vicinity of a community service centre that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100195", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Correctional Facility [GENEPIO:0100196]": { + "text": "Correctional Facility [GENEPIO:0100196]", + "description": "A process occuring within or in the vicinity of a correctional facility that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100196", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Dormitory [GENEPIO:0100197]": { + "text": "Dormitory [GENEPIO:0100197]", + "description": "A process occuring within or in the vicinity of a dormitory that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100197", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Farm [ECTO:1000034]": { + "text": "Farm [ECTO:1000034]", + "description": "A exposure event involving the interaction of an exposure receptor to farm", + "meaning": "ECTO:1000034", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "First Nations Reserve [GENEPIO:0100198]": { + "text": "First Nations Reserve [GENEPIO:0100198]", + "description": "A process occuring within or in the vicinity of a first nations reserve that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100198", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Funeral Home [GENEPIO:0100199]": { + "text": "Funeral Home [GENEPIO:0100199]", + "description": "A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100199", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Group Home [GENEPIO:0100200]": { + "text": "Group Home [GENEPIO:0100200]", + "description": "A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100200", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Healthcare Setting [GENEPIO:0100201]": { + "text": "Healthcare Setting [GENEPIO:0100201]", + "description": "A process occuring within or in the vicinity of a healthcare environment that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100201", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Ambulance [GENEPIO:0100202]": { + "text": "Ambulance [GENEPIO:0100202]", + "description": "A process occuring within or in the vicinity of an ambulance that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100202", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Acute Care Facility [GENEPIO:0100203]": { + "text": "Acute Care Facility [GENEPIO:0100203]", + "description": "A process occuring within or in the vicinity of an acute care facility that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100203", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Clinic [GENEPIO:0100204]": { + "text": "Clinic [GENEPIO:0100204]", + "description": "A process occuring within or in the vicinity of a medical clinic that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100204", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Community Healthcare (At-Home) Setting [GENEPIO:0100415]": { + "text": "Community Healthcare (At-Home) Setting [GENEPIO:0100415]", + "description": "A process occuring within or in the vicinty of a the individual home where the patient or client is living and health care or supportive care is being being delivered, as opposed to care provided in group accommodations like clinics or nursing home.", + "meaning": "GENEPIO:0100415", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Community Health Centre [GENEPIO:0100205]": { + "text": "Community Health Centre [GENEPIO:0100205]", + "description": "A process occuring within or in the vicinity of a community health centre that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100205", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Hospital [ECTO:1000035]": { + "text": "Hospital [ECTO:1000035]", + "description": "A exposure event involving the interaction of an exposure receptor to hospital.", + "meaning": "ECTO:1000035", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Emergency Department [GENEPIO:0100206]": { + "text": "Emergency Department [GENEPIO:0100206]", + "description": "A process occuring within or in the vicinity of an emergency department that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100206", + "is_a": "Hospital [ECTO:1000035]" + }, + "ICU [GENEPIO:0100207]": { + "text": "ICU [GENEPIO:0100207]", + "description": "A process occuring within or in the vicinity of an ICU that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100207", + "is_a": "Hospital [ECTO:1000035]" + }, + "Ward [GENEPIO:0100208]": { + "text": "Ward [GENEPIO:0100208]", + "description": "A process occuring within or in the vicinity of a hospital ward that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100208", + "is_a": "Hospital [ECTO:1000035]" + }, + "Laboratory [ECTO:1000036]": { + "text": "Laboratory [ECTO:1000036]", + "description": "A exposure event involving the interaction of an exposure receptor to laboratory facility.", + "meaning": "ECTO:1000036", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Long-Term Care Facility [GENEPIO:0100209]": { + "text": "Long-Term Care Facility [GENEPIO:0100209]", + "description": "A process occuring within or in the vicinity of a long-term care facility that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100209", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Pharmacy [GENEPIO:0100210]": { + "text": "Pharmacy [GENEPIO:0100210]", + "description": "A process occuring within or in the vicinity of a pharmacy that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100210", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Physician's Office [GENEPIO:0100211]": { + "text": "Physician's Office [GENEPIO:0100211]", + "description": "A process occuring within or in the vicinity of a physician's office that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100211", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Household [GENEPIO:0100212]": { + "text": "Household [GENEPIO:0100212]", + "description": "A process occuring within or in the vicinity of a household that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100212", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Insecure Housing (Homeless) [GENEPIO:0100213]": { + "text": "Insecure Housing (Homeless) [GENEPIO:0100213]", + "description": "A process occuring that exposes the recipient organism to a material entity as a consequence of said organism having insecure housing.", + "meaning": "GENEPIO:0100213", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Occupational Exposure [GENEPIO:0100214]": { + "text": "Occupational Exposure [GENEPIO:0100214]", + "description": "A process occuring within or in the vicinity of a human occupational environment that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100214", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Worksite [GENEPIO:0100215]": { + "text": "Worksite [GENEPIO:0100215]", + "description": "A process occuring within or in the vicinity of an office that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100215", + "is_a": "Occupational Exposure [GENEPIO:0100214]" + }, + "Office [ECTO:1000037]": { + "text": "Office [ECTO:1000037]", + "description": "A exposure event involving the interaction of an exposure receptor to office.", + "meaning": "ECTO:1000037", + "is_a": "Worksite [GENEPIO:0100215]" + }, + "Outdoors [GENEPIO:0100216]": { + "text": "Outdoors [GENEPIO:0100216]", + "description": "A process occuring outdoors that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100216", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Camp/camping [ECTO:5000009]": { + "text": "Camp/camping [ECTO:5000009]", + "description": "A exposure event involving the interaction of an exposure receptor to campground.", + "meaning": "ECTO:5000009", + "is_a": "Outdoors [GENEPIO:0100216]" + }, + "Hiking Trail [GENEPIO:0100217]": { + "text": "Hiking Trail [GENEPIO:0100217]", + "description": "A process that exposes the recipient organism to a material entity as a consequence of hiking.", + "meaning": "GENEPIO:0100217", + "is_a": "Outdoors [GENEPIO:0100216]" + }, + "Hunting Ground [ECTO:6000030]": { + "text": "Hunting Ground [ECTO:6000030]", + "description": "An exposure event involving hunting behavior", + "meaning": "ECTO:6000030", + "is_a": "Outdoors [GENEPIO:0100216]" + }, + "Petting zoo [ECTO:5000008]": { + "text": "Petting zoo [ECTO:5000008]", + "description": "A exposure event involving the interaction of an exposure receptor to petting zoo.", + "meaning": "ECTO:5000008", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Place of Worship [GENEPIO:0100220]": { + "text": "Place of Worship [GENEPIO:0100220]", + "description": "A process occuring within or in the vicinity of a place of worship that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100220", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Church [GENEPIO:0100221]": { + "text": "Church [GENEPIO:0100221]", + "description": "A process occuring within or in the vicinity of a church that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100221", + "is_a": "Place of Worship [GENEPIO:0100220]" + }, + "Mosque [GENEPIO:0100222]": { + "text": "Mosque [GENEPIO:0100222]", + "description": "A process occuring within or in the vicinity of a mosque that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100222", + "is_a": "Place of Worship [GENEPIO:0100220]" + }, + "Temple [GENEPIO:0100223]": { + "text": "Temple [GENEPIO:0100223]", + "description": "A process occuring within or in the vicinity of a temple that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100223", + "is_a": "Place of Worship [GENEPIO:0100220]" + }, + "Restaurant [ECTO:1000040]": { + "text": "Restaurant [ECTO:1000040]", + "description": "A exposure event involving the interaction of an exposure receptor to restaurant.", + "meaning": "ECTO:1000040", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Retail Store [ECTO:1000041]": { + "text": "Retail Store [ECTO:1000041]", + "description": "A exposure event involving the interaction of an exposure receptor to shop.", + "meaning": "ECTO:1000041", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "School [GENEPIO:0100224]": { + "text": "School [GENEPIO:0100224]", + "description": "A process occuring within or in the vicinity of a school that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100224", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Temporary Residence [GENEPIO:0100225]": { + "text": "Temporary Residence [GENEPIO:0100225]", + "description": "A process occuring within or in the vicinity of a temporary residence that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100225", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Homeless Shelter [GENEPIO:0100226]": { + "text": "Homeless Shelter [GENEPIO:0100226]", + "description": "A process occuring within or in the vicinity of a homeless shelter that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100226", + "is_a": "Temporary Residence [GENEPIO:0100225]" + }, + "Hotel [GENEPIO:0100227]": { + "text": "Hotel [GENEPIO:0100227]", + "description": "A process occuring within or in the vicinity of a hotel exposure that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100227", + "is_a": "Temporary Residence [GENEPIO:0100225]" + }, + "Veterinary Care Clinic [GENEPIO:0100228]": { + "text": "Veterinary Care Clinic [GENEPIO:0100228]", + "description": "A process occuring within or in the vicinity of a veterinary facility that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100228", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Travel Exposure [GENEPIO:0100229]": { + "text": "Travel Exposure [GENEPIO:0100229]", + "description": "A process occuring as a result of travel that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100229" + }, + "Travelled on a Cruise Ship [GENEPIO:0100230]": { + "text": "Travelled on a Cruise Ship [GENEPIO:0100230]", + "description": "A process occuring within or in the vicinity of a cruise ship that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100230", + "is_a": "Travel Exposure [GENEPIO:0100229]" + }, + "Travelled on a Plane [GENEPIO:0100231]": { + "text": "Travelled on a Plane [GENEPIO:0100231]", + "description": "A process occuring within or in the vicinity of an airplane that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100231", + "is_a": "Travel Exposure [GENEPIO:0100229]" + }, + "Travelled on Ground Transport [GENEPIO:0100232]": { + "text": "Travelled on Ground Transport [GENEPIO:0100232]", + "description": "A process occuring within or in the vicinity of ground transport that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100232", + "is_a": "Travel Exposure [GENEPIO:0100229]" + }, + "Travelled outside Province/Territory [GENEPIO:0001118]": { + "text": "Travelled outside Province/Territory [GENEPIO:0001118]", + "meaning": "GENEPIO:0001118", + "is_a": "Travel Exposure [GENEPIO:0100229]" + }, + "Travelled outside Canada [GENEPIO:0001119]": { + "text": "Travelled outside Canada [GENEPIO:0001119]", + "meaning": "GENEPIO:0001119", + "is_a": "Travel Exposure [GENEPIO:0100229]" + }, + "Other Exposure Setting [GENEPIO:0100235]": { + "text": "Other Exposure Setting [GENEPIO:0100235]", + "description": "A process occuring that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100235" + } + } + }, + "HostVaccinationStatusMenu": { + "name": "HostVaccinationStatusMenu", + "title": "host_vaccination_status menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Fully Vaccinated [GENEPIO:0100100]": { + "text": "Fully Vaccinated [GENEPIO:0100100]", + "description": "Completed a full series of an authorized vaccine according to the regional health institutional guidance.", + "meaning": "GENEPIO:0100100" + }, + "Not Vaccinated [GENEPIO:0100102]": { + "text": "Not Vaccinated [GENEPIO:0100102]", + "description": "Have not completed or initiated a vaccine series authorized and administered according to the regional health institutional guidance.", + "meaning": "GENEPIO:0100102" + } + } + }, + "InfluenzaAntiviralTreatmentAdministrationMenu": { + "name": "InfluenzaAntiviralTreatmentAdministrationMenu", + "title": "influenza_antiviral_treatment_administration menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Influenza antiviral treatment administered [GENEPIO:0101194]": { + "text": "Influenza antiviral treatment administered [GENEPIO:0101194]", + "meaning": "GENEPIO:0101194" + }, + "No influenza antiviral treatment administered [GENEPIO:0101195]": { + "text": "No influenza antiviral treatment administered [GENEPIO:0101195]", + "meaning": "GENEPIO:0101195" + } + } + }, + "WaterCatchmentAreaHumanPopulationRangeMenu": { + "name": "WaterCatchmentAreaHumanPopulationRangeMenu", + "title": "water_catchment_area_human_population_range menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "<10 people": { + "text": "<10 people" + }, + "10 - 100 people": { + "text": "10 - 100 people" + }, + "100 - 1,000 people": { + "text": "100 - 1,000 people" + }, + "1,000 - 10,000 people": { + "text": "1,000 - 10,000 people" + }, + "10,000 - 100,000 people": { + "text": "10,000 - 100,000 people" + }, + "100,000 - 1,000,000 people": { + "text": "100,000 - 1,000,000 people" + }, + "1,000,000+ people": { + "text": "1,000,000+ people" + } + } + }, + "WaterCatchmentAreaHumanPopulationDensityUnitMenu": { + "name": "WaterCatchmentAreaHumanPopulationDensityUnitMenu", + "title": "water_catchment_area_human_population_density_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "persons per square mile [GENEPIO:0100989]": { + "text": "persons per square mile [GENEPIO:0100989]", + "description": "A unit of population density that describes the average number of people in a square mile of a given area.", + "meaning": "GENEPIO:0100989" + }, + "persons per square kilometer [GENEPIO:0100990]": { + "text": "persons per square kilometer [GENEPIO:0100990]", + "description": "A unit of population density that describes the average number of people in a square kilometer of a given area.", + "meaning": "GENEPIO:0100990" + }, + "residents per square mile [GENEPIO:0100991]": { + "text": "residents per square mile [GENEPIO:0100991]", + "description": "A unit of population density that describes the average number of registered residents in a square mile of a given area.", + "meaning": "GENEPIO:0100991" + }, + "residents per square kilometer [GENEPIO:0100992]": { + "text": "residents per square kilometer [GENEPIO:0100992]", + "description": "A unit of population density that describes the average number of registered residents in a square kilometer of a given area.", + "meaning": "GENEPIO:0100992" + } + } + }, + "PopulatedAreaTypeMenu": { + "name": "PopulatedAreaTypeMenu", + "title": "populated_area_type menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Suburban [GSSO:011077]": { + "text": "Suburban [GSSO:011077]", + "description": "A mixed-use or residential area, existing either as part of a city/urban area, or as a separate residential community within commuting distance of one. Suburbs might have their own political or legal jurisdiction, especially in the United States, but this is not always the case, especially in the United Kingdom where most suburbs are located within the administrative boundaries of cities.", + "meaning": "GSSO:011077" + }, + "Rural [GSSO:011078]": { + "text": "Rural [GSSO:011078]", + "description": "A geographic area that is located outside towns and cities. Rural areas are primarily used for agriculture or pastoralism and may contain rural settlements.", + "meaning": "GSSO:011078" + }, + "Urban [GSSO:011080]": { + "text": "Urban [GSSO:011080]", + "description": "A human settlement with a high population density and infrastructure of built environment. Urban areas are created through urbanization and are categorized by urban morphology as cities, towns, conurbations or suburbs. In urbanism, the term contrasts to rural areas such as villages and hamlets; in urban sociology or urban anthropology it contrasts with natural environment.", + "meaning": "GSSO:011080" + } + } + }, + "SamplingWeatherConditionsMenu": { + "name": "SamplingWeatherConditionsMenu", + "title": "sampling_weather_conditions menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Cloudy/Overcast [ENVO:03501418]": { + "text": "Cloudy/Overcast [ENVO:03501418]", + "description": "Atmospheric weather in which the sky is mostly or completely obscured by clouds.", + "meaning": "ENVO:03501418" + }, + "Partially cloudy [ENVO:03501419]": { + "text": "Partially cloudy [ENVO:03501419]", + "description": "Atmospheric weather in which the sky is partially obscured by clouds.", + "meaning": "ENVO:03501419", + "is_a": "Cloudy/Overcast [ENVO:03501418]" + }, + "Drizzle [ENVO:03501420]": { + "text": "Drizzle [ENVO:03501420]", + "description": "An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process.", + "meaning": "ENVO:03501420" + }, + "Fog [ENVO:01000844]": { + "text": "Fog [ENVO:01000844]", + "description": "A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body.", + "meaning": "ENVO:01000844" + }, + "Rain [ENVO:01001564]": { + "text": "Rain [ENVO:01001564]", + "description": "An aggregate of raindrops falling to a planetary surface during a precipitation process.", + "meaning": "ENVO:01001564" + }, + "Snow [ENVO:01000406]": { + "text": "Snow [ENVO:01000406]", + "description": "Snow is an environmental material which is primarily composed of flakes of crystalline water ice.", + "meaning": "ENVO:01000406" + }, + "Storm [ENVO:01000876]": { + "text": "Storm [ENVO:01000876]", + "description": "A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates.", + "meaning": "ENVO:01000876" + }, + "Sunny/Clear [ENVO:03501421]": { + "text": "Sunny/Clear [ENVO:03501421]", + "description": "Atmospheric weather in which the sun can be seen to shine brightly.", + "meaning": "ENVO:03501421" + } + } + }, + "PresamplingWeatherConditionsMenu": { + "name": "PresamplingWeatherConditionsMenu", + "title": "presampling_weather_conditions menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Cloudy/Overcast [ENVO:03501418]": { + "text": "Cloudy/Overcast [ENVO:03501418]", + "description": "Atmospheric weather in which the sky is mostly or completely obscured by clouds.", + "meaning": "ENVO:03501418" + }, + "Partially cloudy [ENVO:03501419]": { + "text": "Partially cloudy [ENVO:03501419]", + "description": "Atmospheric weather in which the sky is partially obscured by clouds.", + "meaning": "ENVO:03501419", + "is_a": "Cloudy/Overcast [ENVO:03501418]" + }, + "Drizzle [ENVO:03501420]": { + "text": "Drizzle [ENVO:03501420]", + "description": "An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process.", + "meaning": "ENVO:03501420" + }, + "Fog [ENVO:01000844]": { + "text": "Fog [ENVO:01000844]", + "description": "A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body.", + "meaning": "ENVO:01000844" + }, + "Rain [ENVO:01001564]": { + "text": "Rain [ENVO:01001564]", + "description": "An aggregate of raindrops falling to a planetary surface during a precipitation process.", + "meaning": "ENVO:01001564" + }, + "Snow [ENVO:01000406]": { + "text": "Snow [ENVO:01000406]", + "description": "Snow is an environmental material which is primarily composed of flakes of crystalline water ice.", + "meaning": "ENVO:01000406" + }, + "Storm [ENVO:01000876]": { + "text": "Storm [ENVO:01000876]", + "description": "A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates.", + "meaning": "ENVO:01000876" + }, + "Sunny/Clear [ENVO:03501421]": { + "text": "Sunny/Clear [ENVO:03501421]", + "description": "Atmospheric weather in which the sun can be seen to shine brightly.", + "meaning": "ENVO:03501421" + } + } + }, + "PrecipitationMeasurementUnitMenu": { + "name": "PrecipitationMeasurementUnitMenu", + "title": "precipitation_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "millimeter (mm) [UO:0000016]": { + "text": "millimeter (mm) [UO:0000016]", + "description": "A length unit which is defined as one thousandth of a meter.", + "meaning": "UO:0000016" + }, + "centimeter (cm) [UO:0000015]": { + "text": "centimeter (cm) [UO:0000015]", + "description": "A length unit which is equal to one hundredth of a meter or 10^[-2] m", + "meaning": "UO:0000015" + }, + "meter (m) [UO:0000008]": { + "text": "meter (m) [UO:0000008]", + "description": "An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second.", + "meaning": "UO:0000008" + }, + "inch (in) [UO:0010011]": { + "text": "inch (in) [UO:0010011]", + "description": "A non-SI unit of length defined as one twelfth of a foot.", + "meaning": "UO:0010011" + }, + "foot (ft) [UO:0010013]": { + "text": "foot (ft) [UO:0010013]", + "description": "A non-SI unit of length which is approximately 0.3048 meters.", + "meaning": "UO:0010013" + } + } + }, + "AirPressureMeasurementUnitMenu": { + "name": "AirPressureMeasurementUnitMenu", + "title": "air_pressure_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "atmosphere (atm) [EFO:0005212]": { + "text": "atmosphere (atm) [EFO:0005212]", + "description": "A non-SI unit of pressure defined as 101,325 pascals (Pa).", + "meaning": "EFO:0005212" + }, + "bar": { + "text": "bar" + }, + "pascal [UO:0000110]": { + "text": "pascal [UO:0000110]", + "description": "An SI unit of pressure defined as one newton per square meter (N/m^2).", + "meaning": "UO:0000110" + } + } + }, + "AmbientTemperatureMeasurementUnitMenu": { + "name": "AmbientTemperatureMeasurementUnitMenu", + "title": "ambient_temperature_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "degree Fahrenheit (F) [UO:0000195]": { + "text": "degree Fahrenheit (F) [UO:0000195]", + "description": "A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions.", + "meaning": "UO:0000195" + }, + "degree Celsius (C) [UO:0000027]": { + "text": "degree Celsius (C) [UO:0000027]", + "description": "A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions.", + "meaning": "UO:0000027" + } + } + }, + "TotalDailyFlowRateMeasurementUnitMenu": { + "name": "TotalDailyFlowRateMeasurementUnitMenu", + "title": "total_daily_flow_rate_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "cubic meter per second (m^3/s)": { + "text": "cubic meter per second (m^3/s)" + }, + "cubic meter per minute (m^3/min)": { + "text": "cubic meter per minute (m^3/min)" + }, + "cubic meter per hour (m^3/h)": { + "text": "cubic meter per hour (m^3/h)" + }, + "liter per second (L/s)": { + "text": "liter per second (L/s)" + }, + "liter per minute (L/min)": { + "text": "liter per minute (L/min)" + }, + "liter per hour (L/h)": { + "text": "liter per hour (L/h)" + }, + "liter per day (L/day)": { + "text": "liter per day (L/day)" + }, + "million gallons per day (MGD)": { + "text": "million gallons per day (MGD)" + } + } + }, + "InstantaneousFlowRateMeasurementUnitMenu": { + "name": "InstantaneousFlowRateMeasurementUnitMenu", + "title": "instantaneous_flow_rate_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "cubic meter per second (m^3/s)": { + "text": "cubic meter per second (m^3/s)" + }, + "cubic meter per minute (m^3/min)": { + "text": "cubic meter per minute (m^3/min)" + }, + "cubic meter per hour (m^3/h)": { + "text": "cubic meter per hour (m^3/h)" + }, + "liter per second (L/s)": { + "text": "liter per second (L/s)" + }, + "liter per minute (L/min)": { + "text": "liter per minute (L/min)" + }, + "liter per hour (L/h)": { + "text": "liter per hour (L/h)" + }, + "liter per day (L/day)": { + "text": "liter per day (L/day)" + }, + "million gallons per day (MGD)": { + "text": "million gallons per day (MGD)" + } + } + }, + "TurbidityMeasurementUnitMenu": { + "name": "TurbidityMeasurementUnitMenu", + "title": "turbidity_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "nephelometric turbidity unit (NTU)": { + "text": "nephelometric turbidity unit (NTU)" + }, + "formazin nephelometric unit (FNU) [UO:0000318]": { + "text": "formazin nephelometric unit (FNU) [UO:0000318]", + "description": "A measure of turbidity calculated by comparing how infrared light is scattered in a water sample against the amount of infrared light scattered in a reference solution containing formazin.", + "meaning": "UO:0000318" + } + } + }, + "DissolvedOxygenMeasurementUnitMenu": { + "name": "DissolvedOxygenMeasurementUnitMenu", + "title": "dissolved_oxygen_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", + "meaning": "UO:0000273" + }, + "kilogram per cubic meter (kg/m^3) [UO:0000083]": { + "text": "kilogram per cubic meter (kg/m^3) [UO:0000083]", + "description": "An SI unit of density that is one thousandth of the density of water.", + "meaning": "UO:0000083" + }, + "part per million (ppm) [UO:0000169]": { + "text": "part per million (ppm) [UO:0000169]", + "description": "A unitless measure of density that represents one item out of a million.", + "meaning": "UO:0000169" + } + } + }, + "OxygenReductionPotentialOrpMeasurementUnitMenu": { + "name": "OxygenReductionPotentialOrpMeasurementUnitMenu", + "title": "oxygen_reduction_potential_(ORP)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milliVolt (mV) [UO:0000247]": { + "text": "milliVolt (mV) [UO:0000247]", + "description": "A non-SI unit of electromotive force that is one thousandth of a volt.", + "meaning": "UO:0000247" + } + } + }, + "ChemicalOxygenDemandCodMeasurementUnitMenu": { + "name": "ChemicalOxygenDemandCodMeasurementUnitMenu", + "title": "chemical_oxygen_demand_(COD)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", + "meaning": "UO:0000273" + } + } + }, + "CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu": { + "name": "CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu", + "title": "carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", + "meaning": "UO:0000273" + } + } + }, + "TotalSuspendedSolidsTssMeasurementUnitMenu": { + "name": "TotalSuspendedSolidsTssMeasurementUnitMenu", + "title": "total_suspended_solids_(TSS)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "percent (%) [UO:0000187]": { + "text": "percent (%) [UO:0000187]", + "description": "A unitless measure that represents one in a hundred.", + "meaning": "UO:0000187" + }, + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", + "meaning": "UO:0000175" + } + } + }, + "TotalDissolvedSolidsTdsMeasurementUnitMenu": { + "name": "TotalDissolvedSolidsTdsMeasurementUnitMenu", + "title": "total_dissolved_solids_(TDS)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "percent (%) [UO:0000187]": { + "text": "percent (%) [UO:0000187]", + "description": "A unitless measure that represents one in a hundred.", + "meaning": "UO:0000187" + }, + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", + "meaning": "UO:0000175" + } + } + }, + "TotalSolidsTsMeasurementUnitMenu": { + "name": "TotalSolidsTsMeasurementUnitMenu", + "title": "total_solids_(TS)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "percent (%) [UO:0000187]": { + "text": "percent (%) [UO:0000187]", + "description": "A unitless measure that represents one in a hundred.", + "meaning": "UO:0000187" + }, + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", + "meaning": "UO:0000175" + } + } + }, + "AlkalinityMeasurementUnitMenu": { + "name": "AlkalinityMeasurementUnitMenu", + "title": "alkalinity_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milliequivalent per liter (meq/L)": { + "text": "milliequivalent per liter (meq/L)" + }, + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", + "meaning": "UO:0000273" + }, + "parts per million [UO:0000169]": { + "text": "parts per million [UO:0000169]", + "description": "A unitless measure of density that represents one item out of a million.", + "meaning": "UO:0000169" + } + } + }, + "ConductivityMeasurementUnitMenu": { + "name": "ConductivityMeasurementUnitMenu", + "title": "conductivity_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milliSiemen per centimeter (mS/cm)": { + "text": "milliSiemen per centimeter (mS/cm)" + }, + "microSiemen per centimeter (μS/cm)": { + "text": "microSiemen per centimeter (μS/cm)" + }, + "Siemen per meter (S/m)": { + "text": "Siemen per meter (S/m)" + } + } + }, + "SalinityMeasurementUnitMenu": { + "name": "SalinityMeasurementUnitMenu", + "title": "salinity_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "practical salinity unit (PSU)": { + "text": "practical salinity unit (PSU)" + }, + "weight for weight (% w/w)": { + "text": "weight for weight (% w/w)" + }, + "parts per thousand [UO:0000168]": { + "text": "parts per thousand [UO:0000168]", + "description": "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same.", + "meaning": "UO:0000168" + }, + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", + "meaning": "UO:0000175" + } + } + }, + "TotalNitrogenTnMeasurementUnitMenu": { + "name": "TotalNitrogenTnMeasurementUnitMenu", + "title": "total_nitrogen_(TN)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", + "meaning": "UO:0000273" + }, + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", + "meaning": "UO:0000175" + }, + "gram per total solids (g/gTS)": { + "text": "gram per total solids (g/gTS)" + } + } + }, + "TotalPhosphorpusTpMeasurementUnitMenu": { + "name": "TotalPhosphorpusTpMeasurementUnitMenu", + "title": "total_phosphorpus_(TP)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "gram per total solids (g/gTS)": { + "text": "gram per total solids (g/gTS)" + }, + "orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]": { + "text": "orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]", + "description": "A substance unit which describes the weight of orthophosphate as phosphorus (gPO4-P) within a sample to the weight of total solids.", + "meaning": "GENEPIO:0100998" + }, + "milligrams per liter (mg/L) [UO:0000273]": { + "text": "milligrams per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", + "meaning": "UO:0000273" + }, + "milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999]": { + "text": "milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999]", + "description": "A density unit comparing the weight of orthophosphate as phosphorus (PO4-P) in milligrams within a standard liter volume.", + "meaning": "GENEPIO:0100999" + } + } + }, + "FecalContaminationIndicatorMenu": { + "name": "FecalContaminationIndicatorMenu", + "title": "fecal contamination indicator menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "crAssphage [NCBITaxon:1211417]": { + "text": "crAssphage [NCBITaxon:1211417]", + "description": "CrAss-like phage, a bacteriophage discovered in 2014 in the human fecal metagenome.", + "meaning": "NCBITaxon:1211417" + }, + "PMMoV / pepper mild mottle virus [NCBITaxon:12239]": { + "text": "PMMoV / pepper mild mottle virus [NCBITaxon:12239]", + "description": "A plant RNA virus that is abundant in human feces.", + "meaning": "NCBITaxon:12239" + }, + "Bacteroides HF183": { + "text": "Bacteroides HF183", + "description": "A fecal indicator which is the most commonly used sewage-associated marker gene, belonging to the Bacteroides genus.", + "meaning": "GENEPIO:0101000" + }, + "Lachnospiraceae Lachno3": { + "text": "Lachnospiraceae Lachno3", + "description": "A fecal indicator which is a human-associated genetic marker in the Lachnospiraceae family of bacteria.", + "meaning": "GENEPIO:0101001" + }, + "F+ (male specific) coliphages": { + "text": "F+ (male specific) coliphages", + "description": "A fecal indicator which is a bacteriophage that infects coliform bacteria and is used in water assessment.", + "meaning": "GENEPIO:0101002" + }, + "Stercobilin": { + "text": "Stercobilin", + "description": "Bile pigment found in fecal material.", + "meaning": "CHEBI:26756" + } + } + }, + "FecalContaminationUnitMenu": { + "name": "FecalContaminationUnitMenu", + "title": "fecal_contamination_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "log10 gene copies per 100 milliliter (log10 GC/100 mL)": { + "text": "log10 gene copies per 100 milliliter (log10 GC/100 mL)" + }, + "gene copies per liter (GC/L)": { + "text": "gene copies per liter (GC/L)" + }, + "PCR quantification cycle [UO:0010077]": { + "text": "PCR quantification cycle [UO:0010077]", + "description": "A count unit of how many Polymerase Chain Reaction (PCR) cycles it took to detect a real signal from a sample. Equivalent to the PCR cycle number at which a sample's reaction curve intersects the threshold line.", + "meaning": "UO:0010077" + }, + "log10 gene copies per nanogram total DNA": { + "text": "log10 gene copies per nanogram total DNA" + } + } + }, + "UrinaryContaminationIndicatorMenu": { + "name": "UrinaryContaminationIndicatorMenu", + "title": "urinary_contamination_indicator menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Urobilin [CHEBI:36378]": { + "text": "Urobilin [CHEBI:36378]", + "description": "A tetrapyrroledicarboxylic acid that causes the yellow color in urine. Also known as urochrome.", + "meaning": "CHEBI:36378" + } + } + }, + "UrinaryContaminationUnitMenu": { + "name": "UrinaryContaminationUnitMenu", + "title": "urinary_contamination_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "nanograms per liter (ng/L) [EFO:0004382]": { + "text": "nanograms per liter (ng/L) [EFO:0004382]", + "description": "A mass unit density which is equal to mass of an object in nanograms divided by the volume in liters.", + "meaning": "EFO:0004382" + } + } + }, + "FecalColiformCountUnitMenu": { + "name": "FecalColiformCountUnitMenu", + "title": "fecal_coliform_count_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "colony forming units per milliliter (CFU/mL) [UO:0000213]": { + "text": "colony forming units per milliliter (CFU/mL) [UO:0000213]", + "description": "A unit of microbial density that describes the number of colony forming units within a milliliter of material.", + "meaning": "UO:0000213" + }, + "colony forming units per 100 milliliter (CFU/100 mL)": { + "text": "colony forming units per 100 milliliter (CFU/100 mL)" + }, + "colony forming units per grams total solids (CFU/gTS)": { + "text": "colony forming units per grams total solids (CFU/gTS)" + }, + "most probable number per milliliter (MPN/mL)": { + "text": "most probable number per milliliter (MPN/mL)" + }, + "most probable number per 100 milliliter (MPN/100 mL)": { + "text": "most probable number per 100 milliliter (MPN/100 mL)" + } + } + }, + "SampleTemperatureUnitAtCollectionMenu": { + "name": "SampleTemperatureUnitAtCollectionMenu", + "title": "sample_temperature_unit_(at collection) menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "degree Fahrenheit (F) [UO:0000195]": { + "text": "degree Fahrenheit (F) [UO:0000195]", + "description": "A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions.", + "meaning": "UO:0000195" + }, + "degree Celsius (C) [UO:0000027]": { + "text": "degree Celsius (C) [UO:0000027]", + "description": "A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions.", + "meaning": "UO:0000027" + } + } + }, + "SampleTemperatureUnitWhenReceivedMenu": { + "name": "SampleTemperatureUnitWhenReceivedMenu", + "title": "sample_temperature_unit_(when received) menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "degree Fahrenheit (F) [UO:0000195]": { + "text": "degree Fahrenheit (F) [UO:0000195]", + "description": "A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions.", + "meaning": "UO:0000195" + }, + "degree Celsius (C) [UO:0000027]": { + "text": "degree Celsius (C) [UO:0000027]", + "description": "A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions.", + "meaning": "UO:0000027" + } + } + }, + "SequencingAssayTypeMenu": { + "name": "SequencingAssayTypeMenu", + "title": "sequencing_assay_type menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Amplicon sequencing assay [OBI:0002767]": { + "text": "Amplicon sequencing assay [OBI:0002767]", + "description": "A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced.", + "meaning": "OBI:0002767" + }, + "16S ribosomal gene sequencing assay [OBI:0002763]": { + "text": "16S ribosomal gene sequencing assay [OBI:0002763]", + "description": "An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample.", + "meaning": "OBI:0002763", + "is_a": "Amplicon sequencing assay [OBI:0002767]" + }, + "CRISPR amplicon sequencing assay [GENEPIO:0101128]": { + "text": "CRISPR amplicon sequencing assay [GENEPIO:0101128]", + "meaning": "GENEPIO:0101128", + "is_a": "Amplicon sequencing assay [OBI:0002767]" + }, + "Primal tiling amplicon sequencing assay [GENEPIO:0101129]": { + "text": "Primal tiling amplicon sequencing assay [GENEPIO:0101129]", + "meaning": "GENEPIO:0101129", + "is_a": "Amplicon sequencing assay [OBI:0002767]" + }, + "Whole genome sequencing assay [OBI:0002117]": { + "text": "Whole genome sequencing assay [OBI:0002117]", + "description": "A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.", + "meaning": "OBI:0002117" + }, + "Whole metagenome sequencing assay [OBI:0002623]": { + "text": "Whole metagenome sequencing assay [OBI:0002623]", + "description": "A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.", + "meaning": "OBI:0002623" + }, + "Whole virome sequencing assay [OBI:0002768]": { + "text": "Whole virome sequencing assay [OBI:0002768]", + "description": "A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample.", + "meaning": "OBI:0002768", + "is_a": "Whole metagenome sequencing assay [OBI:0002623]" + } + } + }, + "PurposeOfSequencingMenu": { + "name": "PurposeOfSequencingMenu", + "title": "purpose_of_sequencing menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Baseline surveillance (random sampling) [GENEPIO:0100005]": { + "text": "Baseline surveillance (random sampling) [GENEPIO:0100005]", + "description": "A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling.", + "meaning": "GENEPIO:0100005" + }, + "Targeted surveillance (non-random sampling) [GENEPIO:0100006]": { + "text": "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", + "description": "A surveillance sampling strategy in which an aspired outcome is explicitly stated.", + "meaning": "GENEPIO:0100006" + }, + "Priority surveillance project [GENEPIO:0100007]": { + "text": "Priority surveillance project [GENEPIO:0100007]", + "description": "A targeted surveillance strategy which is considered important and/or urgent.", + "meaning": "GENEPIO:0100007", + "is_a": "Targeted surveillance (non-random sampling) [GENEPIO:0100006]" + }, + "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]": { + "text": "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]", + "description": "A surveillance strategy in which an individual or site is selected to undergo repeat sampling over a defined period of time.", + "meaning": "GENEPIO:0100009", + "is_a": "Priority surveillance project [GENEPIO:0100007]" + }, + "Cluster/Outbreak investigation [GENEPIO:0100019]": { + "text": "Cluster/Outbreak investigation [GENEPIO:0100019]", + "description": "A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak.", + "meaning": "GENEPIO:0100019" + }, + "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]": { + "text": "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]", + "description": "An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that has connections to two or more jurisdictions.", + "meaning": "GENEPIO:0100020", + "is_a": "Cluster/Outbreak investigation [GENEPIO:0100019]" + }, + "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]": { + "text": "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]", + "description": "An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that only has connections within a single jurisdiction.", + "meaning": "GENEPIO:0100021", + "is_a": "Cluster/Outbreak investigation [GENEPIO:0100019]" + }, + "Research [GENEPIO:0100022]": { + "text": "Research [GENEPIO:0100022]", + "description": "A sampling strategy in which sites are sampled in order to perform research.", + "meaning": "GENEPIO:0100022" + }, + "Viral passage experiment [GENEPIO:0100023]": { + "text": "Viral passage experiment [GENEPIO:0100023]", + "description": "A research sampling strategy in which samples are selected in order to perform a viral passage experiment.", + "meaning": "GENEPIO:0100023", + "is_a": "Research [GENEPIO:0100022]" + }, + "Protocol testing experiment [GENEPIO:0100024]": { + "text": "Protocol testing experiment [GENEPIO:0100024]", + "description": "A research sampling strategy in which samples are collected in order to test a method or protocol.", + "meaning": "GENEPIO:0100024", + "is_a": "Research [GENEPIO:0100022]" + }, + "Retrospective sequencing [GENEPIO:0100356]": { + "text": "Retrospective sequencing [GENEPIO:0100356]", + "description": "A sampling strategy in which stored samples from past events are sequenced.", + "meaning": "GENEPIO:0100356" + } + } + }, + "GeoLocNameCountryMenu": { + "name": "GeoLocNameCountryMenu", + "title": "geo_loc_name_(country) menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Afghanistan [GAZ:00006882]": { + "text": "Afghanistan [GAZ:00006882]", + "description": "A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ]", + "meaning": "GAZ:00006882" + }, + "Albania [GAZ:00002953]": { + "text": "Albania [GAZ:00002953]", + "description": "A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ]", + "meaning": "GAZ:00002953" + }, + "Algeria [GAZ:00000563]": { + "text": "Algeria [GAZ:00000563]", + "description": "A country in North Africa. It is bordered by Tunisia in the northeast, Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, a few km of the Western Sahara in the west, Morocco in the northwest, and the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). [ url:http://en.wikipedia.org/wiki/Algeria ]", + "meaning": "GAZ:00000563" + }, + "American Samoa [GAZ:00003957]": { + "text": "American Samoa [GAZ:00003957]", + "description": "An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa ]", + "meaning": "GAZ:00003957" + }, + "Andorra [GAZ:00002948]": { + "text": "Andorra [GAZ:00002948]", + "description": "A small landlocked country in western Europe, located in the eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. Andorra consists of seven communities known as parishes (Catalan: parroquies, singular - parroquia). Until relatively recently, it had only six parishes; the seventh, Escaldes-Engordany, was created in 1978. Some parishes have a further territorial subdivision. Ordino, La Massana and Sant Julia de Loria are subdivided into quarts (quarters), while Canillo is subdivided into veinats (neighborhoods). Those mostly coincide with villages, which are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ]", + "meaning": "GAZ:00002948" + }, + "Angola [GAZ:00001095]": { + "text": "Angola [GAZ:00001095]", + "description": "A country in south-central Africa bordering Namibia to the south, Democratic Republic of the Congo to the north, and Zambia to the east, and with a west coast along the Atlantic Ocean. The exclave province Cabinda has a border with the Republic of the Congo and the Democratic Republic of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ]", + "meaning": "GAZ:00001095" + }, + "Anguilla [GAZ:00009159]": { + "text": "Anguilla [GAZ:00009159]", + "description": "A British overseas territory in the Caribbean, one of the most northerly of the Leeward Islands in the Lesser Antilles. It consists of the main island of Anguilla itself, approximately 26 km long by 5 km wide at its widest point, together with a number of much smaller islands and cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila ]", + "meaning": "GAZ:00009159" + }, + "Antarctica [GAZ:00000462]": { + "text": "Antarctica [GAZ:00000462]", + "description": "The Earth's southernmost continent, overlying the South Pole. It is situated in the southern hemisphere, almost entirely south of the Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica ]", + "meaning": "GAZ:00000462" + }, + "Antigua and Barbuda [GAZ:00006883]": { + "text": "Antigua and Barbuda [GAZ:00006883]", + "description": "An island nation located on the eastern boundary of the Caribbean Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda ]", + "meaning": "GAZ:00006883" + }, + "Argentina [GAZ:00002928]": { + "text": "Argentina [GAZ:00002928]", + "description": "A South American country, constituted as a federation of twenty-three provinces and an autonomous city. It is bordered by Paraguay and Bolivia in the north, Brazil and Uruguay in the northeast, and Chile in the west and south. The country claims the British controlled territories of the Falkland Islands and South Georgia and the South Sandwich Islands. Argentina also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping other claims made by Chile and the United Kingdom. Argentina is subdivided into twenty-three provinces (Spanish: provincias, singular provincia) and one federal district (Capital de la Republica or Capital de la Nacion, informally the Capital Federal). The federal district and the provinces have their own constitutions, but exist under a federal system. Provinces are then divided into departments (Spanish: departamentos, singular departamento), except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina ]", + "meaning": "GAZ:00002928" + }, + "Armenia [GAZ:00004094]": { + "text": "Armenia [GAZ:00004094]", + "description": "A landlocked mountainous country in Eurasia between the Black Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan exclave of Azerbaijan to the south. A transcontinental country at the juncture of Eastern Europe and Western Asia. A former republic of the Soviet Union. Armenia is divided into ten marzes (provinces, singular marz), with the city (kaghak) of Yerevan having special administrative status as the country's capital. [ url:http://en.wikipedia.org/wiki/Armenia ]", + "meaning": "GAZ:00004094" + }, + "Aruba [GAZ:00004025]": { + "text": "Aruba [GAZ:00004025]", + "description": "An autonomous region within the Kingdom of the Netherlands, Aruba has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba ]", + "meaning": "GAZ:00004025" + }, + "Ashmore and Cartier Islands [GAZ:00005901]": { + "text": "Ashmore and Cartier Islands [GAZ:00005901]", + "description": "A Territory of Australia that includes two groups of small low-lying uninhabited tropical islands in the Indian Ocean situated on the edge of the continental shelf north-west of Australia and south of the Indonesian island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands ]", + "meaning": "GAZ:00005901" + }, + "Australia [GAZ:00000463]": { + "text": "Australia [GAZ:00000463]", + "description": "A country in the southern hemisphere comprising the mainland of the world's smallest continent, the major island of Tasmania, and a number of other islands in the Indian and Pacific Oceans. The neighbouring countries are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to the south-east. Australia has six states, two major mainland territories, and other minor territories.", + "meaning": "GAZ:00000463" + }, + "Austria [GAZ:00002942]": { + "text": "Austria [GAZ:00002942]", + "description": "A landlocked country in Central Europe. It borders both Germany and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia and Italy to the south, and Switzerland and Liechtenstein to the west. The capital is the city of Vienna on the Danube River. Austria is divided into nine states (Bundeslander). These states are then divided into districts (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities (Gemeinden). Cities have the competencies otherwise granted to both districts and municipalities.", + "meaning": "GAZ:00002942" + }, + "Azerbaijan [GAZ:00004941]": { + "text": "Azerbaijan [GAZ:00004941]", + "description": "A country in the he South Caucasus region of Eurasia, it is bounded by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan is bordered by Armenia to the north and east, Iran to the south and west, and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts in Azerbaijan's southwest, have been controlled by Armenia since the end of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons 11 city districts (saharlar), and one autonomous republic (muxtar respublika).", + "meaning": "GAZ:00004941" + }, + "Bahamas [GAZ:00002733]": { + "text": "Bahamas [GAZ:00002733]", + "description": "A country consisting of two thousand cays and seven hundred islands that form an archipelago. It is located in the Atlantic Ocean, southeast of Florida and the United States, north of Cuba, the island of Hispanola and the Caribbean, and northwest of the British overseas territory of the Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, whose affairs are handled directly by the central government.", + "meaning": "GAZ:00002733" + }, + "Bahrain [GAZ:00005281]": { + "text": "Bahrain [GAZ:00005281]", + "description": "A borderless island country in the Persian Gulf. Saudi Arabia lies to the west and is connected to Bahrain by the King Fahd Causeway, and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into five governorates.", + "meaning": "GAZ:00005281" + }, + "Baker Island [GAZ:00007117]": { + "text": "Baker Island [GAZ:00007117]", + "description": "An uninhabited atoll located just north of the equator in the central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island is an unincorporated and unorganized territory of the US.", + "meaning": "GAZ:00007117" + }, + "Bangladesh [GAZ:00003750]": { + "text": "Bangladesh [GAZ:00003750]", + "description": "A country in South Asia. It is bordered by India on all sides except for a small border with Myanmar to the far southeast and by the Bay of Bengal to the south. Bangladesh is divided into six administrative divisions. Divisions are subdivided into districts (zila). There are 64 districts in Bangladesh, each further subdivided into upazila (subdistricts) or thana (\"police stations\").", + "meaning": "GAZ:00003750" + }, + "Barbados [GAZ:00001251]": { + "text": "Barbados [GAZ:00001251]", + "description": "An island country in the Lesser Antilles of the West Indies, in the Caribbean region of the Americas, and the most easterly of the Caribbean Islands. It is 34 kilometres (21 miles) in length and up to 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is in the western part of the North Atlantic, 100 km (62 mi) east of the Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards, part of the Lesser Antilles, at roughly 13°N of the equator. It is about 168 km (104 mi) east of both the countries of Saint Lucia and Saint Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside the principal Atlantic hurricane belt. Its capital and largest city is Bridgetown.", + "meaning": "GAZ:00001251" + }, + "Bassas da India [GAZ:00005810]": { + "text": "Bassas da India [GAZ:00005810]", + "description": "A roughly circular atoll about 10 km in diameter, which corresponds to a total size (including lagoon) of 80 km2. It is located in the southern Mozambique Channel, about half-way between Madagascar (which is 385 km to the east) and Mozambique, and 110 km northwest of Europa Island. It rises steeply from the seabed 3000 m below.", + "meaning": "GAZ:00005810" + }, + "Belarus [GAZ:00006886]": { + "text": "Belarus [GAZ:00006886]", + "description": "A landlocked country in Eastern Europe, that borders Russia to the north and east, Ukraine to the south, Poland to the west, and Lithuania and Latvia to the north. Its capital is Minsk. Belarus is divided into six voblasts, or provinces. Voblasts are further subdivided into raions (commonly translated as districts or regions). As of 2002, there are six voblasts, 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special status, due to the city serving as the national capital.", + "meaning": "GAZ:00006886" + }, + "Belgium [GAZ:00002938]": { + "text": "Belgium [GAZ:00002938]", + "description": "A country in northwest Europe. Belgium shares borders with France (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each comprise five provinces; the third region, Brussels-Capital Region, is not a province, nor does it contain any Together, these comprise 589 municipalities, which in general consist of several sub-municipalities (which were independent municipalities before the municipal merger operation mainly in 1977).", + "meaning": "GAZ:00002938" + }, + "Belize [GAZ:00002934]": { + "text": "Belize [GAZ:00002934]", + "description": "A country in Central America. It is the only officially English speaking country in the region. Belize was a British colony for more than a century and was known as British Honduras until 1973. It became an independent nation within The Commonwealth in 1981. Belize is divided into 6 districts, which are further divided into 31 constituencies.", + "meaning": "GAZ:00002934" + }, + "Benin [GAZ:00000904]": { + "text": "Benin [GAZ:00000904]", + "description": "A country in Western Africa. It borders Togo to the west, Nigeria to the east and Burkina Faso and Niger to the north; its short coastline to the south leads to the Bight of Benin. Its capital is Porto Novo, but the seat of government is Cotonou. Benin is divided into 12 departments and subdivided into 77 communes.", + "meaning": "GAZ:00000904" + }, + "Bermuda [GAZ:00001264]": { + "text": "Bermuda [GAZ:00001264]", + "description": "A British overseas territory in the North Atlantic Ocean. Located off the east coast of the United States, it is situated around 1770 km NE of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately 138 islands.", + "meaning": "GAZ:00001264" + }, + "Bhutan [GAZ:00003920]": { + "text": "Bhutan [GAZ:00003920]", + "description": "A landlocked nation in South Asia. It is located amidst the eastern end of the Himalaya Mountains and is bordered to the south, east and west by India and to the north by Tibet. Bhutan is separated from Nepal by the Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative zones). Each dzongdey is further divided into dzongkhag (districts). There are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into subdistricts known as dungkhag. At the basic level, groups of villages form a constituency called gewog.", + "meaning": "GAZ:00003920" + }, + "Bolivia [GAZ:00002511]": { + "text": "Bolivia [GAZ:00002511]", + "description": "A landlocked country in central South America. It is bordered by Brazil on the north and east, Paraguay and Argentina on the south, and Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: departamentos). Each of the departments is subdivided into provinces (provincias), which are further subdivided into municipalities (municipios).", + "meaning": "GAZ:00002511" + }, + "Borneo [GAZ:00025355]": { + "text": "Borneo [GAZ:00025355]", + "description": "An island at the grographic centre of Maritime Southeast Adia, in relation to major Indonesian islands, it is located north of Java, west of Sulawesi, and east of Sumatra. It is the third-largest island in the world and the larest in Asia. The island is politically divided among three countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] Approximately 73% of the island is Indonesian territory. In the north, the East Malaysian states of Sabah and Sarawak make up about 26% of the island. Additionally, the Malaysian federal territory of Labuan is situated on a small island just off the coast of Borneo. The sovereign state of Brunei, located on the north coast, comprises about 1% of Borneo's land area. A little more than half of the island is in the Northern Hemisphere, including Brunei and the Malaysian portion, while the Indonesian portion spans the Northern and Southern hemispheres.", + "meaning": "GAZ:00025355" + }, + "Bosnia and Herzegovina [GAZ:00006887]": { + "text": "Bosnia and Herzegovina [GAZ:00006887]", + "description": "A country on the Balkan peninsula of Southern Europe. Bordered by Croatia to the north, west and south, Serbia to the east, and Montenegro to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided into three political regions of which one, the Brcko District is part of the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. All three have an equal constitutional status on the whole territory of Bosnia and Herzegovina.", + "meaning": "GAZ:00006887" + }, + "Botswana [GAZ:00001097]": { + "text": "Botswana [GAZ:00001097]", + "description": "A landlocked nation in Southern Africa. It is bordered by South Africa to the south and southeast, Namibia to the west, Zambia to the north, and Zimbabwe to the northeast. Botswana is divided into nine districts, which are subdivided into a total twenty-eight subdistricts.", + "meaning": "GAZ:00001097" + }, + "Bouvet Island [GAZ:00001453]": { + "text": "Bouvet Island [GAZ:00001453]", + "description": "A sub-antarctic volcanic island in the South Atlantic Ocean, south-southwest of the Cape of Good Hope (South Africa). It is a dependent area of Norway and is not subject to the Antarctic Treaty, as it is north of the latitude south of which claims are suspended.", + "meaning": "GAZ:00001453" + }, + "Brazil [GAZ:00002828]": { + "text": "Brazil [GAZ:00002828]", + "description": "A country in South America. Bordered by the Atlantic Ocean and by Venezuela, Suriname, Guyana and the department of French Guiana to the north, Colombia to the northwest, Bolivia and Peru to the west, Argentina and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six states (estados) and one federal district (Distrito Federal). The states are subdivided into municipalities. For statistical purposes, the States are grouped into five main regions: North, Northeast, Central-West, Southeast and South.", + "meaning": "GAZ:00002828" + }, + "British Virgin Islands [GAZ:00003961]": { + "text": "British Virgin Islands [GAZ:00003961]", + "description": "A British overseas territory, located in the Caribbean to the east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, the remaining islands constituting the US Virgin Islands. The British Virgin Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately fifteen of the islands are inhabited.", + "meaning": "GAZ:00003961" + }, + "Brunei [GAZ:00003901]": { + "text": "Brunei [GAZ:00003901]", + "description": "A country located on the north coast of the island of Borneo, in Southeast Asia. Apart from its coastline with the South China Sea it is completely surrounded by the State of Sarawak, Malaysia, and in fact it is separated into two parts by Limbang, which is part of Sarawak. Brunei is divided into four districts (daerah), the districts are subdivided into thirty-eight mukims, which are then divided into kampong (villages).", + "meaning": "GAZ:00003901" + }, + "Bulgaria [GAZ:00002950]": { + "text": "Bulgaria [GAZ:00002950]", + "description": "A country in Southeastern Europe, borders five other countries; Romania to the north (mostly along the Danube), Serbia and the Republic of Macedonia to the west, and Greece and Turkey to the south. The Black Sea defines the extent of the country to the east. Since 1999, it has consisted of twenty-eight provinces. The provinces subdivide into 264 municipalities.", + "meaning": "GAZ:00002950" + }, + "Burkina Faso [GAZ:00000905]": { + "text": "Burkina Faso [GAZ:00000905]", + "description": "A landlocked nation in West Africa. It is surrounded by six countries: Mali to the north, Niger to the east, Benin to the south east, Togo and Ghana to the south, and Cote d'Ivoire to the south west. Burkina Faso is divided into thirteen regions, forty-five provinces, and 301 departments (communes).", + "meaning": "GAZ:00000905" + }, + "Burundi [GAZ:00001090]": { + "text": "Burundi [GAZ:00001090]", + "description": "A small country in the Great Lakes region of Africa. It is bordered by Rwanda on the north, Tanzania on the south and east, and the Democratic Republic of the Congo on the west. Although the country is landlocked, much of its western border is adjacent to Lake Tanganyika. Burundi is divided into 17 provinces, 117 communes, and 2,638 collines.", + "meaning": "GAZ:00001090" + }, + "Cambodia [GAZ:00006888]": { + "text": "Cambodia [GAZ:00006888]", + "description": "A country in Southeast Asia. The country borders Thailand to its west and northwest, Laos to its northeast, and Vietnam to its east and southeast. In the south it faces the Gulf of Thailand.", + "meaning": "GAZ:00006888" + }, + "Cameroon [GAZ:00001093]": { + "text": "Cameroon [GAZ:00001093]", + "description": "A country of central and western Africa. It borders Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces and 58 divisions or departments. The divisions are further sub-divided into sub-divisions (arrondissements) and districts.", + "meaning": "GAZ:00001093" + }, + "Canada [GAZ:00002560]": { + "text": "Canada [GAZ:00002560]", + "description": "A country occupying most of northern North America, extending from the Atlantic Ocean in the east to the Pacific Ocean in the west and northward into the Arctic Ocean. Canada is a federation composed of ten provinces and three territories; in turn, these may be grouped into regions. Western Canada consists of British Columbia and the three Prairie provinces (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec and Ontario. Atlantic Canada consists of the three Maritime provinces (New Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada together. Three territories (Yukon, Northwest Territories, and Nunavut) make up Northern Canada.", + "meaning": "GAZ:00002560" + }, + "Cape Verde [GAZ:00001227]": { + "text": "Cape Verde [GAZ:00001227]", + "description": "A republic located on an archipelago in the Macaronesia ecoregion of the North Atlantic Ocean, off the western coast of Africa. Cape Verde is divided into 22 municipalities (concelhos), and subdivided into 32 parishes (freguesias).", + "meaning": "GAZ:00001227" + }, + "Cayman Islands [GAZ:00003986]": { + "text": "Cayman Islands [GAZ:00003986]", + "description": "A British overseas territory located in the western Caribbean Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. The Cayman Islands are divided into seven districts.", + "meaning": "GAZ:00003986" + }, + "Central African Republic [GAZ:00001089]": { + "text": "Central African Republic [GAZ:00001089]", + "description": "A landlocked country in Central Africa. It borders Chad in the north, Sudan in the east, the Republic of the Congo and the Democratic Republic of the Congo in the south, and Cameroon in the west. The Central African Republic is divided into 14 administrative prefectures (prefectures), along with 2 economic prefectures (prefectures economiques) and one autonomous commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures).", + "meaning": "GAZ:00001089" + }, + "Chad [GAZ:00000586]": { + "text": "Chad [GAZ:00000586]", + "description": "A landlocked country in central Africa. It is bordered by Libya to the north, Sudan to the east, the Central African Republic to the south, Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided into 18 regions. The departments are divided into 200 sub-prefectures, which are in turn composed of 446 cantons. This is due to change.", + "meaning": "GAZ:00000586" + }, + "Chile [GAZ:00002825]": { + "text": "Chile [GAZ:00002825]", + "description": "A country in South America occupying a long and narrow coastal strip wedged between the Andes mountains and the Pacific Ocean. The Pacific forms the country's entire western border, with Peru to the north, Bolivia to the northeast, Argentina to the east, and the Drake Passage at the country's southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. Chile is divided into 15 regions. Every region is further divided into provinces. Finally each province is divided into communes. Each region is designated by a name and a Roman numeral, assigned from north to south. The only exception is the region housing the nation's capital, which is designated RM, that stands for Region Metropolitana (Metropolitan Region). Two new regions were created in 2006: Arica-Parinacota in the north, and Los Rios in the south. Both became operative in 2007-10.", + "meaning": "GAZ:00002825" + }, + "China [GAZ:00002845]": { + "text": "China [GAZ:00002845]", + "description": "A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions.", + "meaning": "GAZ:00002845" + }, + "Christmas Island [GAZ:00005915]": { + "text": "Christmas Island [GAZ:00005915]", + "description": "An island in the Indian Ocean, 500 km south of Indonesia and about 2600 km northwest of Perth. The island is the flat summit of a submarine mountain.", + "meaning": "GAZ:00005915" + }, + "Clipperton Island [GAZ:00005838]": { + "text": "Clipperton Island [GAZ:00005838]", + "description": "A nine-square km coral atoll in the North Pacific Ocean, southwest of Mexico and west of Costa Rica.", + "meaning": "GAZ:00005838" + }, + "Cocos Islands [GAZ:00009721]": { + "text": "Cocos Islands [GAZ:00009721]", + "description": "Islands that located in the Indian Ocean, about halfway between Australia and Sri Lanka. A territory of Australia. There are two atolls and twenty-seven coral islands in the group.", + "meaning": "GAZ:00009721" + }, + "Colombia [GAZ:00002929]": { + "text": "Colombia [GAZ:00002929]", + "description": "A country located in the northwestern region of South America. Colombia is bordered to the east by Venezuela and Brazil; to the south by Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean Sea; to the north-west by Panama; and to the west by the Pacific Ocean. Besides the countries in South America, the Republic of Colombia is recognized to share maritime borders with the Caribbean countries of Jamaica, Haiti, the Dominican Republic and the Central American countries of Honduras, Nicaragua, and Costa Rica. Colombia is divided into 32 departments and one capital district which is treated as a department. There are in total 10 districts assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia is also subdivided into some municipalities which form departments, each with a municipal seat capital city assigned. Colombia is also subdivided into corregimientos which form municipalities.", + "meaning": "GAZ:00002929" + }, + "Comoros [GAZ:00005820]": { + "text": "Comoros [GAZ:00005820]", + "description": "An island nation in the Indian Ocean, located off the eastern coast of Africa on the northern end of the Mozambique Channel between northern Madagascar and northeastern Mozambique.", + "meaning": "GAZ:00005820" + }, + "Cook Islands [GAZ:00053798]": { + "text": "Cook Islands [GAZ:00053798]", + "description": "A self-governing parliamentary democracy in free association with New Zealand. The fifteen small islands in this South Pacific Ocean country have a total land area of 240 km2, but the Cook Islands Exclusive Economic Zone (EEZ) covers 1.8 million km2 of ocean.", + "meaning": "GAZ:00053798" + }, + "Coral Sea Islands [GAZ:00005917]": { + "text": "Coral Sea Islands [GAZ:00005917]", + "description": "A Territory of Australia which includes a group of small and mostly uninhabited tropical islands and reefs in the Coral Sea, northeast of Queensland, Australia. The only inhabited island is Willis Island. The territory covers 780,000 km2, extending east and south from the outer edge of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, the Willis Group, and fifteen other reef/island groups.", + "meaning": "GAZ:00005917" + }, + "Costa Rica [GAZ:00002901]": { + "text": "Costa Rica [GAZ:00002901]", + "description": "A republic in Central America, bordered by Nicaragua to the north, Panama to the east-southeast, the Pacific Ocean to the west and south, and the Caribbean Sea to the east. Costa Rica is composed of seven provinces, which in turn are divided into 81 cantons.", + "meaning": "GAZ:00002901" + }, + "Cote d'Ivoire [GAZ:00000906]": { + "text": "Cote d'Ivoire [GAZ:00000906]", + "description": "A country in West Africa. It borders Liberia and Guinea to the west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). The regions are further divided into 58 departments.", + "meaning": "GAZ:00000906" + }, + "Croatia [GAZ:00002719]": { + "text": "Croatia [GAZ:00002719]", + "description": "A country at the crossroads of the Mediterranean, Central Europe, and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to the east, Montenegro to the far southeast, and the Adriatic Sea to the south. Croatia is divided into 21 counties (zupanija) and the capital Zagreb's city district.", + "meaning": "GAZ:00002719" + }, + "Cuba [GAZ:00003762]": { + "text": "Cuba [GAZ:00003762]", + "description": "A country that consists of the island of Cuba (the largest and second-most populous island of the Greater Antilles), Isla de la Juventud and several adjacent small islands. Fourteen provinces and one special municipality (the Isla de la Juventud) now compose Cuba.", + "meaning": "GAZ:00003762" + }, + "Curacao [GAZ:00012582]": { + "text": "Curacao [GAZ:00012582]", + "description": "One of five island areas of the Netherlands Antilles.", + "meaning": "GAZ:00012582" + }, + "Cyprus [GAZ:00004006]": { + "text": "Cyprus [GAZ:00004006]", + "description": "The third largest island in the Mediterranean Sea (after Sicily and Sardinia), Cyprus is situated in the eastern Mediterranean, just south of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, it is often included in the Middle East (see also Western Asia and Near East). Turkey is 75 km north; other neighbouring countries include Syria and Lebanon to the east, Israel to the southeast, Egypt to the south, and Greece to the west-north-west.", + "meaning": "GAZ:00004006" + }, + "Czech Republic [GAZ:00002954]": { + "text": "Czech Republic [GAZ:00002954]", + "description": "A landlocked country in Central Europe. It has borders with Poland to the north, Germany to the northwest and southwest, Austria to the south, and Slovakia to the east. The capital and largest city is Prague. The country is composed of the historic regions of Bohemia and Moravia, as well as parts of Silesia. Since 2000, the Czech Republic is divided into thirteen regions (kraje, singular kraj) and the capital city of Prague. The older seventy-six districts (okresy, singular okres) including three 'statutory cities' (without Prague, which had special status) were disbanded in 1999 in an administrative reform; they remain as territorial division and seats of various branches of state administration. Since 2003-01-01, the regions have been divided into around 203 Municipalities with Extended Competence (unofficially named \"Little Districts\" (Czech: 'male okresy') which took over most of the administration of the former District Authorities. Some of these are further divided into Municipalities with Commissioned Local Authority. However, the old districts still exist as territorial units and remain as seats of some of the offices.", + "meaning": "GAZ:00002954" + }, + "Democratic Republic of the Congo [GAZ:00001086]": { + "text": "Democratic Republic of the Congo [GAZ:00001086]", + "description": "A country of central Africa. It borders the Central African Republic and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia and Angola on the south, the Republic of the Congo on the west, and is separated from Tanzania by Lake Tanganyika on the east. The country enjoys access to the ocean through a 40 km stretch of Atlantic coastline at Muanda and the roughly 9 km wide mouth of the Congo river which opens into the Gulf of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed into 25 Provinces from 2.2009. Each Province is divided into Zones.", + "meaning": "GAZ:00001086" + }, + "Denmark [GAZ:00005852]": { + "text": "Denmark [GAZ:00005852]", + "description": "That part of the Kingdom of Denmark located in continental Europe. The mainland is bordered to the south by Germany; Denmark is located to the southwest of Sweden and the south of Norway. Denmark borders both the Baltic and the North Sea. The country consists of a large peninsula, Jutland (Jylland) and a large number of islands, most notably Zealand (Sjaelland), Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds of minor islands often referred to as the Danish Archipelago.", + "meaning": "GAZ:00005852" + }, + "Djibouti [GAZ:00000582]": { + "text": "Djibouti [GAZ:00000582]", + "description": "A country in eastern Africa. Djibouti is bordered by Eritrea in the north, Ethiopia in the west and south, and Somalia in the southeast. The remainder of the border is formed by the Red Sea and the Gulf of Aden. On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. Djibouti is divided into 5 regions and one city. It is further subdivided into 11 districts.", + "meaning": "GAZ:00000582" + }, + "Dominica [GAZ:00006890]": { + "text": "Dominica [GAZ:00006890]", + "description": "An island nation in the Caribbean Sea. Dominica is divided into ten parishes.", + "meaning": "GAZ:00006890" + }, + "Dominican Republic [GAZ:00003952]": { + "text": "Dominican Republic [GAZ:00003952]", + "description": "A country in the West Indies that occupies the E two-thirds of the Hispaniola island. The Dominican Republic's shores are washed by the Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona Passage, a channel about 130 km wide, separates the country (and the Hispaniola) from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, the national capital, Santo Domingo, is contained within its own Distrito Nacional (National District). The provinces are divided into municipalities (municipios; singular municipio).", + "meaning": "GAZ:00003952" + }, + "Ecuador [GAZ:00002912]": { + "text": "Ecuador [GAZ:00002912]", + "description": "A country in South America, bordered by Colombia on the north, by Peru on the east and south, and by the Pacific Ocean to the west. The country also includes the Galapagos Islands (Archipelago de Colon) in the Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, divided into 199 cantons and subdivided into parishes (or parroquias).", + "meaning": "GAZ:00002912" + }, + "Egypt [GAZ:00003934]": { + "text": "Egypt [GAZ:00003934]", + "description": "A country in North Africa that includes the Sinai Peninsula, a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, and the Gaza Strip and Israel to the east. The northern coast borders the Mediterranean Sea and the island of Cyprus; the eastern coast borders the Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, singular muhafazah). The governorates are further divided into regions (markazes).", + "meaning": "GAZ:00003934" + }, + "El Salvador [GAZ:00002935]": { + "text": "El Salvador [GAZ:00002935]", + "description": "A country in Central America, bordering the Pacific Ocean between Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), which, in turn, are subdivided into 267 municipalities (municipios).", + "meaning": "GAZ:00002935" + }, + "Equatorial Guinea [GAZ:00001091]": { + "text": "Equatorial Guinea [GAZ:00001091]", + "description": "A country in Central Africa. It is one of the smallest countries in continental Africa, and comprises two regions: Rio Muni, continental region including several offshore islands; and Insular Region containing Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando Po) that contains the capital, Malabo. Equatorial Guinea is divided into seven provinces which are divided into districts.", + "meaning": "GAZ:00001091" + }, + "Eritrea [GAZ:00000581]": { + "text": "Eritrea [GAZ:00000581]", + "description": "A country situated in northern East Africa. It is bordered by Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. The east and northeast of the country have an extensive coastline on the Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago and several of the Hanish Islands are part of Eritrea. Eritrea is divided into six regions (zobas) and subdivided into districts (\"sub-zobas\").", + "meaning": "GAZ:00000581" + }, + "Estonia [GAZ:00002959]": { + "text": "Estonia [GAZ:00002959]", + "description": "A country in Northern Europe. Estonia has land borders to the south with Latvia and to the east with Russia. It is separated from Finland in the north by the Gulf of Finland and from Sweden in the west by the Baltic Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). Estonian counties are divided into rural (vallad, singular vald) and urban (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) municipalities. The municipalities comprise populated places (asula or asustusuksus) - various settlements and territorial units that have no administrative function. A group of populated places form a rural municipality with local administration. Most towns constitute separate urban municipalities, while some have joined with surrounding rural municipalities.", + "meaning": "GAZ:00002959" + }, + "Eswatini [GAZ:00001099]": { + "text": "Eswatini [GAZ:00001099]", + "description": "A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla).", + "meaning": "GAZ:00001099" + }, + "Ethiopia [GAZ:00000567]": { + "text": "Ethiopia [GAZ:00000567]", + "description": "A country situated in the Horn of Africa that has been landlocked since the independence of its northern neighbor Eritrea in 1993. Apart from Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to the south, Djibouti to the northeast, and Somalia to the east. Since 1996 Ethiopia has had a tiered government system consisting of a federal government overseeing ethnically-based regional states, zones, districts (woredas), and neighborhoods (kebele). It is divided into nine ethnically-based administrative states (kililoch, singular kilil) and subdivided into sixty-eight zones and two chartered cities (astedader akababiwoch, singular astedader akababi): Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and six special woredas.", + "meaning": "GAZ:00000567" + }, + "Europa Island [GAZ:00005811]": { + "text": "Europa Island [GAZ:00005811]", + "description": "A 28 km2 low-lying tropical island in the Mozambique Channel, about a third of the way from southern Madagascar to southern Mozambique.", + "meaning": "GAZ:00005811" + }, + "Falkland Islands (Islas Malvinas) [GAZ:00001412]": { + "text": "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "description": "An archipelago in the South Atlantic Ocean, located 483 km from the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), and 940 km north of Antarctica (Elephant Island). They consist of two main islands, East Falkland and West Falkland, together with 776 smaller islands.", + "meaning": "GAZ:00001412" + }, + "Faroe Islands [GAZ:00059206]": { + "text": "Faroe Islands [GAZ:00059206]", + "description": "An autonomous province of the Kingdom of Denmark since 1948 located in the Faroes. Administratively, the islands are divided into 34 municipalities (kommunur) within which 120 or so cities and villages lie.", + "meaning": "GAZ:00059206" + }, + "Fiji [GAZ:00006891]": { + "text": "Fiji [GAZ:00006891]", + "description": "An island nation in the South Pacific Ocean east of Vanuatu, west of Tonga and south of Tuvalu. The country occupies an archipelago of about 322 islands, of which 106 are permanently inhabited, and 522 islets. The two major islands, Viti Levu and Vanua Levu, account for 87% of the population.", + "meaning": "GAZ:00006891" + }, + "Finland [GAZ:00002937]": { + "text": "Finland [GAZ:00002937]", + "description": "A Nordic country situated in the Fennoscandian region of Northern Europe. It has borders with Sweden to the west, Russia to the east, and Norway to the north, while Estonia lies to its south across the Gulf of Finland. The capital city is Helsinki. Finland is divided into six administrative provinces (laani, plural laanit). These are divided into 20 regions (maakunt), 77 subregions (seutukunta) and then into municipalities (kunta).", + "meaning": "GAZ:00002937" + }, + "France [GAZ:00003940]": { + "text": "France [GAZ:00003940]", + "description": "A part of the country of France that extends from the Mediterranean Sea to the English Channel and the North Sea, and from the Rhine to the Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas departments.", + "meaning": "GAZ:00003940" + }, + "French Guiana [GAZ:00002516]": { + "text": "French Guiana [GAZ:00002516]", + "description": "An overseas department (departement d'outre-mer) of France, located on the northern coast of South America. It is bordered by Suriname, to the E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. French Guiana is divided into 2 departmental arrondissements, 19 cantons and 22 communes.", + "meaning": "GAZ:00002516" + }, + "French Polynesia [GAZ:00002918]": { + "text": "French Polynesia [GAZ:00002918]", + "description": "A French overseas collectivity in the southern Pacific Ocean. It is made up of several groups of Polynesian islands. French Polynesia has five administrative subdivisions (French: subdivisions administratives).", + "meaning": "GAZ:00002918" + }, + "French Southern and Antarctic Lands [GAZ:00003753]": { + "text": "French Southern and Antarctic Lands [GAZ:00003753]", + "description": "The French Southern and Antarctic Lands have formed a territoire d'outre-mer (an overseas territory) of France since 1955. The territory is divided into five districts.", + "meaning": "GAZ:00003753" + }, + "Gabon [GAZ:00001092]": { + "text": "Gabon [GAZ:00001092]", + "description": "A country in west central Africa sharing borders with Equatorial Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital and largest city is Libreville. Gabon is divided into 9 provinces and further divided into 37 departments.", + "meaning": "GAZ:00001092" + }, + "Gambia [GAZ:00000907]": { + "text": "Gambia [GAZ:00000907]", + "description": "A country in Western Africa. It is the smallest country on the African continental mainland and is bordered to the north, east, and south by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing through the centre of the country and discharging to the Atlantic Ocean is the Gambia River. The Gambia is divided into five divisions and one city (Banjul). The divisions are further subdivided into 37 districts.", + "meaning": "GAZ:00000907" + }, + "Gaza Strip [GAZ:00009571]": { + "text": "Gaza Strip [GAZ:00009571]", + "description": "A Palestinian enclave on the eastern coast of the Mediterranean Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel on the east and north along a 51 km (32 mi) border. Gaza and the West Bank are claimed by the de jure sovereign State of Palestine.", + "meaning": "GAZ:00009571" + }, + "Georgia [GAZ:00004942]": { + "text": "Georgia [GAZ:00004942]", + "description": "A Eurasian country in the Caucasus located at the east coast of the Black Sea. In the north, Georgia has a 723 km common border with Russia, specifically with the Northern Caucasus federal district. The following Russian republics/subdivisions: from west to east: border Georgia: Krasnodar Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to the south-west. It is a transcontinental country, located at the juncture of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 autonomous republics (avtonomiuri respublika), and 1 city (k'alak'i). The regions are further subdivided into 69 districts (raioni).", + "meaning": "GAZ:00004942" + }, + "Germany [GAZ:00002646]": { + "text": "Germany [GAZ:00002646]", + "description": "A country in Central Europe. It is bordered to the north by the North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech Republic; to the south by Austria and Switzerland; and to the west by France, Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) and cities (kreisfreie Stadte).", + "meaning": "GAZ:00002646" + }, + "Ghana [GAZ:00000908]": { + "text": "Ghana [GAZ:00000908]", + "description": "A country in West Africa. It borders Cote d'Ivoire to the west, Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the south. Ghana is a divided into 10 regions, subdivided into a total of 138 districts.", + "meaning": "GAZ:00000908" + }, + "Gibraltar [GAZ:00003987]": { + "text": "Gibraltar [GAZ:00003987]", + "description": "A British overseas territory located near the southernmost tip of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory shares a border with Spain to the north.", + "meaning": "GAZ:00003987" + }, + "Glorioso Islands [GAZ:00005808]": { + "text": "Glorioso Islands [GAZ:00005808]", + "description": "A group of islands and rocks totalling 5 km2, in the northern Mozambique channel, about 160 km northwest of Madagascar.", + "meaning": "GAZ:00005808" + }, + "Greece [GAZ:00002945]": { + "text": "Greece [GAZ:00002945]", + "description": "A country in southeastern Europe, situated on the southern end of the Balkan Peninsula. It has borders with Albania, the former Yugoslav Republic of Macedonia and Bulgaria to the north, and Turkey to the east. The Aegean Sea lies to the east and south of mainland Greece, while the Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin feature a vast number of islands. Greece consists of thirteen peripheries subdivided into a total of fifty-one prefectures (nomoi, singular nomos). There is also one autonomous area, Mount Athos, which borders the periphery of Central Macedonia.", + "meaning": "GAZ:00002945" + }, + "Greenland [GAZ:00001507]": { + "text": "Greenland [GAZ:00001507]", + "description": "A self-governing Danish province located between the Arctic and Atlantic Oceans, east of the Canadian Arctic Archipelago.", + "meaning": "GAZ:00001507" + }, + "Grenada [GAZ:02000573]": { + "text": "Grenada [GAZ:02000573]", + "description": "An island country in the West Indies in the Caribbean Sea at the southern end of the Grenadines island chain. Grenada consists of the island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, and several small islands which lie to the north of the main island and are a part of the Grenadines. It is located northwest of Trinidad and Tobago, northeast of Venezuela and southwest of Saint Vincent and the Grenadines. Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated population of 112,523 in July 2020.", + "meaning": "GAZ:02000573" + }, + "Guadeloupe [GAZ:00067142]": { + "text": "Guadeloupe [GAZ:00067142]", + "description": "An archipelago and overseas department and region of France in the Caribbean. It consists of six inhabited islands—Basse-Terre, Grande-Terre, Marie-Galante, La Désirade, and the two inhabited Îles des Saintes—as well as many uninhabited islands and outcroppings. It is south of Antigua and Barbuda and Montserrat, and north of Dominica.", + "meaning": "GAZ:00067142" + }, + "Guam [GAZ:00003706]": { + "text": "Guam [GAZ:00003706]", + "description": "An organized, unincorporated territory of the United States in the Micronesia subregion of the western Pacific Ocean. It is the westernmost point and territory of the United States (reckoned from the geographic center of the U.S.); in Oceania, it is the largest and southernmost of the Mariana Islands and the largest island in Micronesia.", + "meaning": "GAZ:00003706" + }, + "Guatemala [GAZ:00002936]": { + "text": "Guatemala [GAZ:00002936]", + "description": "A country in Central America bordered by Mexico to the northwest, the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the northeast, and Honduras and El Salvador to the southeast. Guatemala is divided into 22 departments (departamentos) and sub-divided into about 332 municipalities (municipios).", + "meaning": "GAZ:00002936" + }, + "Guernsey [GAZ:00001550]": { + "text": "Guernsey [GAZ:00001550]", + "description": "A British Crown Dependency in the English Channel off the coast of Normandy.", + "meaning": "GAZ:00001550" + }, + "Guinea [GAZ:00000909]": { + "text": "Guinea [GAZ:00000909]", + "description": "A nation in West Africa, formerly known as French Guinea. Guinea's territory has a curved shape, with its base at the Atlantic Ocean, inland to the east, and turning south. The base borders Guinea-Bissau and Senegal to the north, and Mali to the north and north-east; the inland part borders Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone to the west of the southern tip.", + "meaning": "GAZ:00000909" + }, + "Guinea-Bissau [GAZ:00000910]": { + "text": "Guinea-Bissau [GAZ:00000910]", + "description": "A country in western Africa, and one of the smallest nations in continental Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west. Formerly the Portuguese colony of Portuguese Guinea, upon independence, the name of its capital, Bissau, was added to the country's name in order to prevent confusion between itself and the Republic of Guinea.", + "meaning": "GAZ:00000910" + }, + "Guyana [GAZ:00002522]": { + "text": "Guyana [GAZ:00002522]", + "description": "A country in the N of South America. Guyana lies north of the equator, in the tropics, and is located on the Atlantic Ocean. Guyana is bordered to the east by Suriname, to the south and southwest by Brazil and to the west by Venezuela. Guyana is divided into 10 regions. The regions of Guyana are divided into 27 neighborhood councils.", + "meaning": "GAZ:00002522" + }, + "Haiti [GAZ:00003953]": { + "text": "Haiti [GAZ:00003953]", + "description": "A country located in the Greater Antilles archipelago on the Caribbean island of Hispaniola, which it shares with the Dominican Republic. Haiti is divided into 10 departments. The departments are further divided into 41 arrondissements, and 133 communes which serve as second and third level administrative divisions.", + "meaning": "GAZ:00003953" + }, + "Heard Island and McDonald Islands [GAZ:00009718]": { + "text": "Heard Island and McDonald Islands [GAZ:00009718]", + "description": "An Australian external territory comprising a volcanic group of mostly barren Antarctic islands, about two-thirds of the way from Madagascar to Antarctica.", + "meaning": "GAZ:00009718" + }, + "Honduras [GAZ:00002894]": { + "text": "Honduras [GAZ:00002894]", + "description": "A republic in Central America. The country is bordered to the west by Guatemala, to the southwest by El Salvador, to the southeast by Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. Honduras is divided into 18 departments. The capital city is Tegucigalpa Central District of the department of Francisco Morazan.", + "meaning": "GAZ:00002894" + }, + "Hong Kong [GAZ:00003203]": { + "text": "Hong Kong [GAZ:00003203]", + "description": "A special administrative region of the People's Republic of China (PRC). The territory lies on the eastern side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east, west and south. Hong Kong was a crown colony of the United Kingdom from 1842 until the transfer of its sovereignty to the People's Republic of China in 1997.", + "meaning": "GAZ:00003203" + }, + "Howland Island [GAZ:00007120]": { + "text": "Howland Island [GAZ:00007120]", + "description": "An uninhabited coral island located just north of the equator in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. The island is almost half way between Hawaii and Australia and is an unincorporated, unorganized territory of the United States, and is often included as one of the Phoenix Islands. For statistical purposes, Howland is grouped as one of the United States Minor Outlying Islands.", + "meaning": "GAZ:00007120" + }, + "Hungary [GAZ:00002952]": { + "text": "Hungary [GAZ:00002952]", + "description": "A landlocked country in the Carpathian Basin of Central Europe, bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: megye). In addition, the capital city (fovaros), Budapest, is independent of any county government. The counties are further subdivided into 173 subregions (kistersegek), and Budapest is comprised of its own subregion. Since 1996, the counties and City of Budapest have been grouped into 7 regions for statistical and development purposes. These seven regions constitute NUTS second-level units of Hungary.", + "meaning": "GAZ:00002952" + }, + "Iceland [GAZ:00000843]": { + "text": "Iceland [GAZ:00000843]", + "description": "A country in northern Europe, comprising the island of Iceland and its outlying islands in the North Atlantic Ocean between the rest of Europe and Greenland.", + "meaning": "GAZ:00000843" + }, + "India [GAZ:00002839]": { + "text": "India [GAZ:00002839]", + "description": "A country in South Asia. Bounded by the Indian Ocean on the south, the Arabian Sea on the west, and the Bay of Bengal on the east, India has a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, and Bhutan to the north-east; and Bangladesh and Burma to the east. India is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian Ocean. India is a federal republic of twenty-eight states and seven Union Territories. Each state or union territory is divided into basic units of government and administration called districts. There are nearly 600 districts in India. The districts in turn are further divided into tehsils and eventually into villages.", + "meaning": "GAZ:00002839" + }, + "Indonesia [GAZ:00003727]": { + "text": "Indonesia [GAZ:00003727]", + "description": "An archipelagic state in Southeast Asia. The country shares land borders with Papua New Guinea, East Timor and Malaysia. Other neighboring countries include Singapore, the Philippines, Australia, and the Indian territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, five of which have special status. The provinces are subdivided into regencies (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), which are further subdivided into subdistricts (kecamatan), and again into village groupings (either desa or kelurahan).", + "meaning": "GAZ:00003727" + }, + "Iran [GAZ:00004474]": { + "text": "Iran [GAZ:00004474]", + "description": "A country in Central Eurasia. Iran is bounded by the Gulf of Oman and the Persian Gulf to the south and the Caspian Sea to its north. It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into 30 provinces (ostan). The provinces are divided into counties (shahrestan), and subdivided into districts (bakhsh) and sub-districts (dehestan).", + "meaning": "GAZ:00004474" + }, + "Iraq [GAZ:00004483]": { + "text": "Iraq [GAZ:00004483]", + "description": "A country in the Middle East spanning most of the northwestern end of the Zagros mountain range, the eastern part of the Syrian Desert and the northern part of the Arabian Desert. It shares borders with Kuwait and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, Turkey to the north, and Iran to the east. It has a very narrow section of coastline at Umm Qasr on the Persian Gulf. There are two major flowing rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates (or provinces) (muhafazah). The governorates are divided into qadhas (or districts).", + "meaning": "GAZ:00004483" + }, + "Ireland [GAZ:00002943]": { + "text": "Ireland [GAZ:00002943]", + "description": "A country in north-western Europe. The modern sovereign state occupies five-sixths of the island of Ireland, which was partitioned in 1921. It is bordered by Northern Ireland (part of the United Kingdom) to the north, by the Atlantic Ocean to the west and by the Irish Sea to the east. Administration follows the 34 \"county-level\" counties and cities of Ireland. Of these twenty-nine are counties, governed by county councils while the five cities of Dublin, Cork, Limerick, Galway and Waterford have city councils, (previously known as corporations), and are administered separately from the counties bearing those names. The City of Kilkenny is the only city in the republic which does not have a \"city council\"; it is still a borough but not a county borough and is administered as part of County Kilkenny. Ireland is split into eight regions for NUTS statistical purposes. These are not related to the four traditional provinces but are based on the administrative counties.", + "meaning": "GAZ:00002943" + }, + "Isle of Man [GAZ:00052477]": { + "text": "Isle of Man [GAZ:00052477]", + "description": "A Crown dependency of the United Kingdom in the centre of the Irish Sea. It is not part of the United Kingdom, European Union or United Nations.", + "meaning": "GAZ:00052477" + }, + "Israel [GAZ:00002476]": { + "text": "Israel [GAZ:00002476]", + "description": "A country in Western Asia located on the eastern edge of the Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, which are partially administrated by the Palestinian National Authority, are also adjacent. The State of Israel is divided into six main administrative districts, known as mehozot (singular mahoz). Districts are further divided into fifteen sub-districts known as nafot (singular: nafa), which are themselves partitioned into fifty natural regions.", + "meaning": "GAZ:00002476" + }, + "Italy [GAZ:00002650]": { + "text": "Italy [GAZ:00002650]", + "description": "A country located on the Italian Peninsula in Southern Europe, and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. Italy shares its northern Alpine boundary with France, Switzerland, Austria and Slovenia. The independent states of San Marino and the Vatican City are enclaves within the Italian Peninsula, while Campione d'Italia is an Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, singular regione). Five of these regions have a special autonomous status that enables them to enact legislation on some of their local matters. It is further divided into 109 provinces (province) and 8,101 municipalities (comuni).", + "meaning": "GAZ:00002650" + }, + "Jamaica [GAZ:00003781]": { + "text": "Jamaica [GAZ:00003781]", + "description": "A nation of the Greater Antilles. Jamaica is divided into 14 parishes, which are grouped into three historic counties that have no administrative relevance.", + "meaning": "GAZ:00003781" + }, + "Jan Mayen [GAZ:00005853]": { + "text": "Jan Mayen [GAZ:00005853]", + "description": "A volcanic island that is part of the Kingdom of Norway, It has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and 1,000 km west of the Norwegian mainland. The island is mountainous, the highest summit being the Beerenberg volcano in the north. The isthmus is the location of the two largest lakes of the island, Sorlaguna (South Lagoon), and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng Lagoon). Jan Mayen was formed by the Jan Mayen hotspot.", + "meaning": "GAZ:00005853" + }, + "Japan [GAZ:00002747]": { + "text": "Japan [GAZ:00002747]", + "description": "An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south.", + "meaning": "GAZ:00002747" + }, + "Jarvis Island [GAZ:00007118]": { + "text": "Jarvis Island [GAZ:00007118]", + "description": "An uninhabited 4.5 km2 coral atoll located in the South Pacific Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated territory of the United States administered from Washington, DC by the United States Fish and Wildlife Service of the United States Department of the Interior as part of the National Wildlife Refuge system. Jarvis is one of the southern Line Islands and for statistical purposes is also grouped as one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount.", + "meaning": "GAZ:00007118" + }, + "Jersey [GAZ:00001551]": { + "text": "Jersey [GAZ:00001551]", + "description": "A British Crown Dependency[6] off the coast of Normandy, France. As well as the island of Jersey itself, the bailiwick includes two groups of small islands that are no longer permanently inhabited, the Minquiers and Ecrehous, and the Pierres de Lecq.", + "meaning": "GAZ:00001551" + }, + "Johnston Atoll [GAZ:00007114]": { + "text": "Johnston Atoll [GAZ:00007114]", + "description": "A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 nm) west of Hawaii. There are four islands located on the coral reef platform, two natural islands, Johnston Island and Sand Island, which have been expanded by coral dredging, as well as North Island (Akau) and East Island (Hikina), artificial islands formed from coral dredging. Johnston is an unincorporated territory of the United States, administered by the US Fish and Wildlife Service of the Department of the Interior as part of the United States Pacific Island Wildlife Refuges. Sits atop Johnston Seamount.", + "meaning": "GAZ:00007114" + }, + "Jordan [GAZ:00002473]": { + "text": "Jordan [GAZ:00002473]", + "description": "A country in Southwest Asia, bordered by Syria to the north, Iraq to the north-east, Israel and the West Bank to the west, and Saudi Arabia to the east and south. It shares the coastlines of the Dead Sea, and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided into 12 provinces called governorates. The Governorates are subdivided into approximately fifty-two nahias.", + "meaning": "GAZ:00002473" + }, + "Juan de Nova Island [GAZ:00005809]": { + "text": "Juan de Nova Island [GAZ:00005809]", + "description": "A 4.4 km2 low, flat, tropical island in the narrowest part of the Mozambique Channel, about one-third of the way between Madagascar and Mozambique.", + "meaning": "GAZ:00005809" + }, + "Kazakhstan [GAZ:00004999]": { + "text": "Kazakhstan [GAZ:00004999]", + "description": "A country in Central Asia and Europe. It is bordered by Russia, Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders on a significant part of the Caspian Sea. Kazakhstan is divided into 14 provinces and two municipal districts. The provinces of Kazakhstan are divided into raions.", + "meaning": "GAZ:00004999" + }, + "Kenya [GAZ:00001101]": { + "text": "Kenya [GAZ:00001101]", + "description": "A country in Eastern Africa. It is bordered by Ethiopia to the north, Somalia to the east, Tanzania to the south, Uganda to the west, and Sudan to the northwest, with the Indian Ocean running along the southeast border. Kenya comprises eight provinces each headed by a Provincial Commissioner (centrally appointed by the president). The provinces (mkoa singular mikoa plural in Swahili) are subdivided into districts (wilaya). There were 69 districts as of 1999 census. Districts are then subdivided into 497 divisions (taarafa). The divisions are then subdivided into 2,427 locations (kata) and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the status of a full administrative province.", + "meaning": "GAZ:00001101" + }, + "Kerguelen Archipelago [GAZ:00005682]": { + "text": "Kerguelen Archipelago [GAZ:00005682]", + "description": "A group of islands in the southern Indian Ocean. It is a territory of France. They are composed primarily of Tertiary flood basalts and a complex of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano at the southern end was active during the late Pleistocene. The Rallier du Baty Peninsula on the SW tip of the island contains two youthful subglacial eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active fumarole field is related to a series of Holocene trachytic lava flows and lahars that extend beyond the icecap.", + "meaning": "GAZ:00005682" + }, + "Kingman Reef [GAZ:00007116]": { + "text": "Kingman Reef [GAZ:00007116]", + "description": "A largely submerged, uninhabited tropical atoll located in the North Pacific Ocean, roughly half way between Hawaiian Islands and American Samoa. It is the northernmost of the Northern Line Islands and lies 65 km NNW of Palmyra Atoll, the next closest island, and has the status of an unincorporated territory of the United States, administered from Washington, DC by the US Navy. Sits atop Kingman Reef Seamount.", + "meaning": "GAZ:00007116" + }, + "Kiribati [GAZ:00006894]": { + "text": "Kiribati [GAZ:00006894]", + "description": "An island nation located in the central tropical Pacific Ocean. It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 km2 straddling the equator and bordering the International Date Line to the east. It is divided into three island groups which have no administrative function, including a group which unites the Line Islands and the Phoenix Islands (ministry at London, Christmas). Each inhabited island has its own council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two councils on Tabiteuea).", + "meaning": "GAZ:00006894" + }, + "Kosovo [GAZ:00011337]": { + "text": "Kosovo [GAZ:00011337]", + "description": "A country on the Balkan Peninsula. Kosovo borders Central Serbia to the north and east, Montenegro to the northwest, Albania to the west and the Republic of Macedonia to the south. Kosovo is divided into 7 districts (Rreth) and 30 municipalities. Serbia does not recognise the unilateral secession of Kosovo[8] and considers it a United Nations-governed entity within its sovereign territory, the Autonomous Province of Kosovo and Metohija.", + "meaning": "GAZ:00011337" + }, + "Kuwait [GAZ:00005285]": { + "text": "Kuwait [GAZ:00005285]", + "description": "A sovereign emirate on the coast of the Persian Gulf, enclosed by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided into six governorates (muhafazat, singular muhafadhah).", + "meaning": "GAZ:00005285" + }, + "Kyrgyzstan [GAZ:00006893]": { + "text": "Kyrgyzstan [GAZ:00006893]", + "description": "A country in Central Asia. Landlocked and mountainous, it is bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan to the southwest and China to the east. Kyrgyzstan is divided into seven provinces (oblast. The capital, Bishkek, and the second large city Osh are administratively the independent cities (shaar) with a status equal to a province. Each province comprises a number of districts (raions).", + "meaning": "GAZ:00006893" + }, + "Laos [GAZ:00006889]": { + "text": "Laos [GAZ:00006889]", + "description": "A landlocked country in southeast Asia, bordered by Burma (Myanmar) and China to the northwest, Vietnam to the east, Cambodia to the south, and Thailand to the west. Laos is divided into sixteen provinces (qwang) and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided into districts (muang).", + "meaning": "GAZ:00006889" + }, + "Latvia [GAZ:00002958]": { + "text": "Latvia [GAZ:00002958]", + "description": "A country in Northern Europe. Latvia shares land borders with Estonia to the north and Lithuania to the south, and both Russia and Belarus to the east. It is separated from Sweden in the west by the Baltic Sea. The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). There are also seven cities (lielpilsetas) that have a separate status. Latvia is also historically, culturally and constitutionally divided in four or more distinct regions.", + "meaning": "GAZ:00002958" + }, + "Lebanon [GAZ:00002478]": { + "text": "Lebanon [GAZ:00002478]", + "description": "A small, mostly mountainous country in Western Asia, on the eastern shore of the Mediterranean Sea. It is bordered by Syria to the north and east, and Israel to the south. Lebanon is divided into six governorates (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, singular: qadaa).", + "meaning": "GAZ:00002478" + }, + "Lesotho [GAZ:00001098]": { + "text": "Lesotho [GAZ:00001098]", + "description": "A land-locked country, entirely surrounded by the Republic of South Africa. Lesotho is divided into ten districts; these are further subdivided into 80 constituencies, which consists of 129 local community councils.", + "meaning": "GAZ:00001098" + }, + "Liberia [GAZ:00000911]": { + "text": "Liberia [GAZ:00000911]", + "description": "A country on the west coast of Africa, bordered by Sierra Leone, Guinea, Cote d'Ivoire, and the Atlantic Ocean.", + "meaning": "GAZ:00000911" + }, + "Libya [GAZ:00000566]": { + "text": "Libya [GAZ:00000566]", + "description": "A country in North Africa. Bordering the Mediterranean Sea to the north, Libya lies between Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west. There are thirty-four municipalities of Libya, known by the Arabic term sha'biyat (singular sha'biyah). These came recently (in the 1990s to replaced old Baladiyat systam. The Baladiyat system in turn was introduced to replace the system of muhafazah (governorates or provinces) that existed from the 1960s to the 1970s.", + "meaning": "GAZ:00000566" + }, + "Liechtenstein [GAZ:00003858]": { + "text": "Liechtenstein [GAZ:00003858]", + "description": "A tiny, doubly landlocked alpine country in Western Europe, bordered by Switzerland to its west and by Austria to its east. The principality of Liechtenstein is divided into 11 municipalities called Gemeinden (singular Gemeinde). The Gemeinden mostly consist only of a single town. Five of them fall within the electoral district Unterland (the lower county), and the remainder within Oberland (the upper county).", + "meaning": "GAZ:00003858" + }, + "Line Islands [GAZ:00007144]": { + "text": "Line Islands [GAZ:00007144]", + "description": "A group of eleven atolls and low coral islands in the central Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, while three are United States territories that are grouped with the United States Minor Outlying Islands.", + "meaning": "GAZ:00007144" + }, + "Lithuania [GAZ:00002960]": { + "text": "Lithuania [GAZ:00002960]", + "description": "A country located along the south-eastern shore of the Baltic Sea, sharing borders with Latvia to the north, Belarus to the southeast, Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. Lithuania has a three-tier administrative division: the country is divided into 10 counties (singular apskritis, plural, apskritys) that are further subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) which consist of over 500 elderates (singular seniunija, plural seniunijos).", + "meaning": "GAZ:00002960" + }, + "Luxembourg [GAZ:00002947]": { + "text": "Luxembourg [GAZ:00002947]", + "description": "A small landlocked country in western Europe, bordered by Belgium, France, and Germany. Luxembourg is divided into 3 districts, which are further divided into 12 cantons and then 116 communes. Twelve of the communes have city status, of which the city of Luxembourg is the largest.", + "meaning": "GAZ:00002947" + }, + "Macau [GAZ:00003202]": { + "text": "Macau [GAZ:00003202]", + "description": "One of the two special administrative regions of the People's Republic of China, the other being Hong Kong. Macau lies on the western side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east and south. Macau is situated 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang (West River) on the west. It borders the Zhuhai Special Economic Zone in mainland China.", + "meaning": "GAZ:00003202" + }, + "Madagascar [GAZ:00001108]": { + "text": "Madagascar [GAZ:00001108]", + "description": "An island nation in the Indian Ocean off the southeastern coast of Africa. The main island, also called Madagascar, is the fourth largest island in the world, and is home to 5% of the world's plant and animal species, of which more than 80% are endemic to Madagascar. Most notable are the lemur infraorder of primates, the carnivorous fossa, three endemic bird families and six endemic baobab species. Madagascar is divided into six autonomous provinces (faritany mizakatena), and 22 regions. The regions are further subdivided into 116 districts, 1,548 communes, and 16,969 fokontany.", + "meaning": "GAZ:00001108" + }, + "Malawi [GAZ:00001105]": { + "text": "Malawi [GAZ:00001105]", + "description": "A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms.", + "meaning": "GAZ:00001105" + }, + "Malaysia [GAZ:00003902]": { + "text": "Malaysia [GAZ:00003902]", + "description": "A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms.", + "meaning": "GAZ:00003902" + }, + "Maldives [GAZ:00006924]": { + "text": "Maldives [GAZ:00006924]", + "description": "An archipelago which consists of approximately 1,196 coral islands grouped in a double chain of 27 atolls, spread over roughly 90,000 km2.", + "meaning": "GAZ:00006924" + }, + "Mali [GAZ:00000584]": { + "text": "Mali [GAZ:00000584]", + "description": "A landlocked country in northern Africa. It borders Algeria on the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the south, Guinea on the south-west, and Senegal and Mauritania on the west. Mali is divided into 8 regions (regions) and 1 district, and subdivided into 49 cercles, totalling 288 arrondissements.", + "meaning": "GAZ:00000584" + }, + "Malta [GAZ:00004017]": { + "text": "Malta [GAZ:00004017]", + "description": "A Southern European country and consists of an archipelago situated centrally in the Mediterranean.", + "meaning": "GAZ:00004017" + }, + "Marshall Islands [GAZ:00007161]": { + "text": "Marshall Islands [GAZ:00007161]", + "description": "An archipelago that consists of twenty-nine atolls and five isolated islands. The most important atolls and islands form two groups: the Ratak Chain and the Ralik Chain (meaning \"sunrise\" and \"sunset\" chains). Two-thirds of the nation's population lives on Majuro (which is also the capital) and Ebeye. The outer islands are sparsely populated.", + "meaning": "GAZ:00007161" + }, + "Martinique [GAZ:00067143]": { + "text": "Martinique [GAZ:00067143]", + "description": "An island and an overseas department/region and single territorial collectivity of France.", + "meaning": "GAZ:00067143" + }, + "Mauritania [GAZ:00000583]": { + "text": "Mauritania [GAZ:00000583]", + "description": "A country in North-West Africa. It is bordered by the Atlantic Ocean on the west, by Senegal on the southwest, by Mali on the east and southeast, by Algeria on the northeast, and by Western Sahara on the northwest (most of which is occupied by Morocco). The capital and largest city is Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 regions (regions) and one capital district, which in turn are subdivided into 44 departments (departements).", + "meaning": "GAZ:00000583" + }, + "Mauritius [GAZ:00003745]": { + "text": "Mauritius [GAZ:00003745]", + "description": "An island nation off the coast of the African continent in the southwest Indian Ocean, about 900 km east of Madagascar. In addition to the island of Mauritius, the republic includes the islands of St. Brandon, Rodrigues and the Agalega Islands.", + "meaning": "GAZ:00003745" + }, + "Mayotte [GAZ:00003943]": { + "text": "Mayotte [GAZ:00003943]", + "description": "An overseas collectivity of France consisting of a main island, Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and several islets around these two.", + "meaning": "GAZ:00003943" + }, + "Mexico [GAZ:00002852]": { + "text": "Mexico [GAZ:00002852]", + "description": "A federal constitutional republic in North America. It is bounded on the north by the United States; on the south and west by the North Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of Mexico. The United Mexican States comprise a federation of thirty-one states and a federal district, the capital Mexico City.", + "meaning": "GAZ:00002852" + }, + "Micronesia [GAZ:00005862]": { + "text": "Micronesia [GAZ:00005862]", + "description": "A subregion of Oceania, comprising hundreds of small islands in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua New Guinea and Melanesia to the west and southwest, and Polynesia to the east.", + "meaning": "GAZ:00005862" + }, + "Midway Islands [GAZ:00007112]": { + "text": "Midway Islands [GAZ:00007112]", + "description": "A 6.2 km2 atoll located in the North Pacific Ocean (near the northwestern end of the Hawaiian archipelago). It is an unincorporated territory of the United States, designated an insular area under the authority of the US Department of the Interior.", + "meaning": "GAZ:00007112" + }, + "Moldova [GAZ:00003897]": { + "text": "Moldova [GAZ:00003897]", + "description": "A landlocked country in Eastern Europe, located between Romania to the west and Ukraine to the north, east and south. Moldova is divided into thirty-two districts (raioane, singular raion); three municipalities (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). The cities of Comrat and Tiraspol also have municipality status, however not as first-tier subdivisions of Moldova, but as parts of the regions of Gagauzia and Transnistria, respectively. The status of Transnistria is however under dispute. Although it is de jure part of Moldova and is recognized as such by the international community, Transnistria is not de facto under the control of the central government of Moldova. It is administered by an unrecognized breakaway authority under the name Pridnestrovian Moldovan Republic.", + "meaning": "GAZ:00003897" + }, + "Monaco [GAZ:00003857]": { + "text": "Monaco [GAZ:00003857]", + "description": "A small country that is completely bordered by France to the north, west, and south; to the east it is bordered by the Mediterranean Sea. It consists of a single municipality (commune) currently divided into 4 quartiers and 10 wards.", + "meaning": "GAZ:00003857" + }, + "Mongolia [GAZ:00008744]": { + "text": "Mongolia [GAZ:00008744]", + "description": "A country in East-Central Asia. The landlocked country borders Russia to the north and China to the south. The capital and largest city is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are in turn divided into 315 sums (districts). The capital Ulan Bator is administrated separately as a khot (municipality) with provincial status.", + "meaning": "GAZ:00008744" + }, + "Montenegro [GAZ:00006898]": { + "text": "Montenegro [GAZ:00006898]", + "description": "A country located in Southeastern Europe. It has a coast on the Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina to the northwest, Serbia and its partially recognized breakaway southern province of Kosovo to the northeast and Albania to the southeast. Its capital and largest city is Podgorica. Montenegro is divided into twenty-one municipalities (opstina), and two urban municipalities, subdivisions of Podgorica municipality.", + "meaning": "GAZ:00006898" + }, + "Montserrat [GAZ:00003988]": { + "text": "Montserrat [GAZ:00003988]", + "description": "A British overseas territory located in the Leeward Islands. Montserrat is divided into three parishes.", + "meaning": "GAZ:00003988" + }, + "Morocco [GAZ:00000565]": { + "text": "Morocco [GAZ:00000565]", + "description": "A country in North Africa. It has a coast on the Atlantic Ocean that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco has international borders with Algeria to the east, Spain to the north (a water border through the Strait and land borders with two small Spanish autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco is divided into 16 regions, and subdivided into 62 prefectures and provinces. Because of the conflict over Western Sahara, the status of both regions of \"Saguia el-Hamra\" and \"Rio de Oro\" is disputed.", + "meaning": "GAZ:00000565" + }, + "Mozambique [GAZ:00001100]": { + "text": "Mozambique [GAZ:00001100]", + "description": "A country in southeastern Africa bordered by the Indian Ocean to the east, Tanzania to the north, Malawi and Zambia to the northwest, Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique is divided into ten provinces (provincias) and one capital city (cidade capital) with provincial status. The provinces are subdivided into 129 districts (distritos). Districts are further divided in \"Postos Administrativos\" (Administrative Posts) and these in Localidades (Localities) the lowest geographical level of central state administration.", + "meaning": "GAZ:00001100" + }, + "Myanmar [GAZ:00006899]": { + "text": "Myanmar [GAZ:00006899]", + "description": "A country in SE Asia that is bordered by China on the north, Laos on the east, Thailand on the southeast, Bangladesh on the west, and India on the northwest, with the Bay of Bengal to the southwest. Myanmar is divided into seven states and seven divisions. The administrative divisions are further subdivided into districts, which are further subdivided into townships, wards, and villages.", + "meaning": "GAZ:00006899" + }, + "Namibia [GAZ:00001096]": { + "text": "Namibia [GAZ:00001096]", + "description": "A country in southern Africa on the Atlantic coast. It shares borders with Angola and Zambia to the north, Botswana to the east, and South Africa to the south. Namibia is divided into 13 regions and subdivided into 102 constituencies.", + "meaning": "GAZ:00001096" + }, + "Nauru [GAZ:00006900]": { + "text": "Nauru [GAZ:00006900]", + "description": "An island nation in the Micronesian South Pacific. The nearest neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. Nauru is divided into fourteen administrative districts which are grouped into eight electoral constituencies.", + "meaning": "GAZ:00006900" + }, + "Navassa Island [GAZ:00007119]": { + "text": "Navassa Island [GAZ:00007119]", + "description": "A small, uninhabited island in the Caribbean Sea, and is an unorganized unincorporated territory of the United States, which administers it through the US Fish and Wildlife Service. The island is also claimed by Haiti.", + "meaning": "GAZ:00007119" + }, + "Nepal [GAZ:00004399]": { + "text": "Nepal [GAZ:00004399]", + "description": "A landlocked nation in South Asia. It is bordered by the Tibet Autonomous Region of the People's Republic of China to the northeast and India to the south and west; it is separated from Bhutan by the Indian State of Sikkim and from Bangladesh by a small strip of the Indian State of West Bengal, known as the \"Chicken's Neck\". The Himalaya mountain range runs across Nepal's north and western parts, and eight of the world's ten highest mountains, including the highest, Mount Everest are situated within its territory. Nepal is divided into 14 zones and 75 districts, grouped into 5 development regions.", + "meaning": "GAZ:00004399" + }, + "Netherlands [GAZ:00002946]": { + "text": "Netherlands [GAZ:00002946]", + "description": "The European part of the Kingdom of the Netherlands. It is bordered by the North Sea to the north and west, Belgium to the south, and Germany to the east. The Netherlands is divided into twelve administrative regions, called provinces. All provinces of the Netherlands are divided into municipalities (gemeenten), together 443 (2007).", + "meaning": "GAZ:00002946" + }, + "New Caledonia [GAZ:00005206]": { + "text": "New Caledonia [GAZ:00005206]", + "description": "A \"sui generis collectivity\" (in practice an overseas territory) of France, made up of a main island (Grande Terre), the Loyalty Islands, and several smaller islands. It is located in the region of Melanesia in the southwest Pacific. Administratively, the archipelago is divided into three provinces, and then into 33 communes.", + "meaning": "GAZ:00005206" + }, + "New Zealand [GAZ:00000469]": { + "text": "New Zealand [GAZ:00000469]", + "description": "A nation in the south-western Pacific Ocean comprising two large islands (the North Island and the South Island) and numerous smaller islands, most notably Stewart Island/Rakiura and the Chatham Islands.", + "meaning": "GAZ:00000469" + }, + "Nicaragua [GAZ:00002978]": { + "text": "Nicaragua [GAZ:00002978]", + "description": "A republic in Central America. It is also the least densely populated with a demographic similar in size to its smaller neighbors. The country is bordered by Honduras to the north and by Costa Rica to the south. The Pacific Ocean lies to the west of the country, while the Caribbean Sea lies to the east. For administrative purposes it is divided into 15 departments (departamentos) and two self-governing regions (autonomous communities) based on the Spanish model. The departments are then subdivided into 153 municipios (municipalities). The two autonomous regions are Region Autonoma del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 they formed the single department of Zelaya.", + "meaning": "GAZ:00002978" + }, + "Niger [GAZ:00000585]": { + "text": "Niger [GAZ:00000585]", + "description": "A landlocked country in Western Africa, named after the Niger River. It borders Nigeria and Benin to the south, Burkina Faso and Mali to the west, Algeria and Libya to the north and Chad to the east. The capital city is Niamey. Niger is divided into 7 departments and one capital district. The departments are subdivided into 36 arrondissements and further subdivided into 129 communes.", + "meaning": "GAZ:00000585" + }, + "Nigeria [GAZ:00000912]": { + "text": "Nigeria [GAZ:00000912]", + "description": "A federal constitutional republic comprising thirty-six states and one Federal Capital Territory. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in the north. Its coast lies on the Gulf of Guinea, part of the Atlantic Ocean, in the south. The capital city is Abuja. Nigeria is divided into thirty-six states and one Federal Capital Territory, which are further sub-divided into 774 Local Government Areas (LGAs).", + "meaning": "GAZ:00000912" + }, + "Niue [GAZ:00006902]": { + "text": "Niue [GAZ:00006902]", + "description": "An island nation located in the South Pacific Ocean. Although self-governing, Niue is in free association with New Zealand, meaning that the Sovereign in Right of New Zealand is also Niue's head of state.", + "meaning": "GAZ:00006902" + }, + "Norfolk Island [GAZ:00005908]": { + "text": "Norfolk Island [GAZ:00005908]", + "description": "A Territory of Australia that includes Norfolk Island and neighboring islands.", + "meaning": "GAZ:00005908" + }, + "North Korea [GAZ:00002801]": { + "text": "North Korea [GAZ:00002801]", + "description": "A state in East Asia in the northern half of the Korean Peninsula, with its capital in the city of Pyongyang. To the south and separated by the Korean Demilitarized Zone is South Korea, with which it formed one nation until division following World War II. At its northern Amnok River border are China and, separated by the Tumen River in the extreme north-east, Russia.", + "meaning": "GAZ:00002801" + }, + "North Macedonia [GAZ:00006895]": { + "text": "North Macedonia [GAZ:00006895]", + "description": "A landlocked country on the Balkan peninsula in southeastern Europe. It is bordered by Serbia and Kosovo to the north, Albania to the west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), 10 of which comprise Greater Skopje. This is reduced from the previous 123 municipalities established in 1996-09. Prior to this, local government was organised into 34 administrative districts.", + "meaning": "GAZ:00006895" + }, + "North Sea [GAZ:00002284]": { + "text": "North Sea [GAZ:00002284]", + "description": "A sea situated between the eastern coasts of the British Isles and the western coast of Europe.", + "meaning": "GAZ:00002284" + }, + "Northern Mariana Islands [GAZ:00003958]": { + "text": "Northern Mariana Islands [GAZ:00003958]", + "description": "A group of 15 islands about three-quarters of the way from Hawaii to the Philippines.", + "meaning": "GAZ:00003958" + }, + "Norway [GAZ:00002699]": { + "text": "Norway [GAZ:00002699]", + "description": "A country and constitutional monarchy in Northern Europe that occupies the western portion of the Scandinavian Peninsula. It is bordered by Sweden, Finland, and Russia. The Kingdom of Norway also includes the Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty over Svalbard is based upon the Svalbard Treaty, but that treaty does not apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter I Island and Queen Maud Land in Antarctica are external dependencies, but those three entities do not form part of the kingdom.", + "meaning": "GAZ:00002699" + }, + "Oman [GAZ:00005283]": { + "text": "Oman [GAZ:00005283]", + "description": "A country in southwest Asia, on the southeast coast of the Arabian Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia on the west, and Yemen on the southwest. The coast is formed by the Arabian Sea on the south and east, and the Gulf of Oman on the northeast. The country also contains Madha, an exclave enclosed by the United Arab Emirates, and Musandam, an exclave also separated by Emirati territory. Oman is divided into four governorates (muhafazah) and five regions (mintaqat). The regions are subdivided into provinces (wilayat).", + "meaning": "GAZ:00005283" + }, + "Pakistan [GAZ:00005246]": { + "text": "Pakistan [GAZ:00005246]", + "description": "A country in Middle East which lies on the Iranian Plateau and some parts of South Asia. It is located in the region where South Asia converges with Central Asia and the Middle East. It has a 1,046 km coastline along the Arabian Sea in the south, and is bordered by Afghanistan and Iran in the west, India in the east and China in the far northeast. Pakistan is subdivided into four provinces and two territories. In addition, the portion of Kashmir that is administered by the Pakistani government is divided into two separate administrative units. The provinces are divided into a total of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly equivalent to counties). Tehsils may contain villages or municipalities. There are over five thousand local governments in Pakistan.", + "meaning": "GAZ:00005246" + }, + "Palau [GAZ:00006905]": { + "text": "Palau [GAZ:00006905]", + "description": "A nation that consists of eight principal islands and more than 250 smaller ones lying roughly 500 miles southeast of the Philippines.", + "meaning": "GAZ:00006905" + }, + "Panama [GAZ:00002892]": { + "text": "Panama [GAZ:00002892]", + "description": "The southernmost country of Central America. Situated on an isthmus, some categorize it as a transcontinental nation connecting the north and south part of America. It borders Costa Rica to the north-west, Colombia to the south-east, the Caribbean Sea to the north and the Pacific Ocean to the south. Panama's major divisions are nine provinces and five indigenous territories (comarcas indigenas). The provincial borders have not changed since they were determined at independence in 1903. The provinces are divided into districts, which in turn are subdivided into sections called corregimientos. Configurations of the corregimientos are changed periodically to accommodate population changes as revealed in the census reports.", + "meaning": "GAZ:00002892" + }, + "Papua New Guinea [GAZ:00003922]": { + "text": "Papua New Guinea [GAZ:00003922]", + "description": "A country in Oceania that comprises the eastern half of the island of New Guinea and its offshore islands in Melanesia (a region of the southwestern Pacific Ocean north of Australia).", + "meaning": "GAZ:00003922" + }, + "Paracel Islands [GAZ:00010832]": { + "text": "Paracel Islands [GAZ:00010832]", + "description": "A group of small islands and reefs in the South China Sea, about one-third of the way from Vietnam to the Philippines.", + "meaning": "GAZ:00010832" + }, + "Paraguay [GAZ:00002933]": { + "text": "Paraguay [GAZ:00002933]", + "description": "A landlocked country in South America. It lies on both banks of the Paraguay River, bordering Argentina to the south and southwest, Brazil to the east and northeast, and Bolivia to the northwest, and is located in the very heart of South America. Paraguay consists of seventeen departments and one capital district (distrito capital). Each department is divided into districts.", + "meaning": "GAZ:00002933" + }, + "Peru [GAZ:00002932]": { + "text": "Peru [GAZ:00002932]", + "description": "A country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean. Peru is divided into 25 regions and the province of Lima. These regions are subdivided into provinces, which are composed of districts (provincias and distritos). There are 195 provinces and 1833 districts in Peru. The Lima Province, located in the central coast of the country, is unique in that it doesn't belong to any of the twenty-five regions. The city of Lima, which is the nation's capital, is located in this province. Callao is its own region, even though it only contains one province, the Constitutional Province of Callao.", + "meaning": "GAZ:00002932" + }, + "Philippines [GAZ:00004525]": { + "text": "Philippines [GAZ:00004525]", + "description": "An archipelagic nation located in Southeast Asia. The Philippine archipelago comprises 7,107 islands in the western Pacific Ocean, bordering countries such as Indonesia, Malaysia, Palau and the Republic of China, although it is the only Southeast Asian country to share no land borders with its neighbors. The Philippines is divided into three island groups: Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, 136 cities, 1,494 municipalities and 41,995 barangays.", + "meaning": "GAZ:00004525" + }, + "Pitcairn Islands [GAZ:00005867]": { + "text": "Pitcairn Islands [GAZ:00005867]", + "description": "A group of four islands in the southern Pacific Ocean. The Pitcairn Islands form the southeasternmost extension of the geological archipelago of the Tuamotus of French Polynesia.", + "meaning": "GAZ:00005867" + }, + "Poland [GAZ:00002939]": { + "text": "Poland [GAZ:00002939]", + "description": "A country in Central Europe. Poland is bordered by Germany to the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a Russian exclave, to the north. The administrative division of Poland since 1999 has been based on three levels of subdivision. The territory of Poland is divided into voivodeships (provinces); these are further divided into powiats (counties), and these in turn are divided into gminas (communes or municipalities). Major cities normally have the status of both gmina and powiat. Poland currently has 16 voivodeships, 379 powiats (including 65 cities with powiat status), and 2,478 gminas.", + "meaning": "GAZ:00002939" + }, + "Portugal [GAZ:00004126]": { + "text": "Portugal [GAZ:00004126]", + "description": "That part of the Portugese Republic that occupies the W part of the Iberian Peninsula, and immediately adjacent islands.", + "meaning": "GAZ:00004126" + }, + "Puerto Rico [GAZ:00006935]": { + "text": "Puerto Rico [GAZ:00006935]", + "description": "A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States).", + "meaning": "GAZ:00006935" + }, + "Qatar [GAZ:00005286]": { + "text": "Qatar [GAZ:00005286]", + "description": "An Arab emirate in Southwest Asia, occupying the small Qatar Peninsula on the northeasterly coast of the larger Arabian Peninsula. It is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds the state. Qatar is divided into ten municipalities (Arabic: baladiyah), which are further divided into zones (districts).", + "meaning": "GAZ:00005286" + }, + "Republic of the Congo [GAZ:00001088]": { + "text": "Republic of the Congo [GAZ:00001088]", + "description": "A country in Central Africa. It is bordered by Gabon, Cameroon, the Central African Republic, the Democratic Republic of the Congo, the Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic of the Congo is divided into 10 regions (regions) and one commune, the capital Brazzaville. The regions are subdivided into forty-six districts.", + "meaning": "GAZ:00001088" + }, + "Reunion [GAZ:00003945]": { + "text": "Reunion [GAZ:00003945]", + "description": "An island, located in the Indian Ocean east of Madagascar, about 200 km south west of Mauritius, the nearest island.", + "meaning": "GAZ:00003945" + }, + "Romania [GAZ:00002951]": { + "text": "Romania [GAZ:00002951]", + "description": "A country in Southeastern Europe. It shares a border with Hungary and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, and Bulgaria to the south. Romania has a stretch of sea coast along the Black Sea. It is located roughly in the lower basin of the Danube and almost all of the Danube Delta is located within its territory. Romania is divided into forty-one counties (judete), as well as the municipality of Bucharest (Bucuresti) - which is its own administrative unit. The country is further subdivided into 319 cities and 2686 communes (rural localities).", + "meaning": "GAZ:00002951" + }, + "Ross Sea [GAZ:00023304]": { + "text": "Ross Sea [GAZ:00023304]", + "description": "A large embayment of the Southern Ocean, extending deeply into Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck on the east, at 158degW.", + "meaning": "GAZ:00023304" + }, + "Russia [GAZ:00002721]": { + "text": "Russia [GAZ:00002721]", + "description": "A transcontinental country extending over much of northern Eurasia. Russia shares land borders with the following countries (counter-clockwise from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais (territories), 4 autonomous okrugs (autonomous districts), one autonomous oblast, and two federal cities. The federal subjects are grouped into seven federal districts. These subjects are divided into districts (raions), cities/towns and urban-type settlements, and, at level 4, selsovets (rural councils), towns and urban-type settlements under the jurisdiction of the district and city districts.", + "meaning": "GAZ:00002721" + }, + "Rwanda [GAZ:00001087]": { + "text": "Rwanda [GAZ:00001087]", + "description": "A small landlocked country in the Great Lakes region of east-central Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo and Tanzania. Rwanda is divided into five provinces (intara) and subdivided into thirty districts (akarere). The districts are divided into sectors (imirenge).", + "meaning": "GAZ:00001087" + }, + "Saint Helena [GAZ:00000849]": { + "text": "Saint Helena [GAZ:00000849]", + "description": "An island of volcanic origin and a British overseas territory in the South Atlantic Ocean.", + "meaning": "GAZ:00000849" + }, + "Saint Kitts and Nevis [GAZ:00006906]": { + "text": "Saint Kitts and Nevis [GAZ:00006906]", + "description": "A federal two-island nation in the West Indies. Located in the Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast are Antigua and Barbuda, and to the southeast is the small uninhabited island of Redonda, and the island of Montserrat. The federation of Saint Kitts and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts and five on Nevis.", + "meaning": "GAZ:00006906" + }, + "Saint Lucia [GAZ:00006909]": { + "text": "Saint Lucia [GAZ:00006909]", + "description": "An island nation in the eastern Caribbean Sea on the boundary with the Atlantic Ocean.", + "meaning": "GAZ:00006909" + }, + "Saint Pierre and Miquelon [GAZ:00003942]": { + "text": "Saint Pierre and Miquelon [GAZ:00003942]", + "description": "An Overseas Collectivity of France located in a group of small islands in the North Atlantic Ocean, the main ones being Saint Pierre and Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and Miquelon became an overseas department in 1976, but its status changed to that of an Overseas collectivity in 1985.", + "meaning": "GAZ:00003942" + }, + "Saint Martin [GAZ:00005841]": { + "text": "Saint Martin [GAZ:00005841]", + "description": "An overseas collectivity of France that came into being on 2007-02-22, encompassing the northern parts of the island of Saint Martin and neighboring islets. The southern part of the island, Sint Maarten, is part of the Netherlands Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe.", + "meaning": "GAZ:00005841" + }, + "Saint Vincent and the Grenadines [GAZ:02000565]": { + "text": "Saint Vincent and the Grenadines [GAZ:02000565]", + "description": "An island nation in the Lesser Antilles chain of the Caribbean Sea.", + "meaning": "GAZ:02000565" + }, + "Samoa [GAZ:00006910]": { + "text": "Samoa [GAZ:00006910]", + "description": "A country governing the western part of the Samoan Islands archipelago in the South Pacific Ocean. Samoa is made up of eleven itumalo (political districts).", + "meaning": "GAZ:00006910" + }, + "San Marino [GAZ:00003102]": { + "text": "San Marino [GAZ:00003102]", + "description": "A country in the Apennine Mountains. It is a landlocked enclave, completely surrounded by Italy. San Marino is an enclave in Italy, on the border between the regioni of Emilia Romagna and Marche. Its topography is dominated by the Apennines mountain range. San Marino is divided into nine municipalities, known locally as Castelli (singular castello).", + "meaning": "GAZ:00003102" + }, + "Sao Tome and Principe [GAZ:00006927]": { + "text": "Sao Tome and Principe [GAZ:00006927]", + "description": "An island nation in the Gulf of Guinea, off the western equatorial coast of Africa. It consists of two islands: Sao Tome and Principe, located about 140 km apart and about 250 and 225 km respectively, off of the northwestern coast of Gabon. Both islands are part of an extinct volcanic mountain range. Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The provinces are further divided into seven districts, six on Sao Tome and one on Principe (with Principe having self-government since 1995-04-29).", + "meaning": "GAZ:00006927" + }, + "Saudi Arabia [GAZ:00005279]": { + "text": "Saudi Arabia [GAZ:00005279]", + "description": "A country on the Arabian Peninsula. It is bordered by Jordan on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, and the United Arab Emirates on the east, Oman on the southeast, and Yemen on the south. The Persian Gulf lies to the northeast and the Red Sea to its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; singular mintaqah). Each is then divided into Governorates.", + "meaning": "GAZ:00005279" + }, + "Senegal [GAZ:00000913]": { + "text": "Senegal [GAZ:00000913]", + "description": "A country south of the Senegal River in western Africa. Senegal is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies almost entirely within Senegal, surrounded on the north, east and south; from its western coast Gambia's territory follows the Gambia River more than 300 km inland. Dakar is the capital city of Senegal, located on the Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided into 11 regions and further subdivided into 34 Departements, 103 Arrondissements (neither of which have administrative function) and by Collectivites Locales.", + "meaning": "GAZ:00000913" + }, + "Serbia [GAZ:00002957]": { + "text": "Serbia [GAZ:00002957]", + "description": "A landlocked country in Central and Southeastern Europe, covering the southern part of the Pannonian Plain and the central part of the Balkan Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria to the east; Republic of Macedonia, Montenegro to the south; Croatia and Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided into 29 districts plus the City of Belgrade. The districts and the city of Belgrade are further divided into municipalities. Serbia has two autonomous provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), and Vojvodina in the north (7 districts, 46 municipalities).", + "meaning": "GAZ:00002957" + }, + "Seychelles [GAZ:00006922]": { + "text": "Seychelles [GAZ:00006922]", + "description": "An archipelagic island country in the Indian Ocean at the eastern edge of the Somali Sea. It consists of 115 islands.", + "meaning": "GAZ:00006922" + }, + "Sierra Leone [GAZ:00000914]": { + "text": "Sierra Leone [GAZ:00000914]", + "description": "A country in West Africa. It is bordered by Guinea in the north and east, Liberia in the southeast, and the Atlantic Ocean in the southwest and west. The Republic of Sierra Leone is composed of 3 provinces and one area called the Western Area; the provinces are further divided into 12 districts. The Western Area is also divided into 2 districts.", + "meaning": "GAZ:00000914" + }, + "Singapore [GAZ:00003923]": { + "text": "Singapore [GAZ:00003923]", + "description": "An island nation located at the southern tip of the Malay Peninsula. It lies 137 km north of the Equator, south of the Malaysian State of Johor and north of Indonesia's Riau Islands. Singapore consists of 63 islands, including mainland Singapore. There are two man-made connections to Johor, Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in the west. Since 2001-11-24, Singapore has had an administrative subdivision into 5 districts. It is also divided into five Regions, urban planning subdivisions with no administrative role.", + "meaning": "GAZ:00003923" + }, + "Sint Maarten [GAZ:00012579]": { + "text": "Sint Maarten [GAZ:00012579]", + "description": "One of five island areas (Eilandgebieden) of the Netherlands Antilles, encompassing the southern half of the island of Saint Martin/Sint Maarten.", + "meaning": "GAZ:00012579" + }, + "Slovakia [GAZ:00002956]": { + "text": "Slovakia [GAZ:00002956]", + "description": "A landlocked country in Central Europe. The Slovak Republic borders the Czech Republic and Austria to the west, Poland to the north, Ukraine to the east and Hungary to the south. The largest city is its capital, Bratislava. Slovakia is subdivided into 8 kraje (singular - kraj, usually translated as regions. The kraje are subdivided into many okresy (singular okres, usually translated as districts). Slovakia currently has 79 districts.", + "meaning": "GAZ:00002956" + }, + "Slovenia [GAZ:00002955]": { + "text": "Slovenia [GAZ:00002955]", + "description": "A country in southern Central Europe bordering Italy to the west, the Adriatic Sea to the southwest, Croatia to the south and east, Hungary to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. As of 2005-05 Slovenia is divided into 12 statistical regions for legal and statistical purposes. Slovenia is divided into 210 local municipalities, eleven of which have urban status.", + "meaning": "GAZ:00002955" + }, + "Solomon Islands [GAZ:00005275]": { + "text": "Solomon Islands [GAZ:00005275]", + "description": "A nation in Melanesia, east of Papua New Guinea, consisting of nearly one thousand islands. Together they cover a land mass of 28,400 km2. The capital is Honiara, located on the island of Guadalcanal.", + "meaning": "GAZ:00005275" + }, + "Somalia [GAZ:00001104]": { + "text": "Somalia [GAZ:00001104]", + "description": "A country located in the Horn of Africa. It is bordered by Djibouti to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on its north, the Indian Ocean at its east, and Ethiopia to the west. Prior to the civil war, Somalia was divided into eighteen regions (gobollada, singular gobol), which were in turn subdivided into districts. On a de facto basis, northern Somalia is now divided up among the quasi-independent states of Puntland, Somaliland, Galmudug and Maakhir.", + "meaning": "GAZ:00001104" + }, + "South Africa [GAZ:00001094]": { + "text": "South Africa [GAZ:00001094]", + "description": "A country located at the southern tip of Africa. It borders the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, Swaziland, and Lesotho, an independent enclave surrounded by South African territory. It is divided into nine provinces which are further subdivided into 52 districts: 6 metropolitan and 46 district municipalities. The 46 district municipalities are further subdivided into 231 local municipalities. The district municipalities also contain 20 district management areas (mostly game parks) that are directly governed by the district municipalities. The six metropolitan municipalities perform the functions of both district and local municipalities.", + "meaning": "GAZ:00001094" + }, + "South Georgia and the South Sandwich Islands [GAZ:00003990]": { + "text": "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "description": "A British overseas territory in the southern Atlantic Ocean. It iconsists of South Georgia and the Sandwich Islands, some 640 km to the SE.", + "meaning": "GAZ:00003990" + }, + "South Korea [GAZ:00002802]": { + "text": "South Korea [GAZ:00002802]", + "description": "A republic in East Asia, occupying the southern half of the Korean Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 special city (teukbyeolsi). These are further subdivided into a variety of smaller entities, including cities (si), counties (gun), districts (gu), towns (eup), townships (myeon), neighborhoods (dong) and villages (ri).", + "meaning": "GAZ:00002802" + }, + "South Sudan [GAZ:00233439]": { + "text": "South Sudan [GAZ:00233439]", + "description": "A state located in Africa with Juba as its capital city. It's bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic of the Congo to the south, and the Central African Republic to the west and Sudan to the North. Southern Sudan includes the vast swamp region of the Sudd formed by the White Nile, locally called the Bahr el Jebel.", + "meaning": "GAZ:00233439" + }, + "Spain [GAZ:00003936]": { + "text": "Spain [GAZ:00003936]", + "description": "That part of the Kingdom of Spain that occupies the Iberian Peninsula plus the Balaeric Islands. The Spanish mainland is bordered to the south and east almost entirely by the Mediterranean Sea (except for a small land boundary with Gibraltar); to the north by France, Andorra, and the Bay of Biscay; and to the west by the Atlantic Ocean and Portugal.", + "meaning": "GAZ:00003936" + }, + "Spratly Islands [GAZ:00010831]": { + "text": "Spratly Islands [GAZ:00010831]", + "description": "A group of >100 islands located in the Southeastern Asian group of reefs and islands in the South China Sea, about two-thirds of the way from southern Vietnam to the southern Philippines.", + "meaning": "GAZ:00010831" + }, + "Sri Lanka [GAZ:00003924]": { + "text": "Sri Lanka [GAZ:00003924]", + "description": "An island nation in South Asia, located about 31 km off the southern coast of India. Sri Lanka is divided into 9 provinces and 25 districts. Districts are divided into Divisional Secretariats.", + "meaning": "GAZ:00003924" + }, + "State of Palestine [GAZ:00002475]": { + "text": "State of Palestine [GAZ:00002475]", + "description": "The territory under the administration of the Palestine National Authority, as established by the Oslo Accords. The PNA divides the Palestinian territories into 16 governorates.", + "meaning": "GAZ:00002475" + }, + "Sudan [GAZ:00000560]": { + "text": "Sudan [GAZ:00000560]", + "description": "A country in North Africa. It is bordered by Egypt to the north, the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and Uganda to the southeast, Democratic Republic of the Congo and the Central African Republic to the southwest, Chad to the west and Libya to the northwest. Sudan is divided into twenty-six states (wilayat, singular wilayah) which in turn are subdivided into 133 districts.", + "meaning": "GAZ:00000560" + }, + "Suriname [GAZ:00002525]": { + "text": "Suriname [GAZ:00002525]", + "description": "A country in northern South America. It is situated between French Guiana to the east and Guyana to the west. The southern border is shared with Brazil and the northern border is the Atlantic coast. The southernmost border with French Guiana is disputed along the Marowijne river. Suriname is divided into 10 districts, each of which is divided into Ressorten.", + "meaning": "GAZ:00002525" + }, + "Svalbard [GAZ:00005396]": { + "text": "Svalbard [GAZ:00005396]", + "description": "An archipelago of continental islands lying in the Arctic Ocean north of mainland Europe, about midway between Norway and the North Pole.", + "meaning": "GAZ:00005396" + }, + "Swaziland [GAZ:00001099]": { + "text": "Swaziland [GAZ:00001099]", + "description": "A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla).", + "meaning": "GAZ:00001099" + }, + "Sweden [GAZ:00002729]": { + "text": "Sweden [GAZ:00002729]", + "description": "A Nordic country on the Scandinavian Peninsula in Northern Europe. It has borders with Norway (west and north) and Finland (northeast). Sweden is a unitary state, currently divided into twenty-one counties (lan). Each county further divides into a number of municipalities or kommuner, with a total of 290 municipalities in 2004.", + "meaning": "GAZ:00002729" + }, + "Switzerland [GAZ:00002941]": { + "text": "Switzerland [GAZ:00002941]", + "description": "A federal republic in Europe. Switzerland is bordered by Germany, France, Italy, Austria and Liechtenstein. The Swiss Confederation consists of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within Switzerland there are two enclaves: Busingen belongs to Germany, Campione d'Italia belongs to Italy.", + "meaning": "GAZ:00002941" + }, + "Syria [GAZ:00002474]": { + "text": "Syria [GAZ:00002474]", + "description": "A country in Southwest Asia, bordering Lebanon, the Mediterranean Sea and the island of Cyprus to the west, Israel to the southwest, Jordan to the south, Iraq to the east, and Turkey to the north. Syria has fourteen governorates, or muhafazat (singular: muhafazah). The governorates are divided into sixty districts, or manatiq (singular: mintaqah), which are further divided into sub-districts, or nawahi (singular: nahia).", + "meaning": "GAZ:00002474" + }, + "Taiwan [GAZ:00005341]": { + "text": "Taiwan [GAZ:00005341]", + "description": "A state in East Asia with de facto rule of the island of Tawain and adjacent territory. The Republic of China currently administers two historical provinces of China (one completely and a small part of another one) and centrally administers two direct-controlled municipalities.", + "meaning": "GAZ:00005341" + }, + "Tajikistan [GAZ:00006912]": { + "text": "Tajikistan [GAZ:00006912]", + "description": "A mountainous landlocked country in Central Asia. Afghanistan borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and People's Republic of China to the east. Tajikistan consists of 4 administrative divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly known as Karotegin Province). Each region is divided into several districts (nohiya or raion).", + "meaning": "GAZ:00006912" + }, + "Tanzania [GAZ:00001103]": { + "text": "Tanzania [GAZ:00001103]", + "description": "A country in East Africa bordered by Kenya and Uganda on the north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, and Zambia, Malawi and Mozambique on the south. To the east it borders the Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight districts (wilaya), each with at least one council, have been created to further increase local authority; the councils are also known as local government authorities. Currently there are 114 councils operating in 99 districts; 22 are urban and 92 are rural. The 22 urban units are further classified as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) or town councils (the remaining eleven communities).", + "meaning": "GAZ:00001103" + }, + "Thailand [GAZ:00003744]": { + "text": "Thailand [GAZ:00003744]", + "description": "A country in Southeast Asia. To its east lie Laos and Cambodia; to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided into 75 provinces (changwat), which are gathered into 5 groups of provinces by location. There are also 2 special governed districts: the capital Bangkok (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial level and thus often counted as a 76th province.", + "meaning": "GAZ:00003744" + }, + "Timor-Leste [GAZ:00006913]": { + "text": "Timor-Leste [GAZ:00006913]", + "description": "A country in Southeast Asia. It comprises the eastern half of the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, an exclave on the northwestern side of the island, within Indonesian West Timor. The small country of 15,410 km2 is located about 640 km northwest of Darwin, Australia. East Timor is divided into thirteen administrative districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, villages and hamlets.", + "meaning": "GAZ:00006913" + }, + "Togo [GAZ:00000915]": { + "text": "Togo [GAZ:00000915]", + "description": "A country in West Africa bordering Ghana in the west, Benin in the east and Burkina Faso in the north. In the south, it has a short Gulf of Guinea coast, on which the capital Lome is located.", + "meaning": "GAZ:00000915" + }, + "Tokelau [GAZ:00260188]": { + "text": "Tokelau [GAZ:00260188]", + "description": "A dependent territory of New Zealand in the southern Pacific Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and Fakaofo. They have a combined land area of 10 km2 (4 sq mi).", + "meaning": "GAZ:00260188" + }, + "Tonga [GAZ:00006916]": { + "text": "Tonga [GAZ:00006916]", + "description": "A Polynesian country, and also an archipelago comprising 169 islands, of which 36 are inhabited. The archipelago's total surface area is about 750 square kilometres (290 sq mi) scattered over 700,000 square kilometres (270,000 sq mi) of the southern Pacific Ocean.", + "meaning": "GAZ:00006916" + }, + "Trinidad and Tobago [GAZ:00003767]": { + "text": "Trinidad and Tobago [GAZ:00003767]", + "description": "An archipelagic state in the southern Caribbean, lying northeast of the South American nation of Venezuela and south of Grenada in the Lesser Antilles. It also shares maritime boundaries with Barbados to the northeast and Guyana to the southeast. The country covers an area of 5,128 km2and consists of two main islands, Trinidad and Tobago, and 21 smaller islands.", + "meaning": "GAZ:00003767" + }, + "Tromelin Island [GAZ:00005812]": { + "text": "Tromelin Island [GAZ:00005812]", + "description": "A low, flat 0.8 km2 island in the Indian Ocean, about 350 km east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 m long and 700 m wide, surrounded by coral reefs. The island is 7 m high at its highest point.", + "meaning": "GAZ:00005812" + }, + "Tunisia [GAZ:00000562]": { + "text": "Tunisia [GAZ:00000562]", + "description": "A country situated on the Mediterranean coast of North Africa. It is bordered by Algeria to the west and Libya to the southeast. Tunisia is subdivided into 24 governorates, divided into 262 \"delegations\" or \"districts\" (mutamadiyat), and further subdivided into municipalities (shaykhats).", + "meaning": "GAZ:00000562" + }, + "Turkey [GAZ:00000558]": { + "text": "Turkey [GAZ:00000558]", + "description": "A Eurasian country that stretches across the Anatolian peninsula in western Asia and Thrace (Rumelia) in the Balkan region of southeastern Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago are to the west; and the Black Sea is to the north. Separating Anatolia and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus and the Dardanelles), which are commonly reckoned to delineate the border between Asia and Europe, thereby making Turkey transcontinental. The territory of Turkey is subdivided into 81 provinces for administrative purposes. The provinces are organized into 7 regions for census purposes; however, they do not represent an administrative structure. Each province is divided into districts, for a total of 923 districts.", + "meaning": "GAZ:00000558" + }, + "Turkmenistan [GAZ:00005018]": { + "text": "Turkmenistan [GAZ:00005018]", + "description": "A country in Central Asia. It is bordered by Afghanistan to the southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan to the northwest, and the Caspian Sea to the west. It was a constituent republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan is divided into five provinces or welayatlar (singular - welayat) and one independent city.", + "meaning": "GAZ:00005018" + }, + "Turks and Caicos Islands [GAZ:00003955]": { + "text": "Turks and Caicos Islands [GAZ:00003955]", + "description": "A British Overseas Territory consisting of two groups of tropical islands in the West Indies. The Turks and Caicos Islands are divided into six administrative districts (two in the Turks Islands and four in the Caicos Islands.", + "meaning": "GAZ:00003955" + }, + "Tuvalu [GAZ:00009715]": { + "text": "Tuvalu [GAZ:00009715]", + "description": "A Polynesian island nation located in the Pacific Ocean midway between Hawaii and Australia.", + "meaning": "GAZ:00009715" + }, + "United States of America [GAZ:00002459]": { + "text": "United States of America [GAZ:00002459]", + "description": "A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into \"census areas\"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a \"charter township\", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county.", + "meaning": "GAZ:00002459" + }, + "Uganda [GAZ:00001102]": { + "text": "Uganda [GAZ:00001102]", + "description": "A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties.", + "meaning": "GAZ:00001102" + }, + "Ukraine [GAZ:00002724]": { + "text": "Ukraine [GAZ:00002724]", + "description": "A country in Eastern Europe. It borders Russia to the east, Belarus to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine is subdivided into twenty-four oblasts (provinces) and one autonomous republic (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, and Sevastopol, both have a special legal status. The 24 oblasts and Crimea are subdivided into 490 raions (districts), or second-level administrative units.", + "meaning": "GAZ:00002724" + }, + "United Arab Emirates [GAZ:00005282]": { + "text": "United Arab Emirates [GAZ:00005282]", + "description": "A Middle Eastern federation of seven states situated in the southeast of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain.", + "meaning": "GAZ:00005282" + }, + "United Kingdom [GAZ:00002637]": { + "text": "United Kingdom [GAZ:00002637]", + "description": "A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel.", + "meaning": "GAZ:00002637" + }, + "Uruguay [GAZ:00002930]": { + "text": "Uruguay [GAZ:00002930]", + "description": "A country located in the southeastern part of South America. It is bordered by Brazil to the north, by Argentina across the bank of both the Uruguay River to the west and the estuary of Rio de la Plata to the southwest, and the South Atlantic Ocean to the southeast. Uraguay consists of 19 departments (departamentos, singular - departamento).", + "meaning": "GAZ:00002930" + }, + "Uzbekistan [GAZ:00004979]": { + "text": "Uzbekistan [GAZ:00004979]", + "description": "A doubly landlocked country in Central Asia, formerly part of the Soviet Union. It shares borders with Kazakhstan to the west and to the north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one autonomous republic (respublika and one independent city (shahar).", + "meaning": "GAZ:00004979" + }, + "Vanuatu [GAZ:00006918]": { + "text": "Vanuatu [GAZ:00006918]", + "description": "An island country located in the South Pacific Ocean. The archipelago, which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New Guinea, southeast of the Solomon Islands, and west of Fiji.", + "meaning": "GAZ:00006918" + }, + "Venezuela [GAZ:00002931]": { + "text": "Venezuela [GAZ:00002931]", + "description": "A country on the northern coast of South America. The country comprises a continental mainland and numerous islands located off the Venezuelan coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses borders with Guyana to the east, Brazil to the south, and Colombia to the west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just north, off the Venezuelan coast. Venezuela is divided into twenty-three states (Estados), a capital district (distrito capital) corresponding to the city of Caracas, the Federal Dependencies (Dependencias Federales, a special territory), and Guayana Esequiba (claimed in a border dispute with Guyana). Venezuela is further subdivided into 335 municipalities (municipios); these are subdivided into over one thousand parishes (parroquias).", + "meaning": "GAZ:00002931" + }, + "Viet Nam [GAZ:00003756]": { + "text": "Viet Nam [GAZ:00003756]", + "description": "The easternmost country on the Indochina Peninsula in Southeast Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, alongside China, Laos, and Cambodia.", + "meaning": "GAZ:00003756" + }, + "Virgin Islands [GAZ:00003959]": { + "text": "Virgin Islands [GAZ:00003959]", + "description": "A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts.", + "meaning": "GAZ:00003959" + }, + "Wake Island [GAZ:00007111]": { + "text": "Wake Island [GAZ:00007111]", + "description": "A coral atoll (despite its name) having a coastline of 19 km in the North Pacific Ocean, located about two-thirds of the way from Honolulu (3,700 km west) to Guam (2,430 km east).", + "meaning": "GAZ:00007111" + }, + "Wallis and Futuna [GAZ:00007191]": { + "text": "Wallis and Futuna [GAZ:00007191]", + "description": "A Polynesian French island territory (but not part of, or even contiguous with, French Polynesia) in the South Pacific between Fiji and Samoa. It is made up of three main volcanic tropical islands and a number of tiny islets.", + "meaning": "GAZ:00007191" + }, + "West Bank [GAZ:00009572]": { + "text": "West Bank [GAZ:00009572]", + "description": "A landlocked territory near the Mediterranean coast of Western Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the south, west and north.[2] Under Israeli occupation since 1967, the area is split into 167 Palestinian \"islands\" under partial Palestinian National Authority civil rule, and 230 Israeli settlements into which Israeli law is \"pipelined\".", + "meaning": "GAZ:00009572" + }, + "Western Sahara [GAZ:00000564]": { + "text": "Western Sahara [GAZ:00000564]", + "description": "A territory of northwestern Africa, bordered by Morocco to the north, Algeria in the northeast, Mauritania to the east and south, and the Atlantic Ocean on the west. Western Sahara is administratively divided into four regions.", + "meaning": "GAZ:00000564" + }, + "Yemen [GAZ:00005284]": { + "text": "Yemen [GAZ:00005284]", + "description": "A country located on the Arabian Peninsula in Southwest Asia. Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's territory includes over 200 islands, the largest of which is Socotra, about 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen is divided into twenty governorates (muhafazah) and one municipality. The population of each governorate is listed in the table below. The governorates of Yemen are divided into 333 districts (muderiah). The districts are subdivided into 2,210 sub-districts, and then into 38,284 villages (as of 2001).", + "meaning": "GAZ:00005284" + }, + "Zambia [GAZ:00001107]": { + "text": "Zambia [GAZ:00001107]", + "description": "A landlocked country in Southern Africa. The neighbouring countries are the Democratic Republic of the Congo to the north, Tanzania to the north-east, Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, and Angola to the west. The capital city is Lusaka. Zambia is divided into nine provinces. Each province is subdivided into several districts with a total of 73 districts.", + "meaning": "GAZ:00001107" + }, + "Zimbabwe [GAZ:00001106]": { + "text": "Zimbabwe [GAZ:00001106]", + "description": "A landlocked country in the southern part of the continent of Africa, between the Zambezi and Limpopo rivers. It is bordered by South Africa to the south, Botswana to the southwest, Zambia to the northwest, and Mozambique to the east. Zimbabwe is divided into eight provinces and two cities with provincial status. The provinces are subdivided into 59 districts and 1,200 municipalities.", + "meaning": "GAZ:00001106" + } + } + } + }, + "slots": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen_collector_sample_ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:sample_name" + ], + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "required": true + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen_collector_subsample_ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100752", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled_sample_ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100996", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "description": "The user-defined identifier assigned to a specific location from which samples are taken.", + "title": "sampling_site_ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100760", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sampling_event_id": { + "name": "sampling_event_id", + "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", + "title": "sampling_event_ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100761", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject_accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:bioproject_accession" + ], + "slot_uri": "GENEPIO:0001136", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample_accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMD00000001" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001139", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true, + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101203", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101204", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100762", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "description": "The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_contact_email", + "comments": [ + "Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the \"sample collector contact email\"." + ], + "examples": [ + { + "value": "bloggsj@aglab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101107", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample_collected_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collected_by" + ], + "slot_uri": "GENEPIO:0001153", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001156", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo_loc_name_(country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "slot_uri": "GENEPIO:0001181", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "geo_loc_name_(country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory of origin of the sample.", + "title": "geo_loc_name_(state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "slot_uri": "GENEPIO:0001185", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "description": "The county/region of origin of the sample.", + "title": "geo_loc_name_(county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100280", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "The city of origin of the sample.", + "title": "geo_loc_name_(city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001189", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo_loc_name_(site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100436", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "slot_uri": "GENEPIO:0100309", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "slot_uri": "GENEPIO:0100310", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:organism" + ], + "slot_uri": "GENEPIO:0001191", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_subtype": { + "name": "influenza_subtype", + "title": "influenza_subtype", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101108", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "influenza_subsubtype menu", + "required": true, + "multivalued": true + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "title": "influenza_subtyping_scheme_name", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101109", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "influenza_subtyping_scheme_name menu" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "title": "taxonomic_identification_process", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100583", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "taxonomic_identification_process menu" + }, + "virus_identifier": { + "name": "virus_identifier", + "title": "virus_identifier", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101110", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "who_oie_fao_h5_clade": { + "name": "who_oie_fao_h5_clade", + "title": "WHO/OIE/FAO_H5_clade", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101111", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected, or sampling began for a continuous sample.", + "title": "sample_collection_date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collection_date" + ], + "slot_uri": "GENEPIO:0001174", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "description": "The date on which sample collection ended for a continuous sample.", + "title": "sample_collection_end_date", + "comments": [ + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + ], + "examples": [ + { + "value": "2020-03-18" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101071", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "description": "The time at which sample collection began.", + "title": "sample_collection_start_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "17:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101072", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "description": "The time at which sample collection ended.", + "title": "sample_collection_end_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "19:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101073", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "description": "The descriptive time of day during which the sample was collected.", + "title": "sample_collection_time_of_day", + "comments": [ + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + ], + "examples": [ + { + "value": "Morning" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100765", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "sample_collection_time_of_day menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "description": "The amount of time over which the sample was collected.", + "title": "sample_collection_time_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100766", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "description": "The units of the time duration measurement of sample collection.", + "title": "sample_collection_time_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Hour" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100767", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "sample_collection_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001179", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100763", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "host_origin_geo_loc_name_country": { + "name": "host_origin_geo_loc_name_country", + "description": "The country of origin of the host.", + "title": "host_origin_geo_loc_name (country)", + "comments": [ + "If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "South Africa [GAZ:00001094]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100438", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product_origin_geo_loc_name_country": { + "name": "food_product_origin_geo_loc_name_country", + "description": "The country of origin of a food product.", + "title": "food_product_origin_geo_loc_name (country)", + "comments": [ + "If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "United States of America [GAZ:00002459]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:food_origin" + ], + "slot_uri": "GENEPIO:0100437", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product": { + "name": "food_product", + "description": "A material consumed and digested for nutritional value or enjoyment.", + "title": "food_product", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feather meal [FOODON:00003927]" + }, + { + "value": "Bone meal [ENVO:02000054]" + }, + { + "value": "Chicken breast [FOODON:00002703]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_product", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:food_product_type" + ], + "slot_uri": "GENEPIO:0100444", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product_properties": { + "name": "food_product_properties", + "description": "Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers.", + "title": "food_product_properties", + "comments": [ + "Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free)." + ], + "examples": [ + { + "value": "Food (chopped) [FOODON:00002777]" + }, + { + "value": "Ready-to-eat (RTE) [FOODON:03316636]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_product_properties", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0100445", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product_properties menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_packaging": { + "name": "food_packaging", + "description": "The type of packaging used to contain a food product.", + "title": "food_packaging", + "comments": [ + "If known, provide information regarding how the food product was packaged." + ], + "examples": [ + { + "value": "Plastic tray or pan [FOODON:03490126]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_packaging", + "BIOSAMPLE_Enterics:food_contain_wrap" + ], + "slot_uri": "GENEPIO:0100447", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_packaging menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_quality_date": { + "name": "food_quality_date", + "description": "A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula.", + "title": "food_quality_date", + "comments": [ + "This date is typically labeled on a food product as \"best if used by\", best by\", \"use by\", or \"freeze by\" e.g. 5/24/2020. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:food_quality_date" + ], + "slot_uri": "GENEPIO:0100615", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "range": "date" + }, + "food_packaging_date": { + "name": "food_packaging_date", + "description": "A food product's packaging date as marked by a food manufacturer or retailer.", + "title": "food_packaging_date", + "comments": [ + "The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100616", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "range": "date" + }, + "environmental_site": { + "name": "environmental_site", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "title": "environmental_site", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Poultry hatchery [ENVO:01001874]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_site", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:animal_env" + ], + "slot_uri": "GENEPIO:0001232", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_site menu" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "title": "environmental_material", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Soil [ENVO:00001998]" + }, + { + "value": "Water [CHEBI:15377]" + }, + { + "value": "Wastewater [ENVO:00002001]" + }, + { + "value": "Broom [ENVO:03501377]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_material", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0001223", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "anatomical_material": { + "name": "anatomical_material", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "title": "anatomical_material", + "comments": [ + "An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Tissue [UBERON:0000479]" + }, + { + "value": "Blood [UBERON:0000178]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:anatomical_material", + "BIOSAMPLE_Enterics:host_tissue_sampled", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0001211", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "body_product": { + "name": "body_product", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "title": "body_product", + "comments": [ + "A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feces [UBERON:0001988]" + }, + { + "value": "Urine [UBERON:0001088]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:body_product", + "BIOSAMPLE_Enterics:host_body_product", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0001216", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "body_product menu" + }, + { + "range": "null value menu" + } + ] + }, + "anatomical_part": { + "name": "anatomical_part", + "description": "An anatomical part of an organism e.g. oropharynx.", + "title": "anatomical_part", + "comments": [ + "An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Snout [UBERON:0006333]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:anatomical_part", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0001214", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_part menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection_device", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Drag swab [OBI:0002822]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_device", + "BIOSAMPLE_Enterics:samp_collect_device", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0001234", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "collection_device menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "title": "collection_method", + "comments": [ + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Rinsing for specimen collection [GENEPIO_0002116]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_method", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0001241", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "collection_method menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100768", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "milliliter (mL) [UO:0000098]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100769", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "sample_volume_measurement_unit menu" + }, + "residual_sample_status": { + "name": "residual_sample_status", + "description": "The status of the residual sample (whether any sample remains after its original use).", + "title": "residual_sample_status", + "comments": [ + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + ], + "examples": [ + { + "value": "No residual sample (sample all used) [GENEPIO:0101088]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101090", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "residual_sample_status menu" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:purpose_of_sampling" + ], + "slot_uri": "GENEPIO:0001198", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sampling menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity": { + "name": "presampling_activity", + "description": "The activities or variables upstream of sample collection that may affect the sample.", + "title": "presampling_activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100433", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "multivalued": true, + "any_of": [ + { + "range": "presampling_activity menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the activities or variables that affected the sample collected.", + "title": "presampling_activity_details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100434", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_storage_method": { + "name": "sample_storage_method", + "description": "The process used to store the sample.", + "title": "sample_storage_method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100448", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The medium in which a sample is stored.", + "title": "sample_storage_medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100449", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101014", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101015", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "sample_storage_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001253", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "multivalued": true, + "any_of": [ + { + "range": "specimen_processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100311", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental_protocol", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101029", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100921", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "multivalued": true, + "any_of": [ + { + "range": "experimental_specimen_role_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "title": "experimental_specimen_details", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101112", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "available_data_types": { + "name": "available_data_types", + "description": "The type of data that is available, that may or may not require permission to access.", + "title": "available_data_types", + "comments": [ + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + ], + "examples": [ + { + "value": "Total coliform count [GENEPIO:0100729]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100690", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "multivalued": true, + "any_of": [ + { + "range": "available_data_types menu" + }, + { + "range": "null value menu" + } + ] + }, + "available_data_type_details": { + "name": "available_data_type_details", + "description": "Detailed information regarding other available data types.", + "title": "available_data_type_details", + "comments": [ + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + ], + "examples": [ + { + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101023", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "host_common_name": { + "name": "host_common_name", + "description": "The commonly used name of the host.", + "title": "host_(common_name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name." + ], + "examples": [ + { + "value": "Cow [NCBITaxon:9913]" + }, + { + "value": "Chicken [NCBITaxon:9913], Human [NCBITaxon:9606]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host" + ], + "slot_uri": "GENEPIO:0001386", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "host (common name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_scientific_name": { + "name": "host_scientific_name", + "description": "The taxonomic, or scientific name of the host.", + "title": "host_(scientific_name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided." + ], + "examples": [ + { + "value": "Bos taurus [NCBITaxon:9913]" + }, + { + "value": "Homo sapiens [NCBITaxon:9103]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:host", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:host" + ], + "slot_uri": "GENEPIO:0001387", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "host (scientific name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_ecotype": { + "name": "host_ecotype", + "description": "The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler.", + "title": "host_(ecotype)", + "comments": [ + "Provide the name of the ecotype of the host organism." + ], + "examples": [ + { + "value": "Sea ecotype" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_variety" + ], + "slot_uri": "GENEPIO:0100450", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "host_breed": { + "name": "host_breed", + "description": "A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding.", + "title": "host_(breed)", + "comments": [ + "Provide the name of the breed of the host organism." + ], + "examples": [ + { + "value": "Holstein" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:host_disease", + "BIOSAMPLE_Enterics:host_animal_breed" + ], + "slot_uri": "GENEPIO:0100451", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "host_food_production_name": { + "name": "host_food_production_name", + "description": "The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity.", + "title": "host_(food production name)", + "comments": [ + "Select the host's food production name from the pick list." + ], + "examples": [ + { + "value": "Calf [FOODON:03411349]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host" + ], + "slot_uri": "GENEPIO:0100452", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host (food production name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_age": { + "name": "host_age", + "description": "Age of host at the time of sampling.", + "title": "host_age", + "comments": [ + "If known, provide age. Age-binning is also acceptable." + ], + "examples": [ + { + "value": "79" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Patient%20age", + "CNPHI:host_age" + ], + "slot_uri": "GENEPIO:0001392", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "required": true, + "maximum_value": 130, + "any_of": [ + { + "range": "decimal" + }, + { + "range": "null value menu" + } + ] + }, + "host_age_unit": { + "name": "host_age_unit", + "description": "The units used to measure the host's age.", + "title": "host_age_unit", + "comments": [ + "If known, provide the age units used to measure the host's age from the pick list." + ], + "examples": [ + { + "value": "year [UO:0000036]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001393", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "host_age_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_age_bin": { + "name": "host_age_bin", + "description": "Age of host at the time of sampling, expressed as an age group.", + "title": "host_age_bin", + "comments": [ + "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_age" + ], + "slot_uri": "GENEPIO:0001394", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host_age_bin menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_disease": { + "name": "host_disease", + "description": "The name of the disease experienced by the host.", + "title": "host_disease", + "comments": [ + "This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”." + ], + "examples": [ + { + "value": "mastitis, gastroenteritis" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_disease" + ], + "slot_uri": "GENEPIO:0001391", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host_disease menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_state": { + "name": "host_health_state", + "description": "Health status of the host at the time of sample collection.", + "title": "host_health_state", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Asymptomatic [NCIT:C3833]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Patient%20status", + "CNPHI:host_health_state" + ], + "slot_uri": "GENEPIO:0001388", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host_health_state menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_status_details": { + "name": "host_health_status_details", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "title": "host_health_status_details", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Hospitalized (ICU) [GENEPIO:0100046]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001389", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host_health_status_details menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_outcome": { + "name": "host_health_outcome", + "description": "Disease outcome in the host.", + "title": "host_health_outcome", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Recovered [NCIT:C49498]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:host_disease_outcome" + ], + "slot_uri": "GENEPIO:0001390", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host_health_outcome menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_subject_id": { + "name": "host_subject_id", + "description": "A unique identifier by which each host can be referred to e.g. #131", + "title": "host_subject_ID", + "comments": [ + "Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward." + ], + "examples": [ + { + "value": "BCxy123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:host_subject_id" + ], + "slot_uri": "GENEPIO:0001398", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "case_id": { + "name": "case_id", + "description": "The identifier used to specify an epidemiologically detected case of disease.", + "title": "case_ID", + "comments": [ + "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing." + ], + "examples": [ + { + "value": "ABCD1234" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100281", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "symptom_onset_date": { + "name": "symptom_onset_date", + "description": "The date on which the symptoms began or were first noted.", + "title": "symptom_onset_date", + "comments": [ + "If known, provide the symptom onset date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001399", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "signs_and_symptoms": { + "name": "signs_and_symptoms", + "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", + "title": "signs_and_symptoms", + "comments": [ + "Select all of the symptoms experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001400", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "signs_and_symptoms menu" + }, + { + "range": "null value menu" + } + ] + }, + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "description": "Patient pre-existing conditions and risk factors.\nPre-existing condition: A medical condition that existed prior to the current infection.\nRisk Factor: A variable associated with an increased risk of disease or infection.", + "title": "pre-existing_conditions_and_risk_factors", + "comments": [ + "Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Asthma [HP:0002099]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001401", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "pre-existing_conditions_and_risk_factors menu" + }, + { + "range": "null value menu" + } + ] + }, + "complications": { + "name": "complications", + "description": "Patient medical complications that are believed to have occurred as a result of host disease.", + "title": "complications", + "comments": [ + "Select all of the complications experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Acute respiratory failure [MONDO:0001208]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001402", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "complications menu" + }, + { + "range": "null value menu" + } + ] + }, + "exposure_event": { + "name": "exposure_event", + "description": "Event leading to exposure.", + "title": "exposure event", + "comments": [ + "Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Social Gathering" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Additional%20location%20information", + "CNPHI:Exposure%20Event", + "NML_LIMS:PH_EXPOSURE" + ], + "slot_uri": "GENEPIO:0001417", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "exposure event menu" + }, + { + "range": "null value menu" + } + ] + }, + "exposure_contact_level": { + "name": "exposure_contact_level", + "description": "The exposure transmission contact type.", + "title": "exposure contact level", + "comments": [ + "Select direct or indirect exposure from the pick-list." + ], + "examples": [ + { + "value": "Direct" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:exposure%20contact%20level" + ], + "slot_uri": "GENEPIO:0001418", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "exposure contact level menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_role": { + "name": "host_role", + "description": "The role of the host in relation to the exposure setting.", + "title": "host role", + "comments": [ + "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Inpatient" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_HOST_ROLE" + ], + "slot_uri": "GENEPIO:0001419", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "host role menu", + "multivalued": true + }, + "exposure_setting": { + "name": "exposure_setting", + "description": "The setting leading to exposure.", + "title": "exposure setting", + "comments": [ + "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Healthcare Setting" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE" + ], + "slot_uri": "GENEPIO:0001428", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "exposure setting menu", + "multivalued": true + }, + "exposure_details": { + "name": "exposure_details", + "description": "Additional host exposure information.", + "title": "exposure details", + "comments": [ + "Free text description of the exposure." + ], + "examples": [ + { + "value": "Case infected family at home" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_DETAILS" + ], + "slot_uri": "GENEPIO:0001431", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "host_vaccination_status": { + "name": "host_vaccination_status", + "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", + "title": "host_vaccination_status", + "comments": [ + "Select the vaccination status of the host from the pick list." + ], + "examples": [ + { + "value": "Fully Vaccinated [GENEPIO:0100100]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:prior_sars_cov_2_vaccination" + ], + "slot_uri": "GENEPIO:0001404", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host_vaccination_status menu" + }, + { + "range": "null value menu" + } + ] + }, + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", + "description": "The number of doses of the vaccine recived by the host.", + "title": "number_of_vaccine_doses_received", + "comments": [ + "Record how many doses of the vaccine the host has received." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001406", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "integer", + "minimum_value": 0 + }, + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", + "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", + "title": "vaccination_dose_1_vaccine_name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100313", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", + "description": "The date the first dose of a vaccine was administered.", + "title": "vaccination_dose_1_vaccination_date", + "comments": [ + "Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-03-01" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100314", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "date" + }, + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", + "description": "The name of the vaccine administered as the second dose of a vaccine regimen.", + "title": "vaccination_dose_2_vaccine_name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100315", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", + "description": "The date the second dose of a vaccine was administered.", + "title": "vaccination_dose_2_vaccination_date", + "comments": [ + "Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-09-01" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100316", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "date" + }, + "vaccination_history": { + "name": "vaccination_history", + "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", + "title": "vaccination history", + "comments": [ + "Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons." + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2021-03-01" + }, + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2022-01-15" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Last%20vaccinated" + ], + "slot_uri": "GENEPIO:0100321", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "influenza_antiviral_treatment_administration": { + "name": "influenza_antiviral_treatment_administration", + "description": "An action of giving or applying an influenza antiviral agent to a patient as part of a treatment regimen.", + "title": "influenza_antiviral_treatment_administration", + "examples": [ + { + "value": "Influenza antiviral treatment administered [GENEPIO:0101194]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101113", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "influenza_antiviral_treatment_administration menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_antiviral_agent__": { + "name": "influenza_antiviral_agent__", + "description": "A substance that destroys or inhibits replication of viruses.", + "title": "influenza_antiviral_agent", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101114", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "influenza_antiviral_treatment_date": { + "name": "influenza_antiviral_treatment_date", + "description": "The date on which the influenza antiviral agent was administered to a patient as part of treatment", + "title": "influenza_antiviral_treatment_date", + "comments": [ + "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given." + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101115", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "date" + }, + "water_catchment_area_human_population_measurement_value": { + "name": "water_catchment_area_human_population_measurement_value", + "description": "The numerical value of the human population measurement that contributes to the composition of water in a catchment area.", + "title": "water_catchment_area_human_population_measurement_value", + "comments": [ + "Where known, provide the numerical value of population size, i.e. the number of people." + ], + "examples": [ + { + "value": "10,500" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100773", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "integer" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_range": { + "name": "water_catchment_area_human_population_range", + "description": "The human population range of the water catchment that contributes effluent to a wastewater site.", + "title": "water_catchment_area_human_population_range", + "comments": [ + "Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist." + ], + "examples": [ + { + "value": "1,000 - 10,000 people" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100774", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "water catchment area human population range menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_measurement_method": { + "name": "water_catchment_area_human_population_measurement_method", + "description": "The method by which a water catchment 's human population size was measured or estimated", + "title": "water_catchment_area_human_population_measurement_method", + "comments": [ + "Provide a brief description of how catchment population size was measured or estimated." + ], + "examples": [ + { + "value": "population of jurisdiction encompassing the wastewater service area" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100775", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_value": { + "name": "water_catchment_area_human_population_density_value", + "description": "The numerical value describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density value", + "comments": [ + "Provide the numerical value of the population density in the catchement area." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100776", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_unit": { + "name": "water_catchment_area_human_population_density_unit", + "description": "The unit describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density unit", + "comments": [ + "Provide the unit of the population density in the catchement area." + ], + "examples": [ + { + "value": "persons per Km^2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100777", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "water catchment area human population density unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "populated_area_type": { + "name": "populated_area_type", + "description": "A type of area that is populated by humans to different degrees.", + "title": "populated area type", + "comments": [ + "Provide the populated area type from the pick list." + ], + "examples": [ + { + "value": "Urban area" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100778", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "populated area type menu" + }, + { + "range": "null value menu" + } + ] + }, + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "sampling weather conditions", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100779", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "multivalued": true, + "any_of": [ + { + "range": "sampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", + "description": "Weather conditions prior to collection that may affect the sample.", + "title": "presampling weather conditions", + "comments": [ + "Provide the weather conditions prior to sample collection." + ], + "examples": [ + { + "value": "Drizzle" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100780", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "multivalued": true, + "any_of": [ + { + "range": "presampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", + "comments": [ + "Provide the quantity of precipitation in the area leading up to the time of sample collection." + ], + "examples": [ + { + "value": "12" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100911", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "water_depth": { + "name": "water_depth", + "description": "The depth of some water.", + "title": "water_depth", + "comments": [ + "Provide the numerical depth only of water only (without units)." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100440", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "water_depth_units": { + "name": "water_depth_units", + "description": "The units of measurement for water depth.", + "title": "water_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101025", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "water_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "sediment_depth": { + "name": "sediment_depth", + "description": "The depth of some sediment.", + "title": "sediment_depth", + "comments": [ + "Provide the numerical depth only of the sediment (without units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100697", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "sediment_depth_units": { + "name": "sediment_depth_units", + "description": "The units of measurement for sediment depth.", + "title": "sediment_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101026", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "sediment_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "air_temperature": { + "name": "air_temperature", + "description": "The temperature of some air.", + "title": "air_temperature", + "comments": [ + "Provide the numerical value for the temperature of the air (without units)." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100441", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "air_temperature_units": { + "name": "air_temperature_units", + "description": "The units of measurement for air temperature.", + "title": "air_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101027", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "air_temperature_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_temperature": { + "name": "water_temperature", + "description": "The temperature of some water.", + "title": "water_temperature", + "comments": [ + "Provide the numerical value for the temperature of the water (without units)." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100698", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "water_temperature_units": { + "name": "water_temperature_units", + "description": "The units of measurement for water temperature.", + "title": "water_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101028", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "water_temperature_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "weather_type": { + "name": "weather_type", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "weather_type", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain [ENVO:01001564]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100442", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "multivalued": true, + "any_of": [ + { + "range": "weather_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_unit": { + "name": "precipitation_measurement_unit", + "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement unit", + "comments": [ + "Provide the units of precipitation by selecting a value from the pick list." + ], + "examples": [ + { + "value": "inch" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100912", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "precipitation measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", + "description": "The process used to measure the amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement 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of a measurement of alkalinity.", + "title": "alkalinity measurement value", + "comments": [ + "Provide the numerical value of the measured alkalinity." + ], + "examples": [ + { + "value": "3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100878", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "alkalinity_measurement_unit": { + "name": "alkalinity_measurement_unit", + "description": "The units of a measurement of alkalinity.", + "title": "alkalinity measurement unit", + "comments": [ + "Provide the units of the measured alkalinity." + ], + "examples": [ + { + "value": "milligram per liter of calcium carbonate (mg/L CaCO3)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100879", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "alkalinity measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "alkalinity_measurement_method": { + "name": "alkalinity_measurement_method", + "description": "The process used to measure alkalinity.", + "title": "alkalinity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure alkalinity." + ], + "examples": [ + { + "value": "Titration method" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100880", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "conductivity_measurement_value": { + "name": "conductivity_measurement_value", + "description": "The numerical value of a measurement of conductivity.", + "title": "conductivity measurement value", + "comments": [ + "Provide the numerical value of the measured conductivity." + ], + "examples": [ + { + "value": "1412" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100916", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "conductivity_measurement_unit": { + "name": "conductivity_measurement_unit", + "description": "The units of a measurement of conductivity.", + "title": "conductivity measurement unit", + "comments": [ + "Provide the units of the measured conductivity." + ], + "examples": [ + { + "value": "microSiemen per centimeter (μS/cm)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100803", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "conductivity measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "conductivity_measurement_method": { + "name": "conductivity_measurement_method", + "description": "The method used to measure conductivity.", + "title": "conductivity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure conductivity." + ], + "examples": [ + { + "value": "Conductivity electrode and meter" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100804", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "salinity_measurement_value": { + "name": "salinity_measurement_value", + "description": "The numerical value of a measurement of salinity.", + "title": "salinity measurement value", + "comments": [ + "Provide the numerical value of the measured salinity." + ], + "examples": [ + { + "value": "35" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100805", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "salinity_measurement_unit": { + "name": "salinity_measurement_unit", + "description": "The units of a measurement of salinity.", + "title": "salinity measurement unit", + "comments": [ + "Provide the units of the measured salinity." + ], + "examples": [ + { + "value": "practical salinity unit (PSU)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100806", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "salinity measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "salinity_measurement_method": { + "name": "salinity_measurement_method", + "description": "The method used to measure salinity.", + "title": "salinity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure salinity." + ], + "examples": [ + { + "value": "conductivity meter" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100807", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "total_nitrogen_tn_measurement_value": { + "name": "total_nitrogen_tn_measurement_value", + "description": "The numerical value of a measurement of total nitrogen (TN).", + "title": "total nitrogen (TN) measurement value", + "comments": [ + "Provide the numerical value of the measured TN." + ], + "examples": [ + { + "value": "120" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100808", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "total_nitrogen_tn_measurement_unit": { + "name": "total_nitrogen_tn_measurement_unit", + "description": "The units of a measurement of total nitrogen (TN).", + "title": "total nitrogen (TN) measurement unit", + "comments": [ + "Provide the units of the measured TN." + ], + "examples": [ + { + "value": "milligram per liter (mg/L)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100809", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "total nitrogen (TN) measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "total_nitrogen_tn_measurement_method": { + "name": "total_nitrogen_tn_measurement_method", + "description": "The method used to measure total nitrogen (TN).", + "title": "total nitrogen (TN) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TN." + ], + "examples": [ + { + "value": "Hach total nitrogen spectrophotometric test" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100810", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "total_phosphorus_tp_measurement_value": { + "name": "total_phosphorus_tp_measurement_value", + "description": "The numerical value of a measurement of total phosphorus (TP).", + "title": "total phosphorus (TP) measurement value", + "comments": [ + "Provide the numerical value of the measured TP." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100811", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "total_phosphorus_tp_measurement_unit": { + "name": "total_phosphorus_tp_measurement_unit", + "description": "The units of a measurement of total phosphorus (TP).", + "title": "total phosphorus (TP) measurement unit", + "comments": [ + "Provide the units of the measured TP." + ], + "examples": [ + { + "value": "milligrams orthophosphate as phosphorus per liter (mg PO4-P/L)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100812", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "total phosphorus (TP) measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "total_phosphorus_tp_measurement_method": { + "name": "total_phosphorus_tp_measurement_method", + "description": "The method used to measure total phosphorus (TP).", + "title": "total phosphorus (TP) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TP." + ], + "examples": [ + { + "value": "Merck phosphate spectrophotometric test kit" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100813", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "fecal_contamination_indicator_": { + "name": "fecal_contamination_indicator_", + "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination.", + "title": "fecal contamination indicator", + "comments": [ + "If a fecal contamination indicator was measured, select it from the picklist." + ], + "examples": [ + { + "value": "crAssphage" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100814", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "fecal contamination indicator menu" + }, + { + "range": "null value menu" + } + ] + }, + "fecal_contamination_value": { + "name": "fecal_contamination_value", + "description": "The numerical value of a measurement of fecal contamination.", + "title": "fecal contamination value", + "comments": [ + "Provide the numerical value of the measured fecal contamination." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100815", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "fecal_contamination_unit": { + "name": "fecal_contamination_unit", + "description": "The units of a measurement of fecal contamination.", + "title": "fecal contamination unit", + "comments": [ + "Provide the units of the measured fecal contamination." + ], + "examples": [ + { + "value": "cycle threshold (Ct) / quantification cycle (Cq)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100816", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "fecal contamination unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "fecal_contamination_method": { + "name": "fecal_contamination_method", + "description": "The method used to measure fecal contamination.", + "title": "fecal contamination method", + "comments": [ + "Provide the name of the procedure or technology used to measure fecal contamination." + ], + "examples": [ + { + "value": "quantitative PCR assay" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100817", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "fecal_coliform_count_value": { + "name": "fecal_coliform_count_value", + "description": "The numerical value of a measurement of fecal coliforms within a sample.", + "title": "fecal coliform count value", + "comments": [ + "Provide the numerical value of the measured fecal coliforms." + ], + "examples": [ + { + "value": "3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100818", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "fecal_coliform_count_unit": { + "name": "fecal_coliform_count_unit", + "description": "The units of a measurement of fecal coliforms.", + "title": "fecal coliform count unit", + "comments": [ + "Provide the units of the measured fecal coliforms." + ], + "examples": [ + { + "value": "most probable number per milliliter (MPN/mL)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100819", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "fecal coliform count unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "fecal_coliform_count_method": { + "name": "fecal_coliform_count_method", + "description": "The method used to measure fecal coliforms.", + "title": "fecal coliform count method", + "comments": [ + "Provide the name of the procedure or technology used to measure fecal coliforms." + ], + "examples": [ + { + "value": "MPN method via serial dilutions until lack of growth" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100820", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "urinary_contamination_indicator": { + "name": "urinary_contamination_indicator", + "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination.", + "title": "urinary contamination indicator", + "comments": [ + "If a urinary contamination indicator was measured, select it from the picklist." + ], + "examples": [ + { + "value": "urobilin" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100837", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "urinary contamination indicator menu" + }, + { + "range": "null value menu" + } + ] + }, + "urinary_contamination_value": { + "name": "urinary_contamination_value", + "description": "The numerical value of a measurement of urinary contamination.", + "title": "urinary contamination value", + "comments": [ + "Provide the numerical value of the measured urinary contamination." + ], + "examples": [ + { + "value": "3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100838", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "urinary_contamination_unit": { + "name": "urinary_contamination_unit", + "description": "The units of a measurement of urinary contamination.", + "title": "urinary contamination unit", + "comments": [ + "Provide the units of the measured urinary contamination." + ], + "examples": [ + { + "value": "nanograms per liter" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100839", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "urinary contamination unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "urinary_contamination_method": { + "name": "urinary_contamination_method", + "description": "The method used to measure urinary contamination.", + "title": "urinary contamination method", + "comments": [ + "Provide the name of the procedure or technology used to measure urinary contamination." + ], + "examples": [ + { + "value": "Urobilin Concentration Test" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100840", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_value_at_collection": { + "name": "sample_temperature_value_at_collection", + "description": "The numerical value of a measurement of temperature of a sample at collection.", + "title": "sample temperature value (at collection)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "20" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100821", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_unit_at_collection": { + "name": "sample_temperature_unit_at_collection", + "description": "The units of a measurement of temperature of a sample at the time of collection.", + "title": "sample temperature unit (at collection)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100822", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "sample temperature unit (at collection) menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", + "description": "The numerical value of a measurement of temperature of a sample upon receipt.", + "title": "sample temperature value (when received)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "22" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100823", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_unit_when_received": { + "name": "sample_temperature_unit_when_received", + "description": "The units of a measurement of temperature of a sample at the time upon receipt.", + "title": "sample temperature unit (when received)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100824", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "sample temperature unit (when received) menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library_ID", + "comments": [ + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "LS_2010_NP_123446" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001448", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing_assay_type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100997", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "sequencing_assay_type menu" + }, + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001447", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "date" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "description": "The reason that the sample was sequenced.", + "title": "purpose_of_sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001445", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sequencing menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose_of_sequencing_details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001446", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:sequenced_by", + "BIOSAMPLE_Enterics:sequenced_by" + ], + "slot_uri": "GENEPIO:0100416", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100470", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100471", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100422", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence_submitted_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001159", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequence_submitter_contact_email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001165", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic_acid_extraction_method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100939", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic_acid_extraction_kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100772", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "description": "The description of the endogenous controls included when extracting a sample.", + "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100923", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "AMR-GRDI (PA-1356)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100472", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing_platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100473", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "sequencing_platform menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing_instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001452", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "sequencing_instrument menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library_preparation_kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001450", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA_fragment_length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100843", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "Integer" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100966", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "genomic_target_enrichment_method menu" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method_details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ + { + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100967", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon_pcr_primer_scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001456", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon_size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001449", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "Integer" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing_flow_cell_version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101102", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing_protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001454", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1_fastq_filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001476", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2_fastq_filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001477", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5_filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "batch1a_sequences.fast5" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001480", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101715", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "assembly_filename": { + "name": "assembly_filename", + "description": "The user-defined filename of the FASTA file.", + "title": "assembly_filename", + "comments": [ + "Provide the FASTA filename." + ], + "examples": [ + { + "value": "pathogenassembly123.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001461", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100557", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100558", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100559", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "multivalued": true, + "any_of": [ + { + "range": "quality_control_determination menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100560", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "multivalued": true, + "any_of": [ + { + "range": "quality_control_issues menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100561", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001458", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001459", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100825", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100826", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001463", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001469", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001472", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001474", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001475", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100844", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001482", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100827", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100828", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100829", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100937", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100830", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001484", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100938", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100845", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100846", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "The length of the genome defined by the most common nucleotides at each position.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001483", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001485", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100831", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001489", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100832", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100833", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100834", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100835", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101074", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101075", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "date" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100836", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "description": "The name of the genetic marker used for testing.", + "title": "genetic target name", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101116", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "genetic_target_region": { + "name": "genetic_target_region", + "description": "The specific region or segment of a genetic sequence used for testing or analysis.", + "title": "genetic target region", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101117", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", + "title": "genetic target region reference genome", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101118", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100962", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "diagnostic target presence menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100963", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100964", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "diagnostic measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100965", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "diagnostic measurement method menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold value", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101104", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold units", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101105", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "description": "Describe any details of the diagnsotic testing.", + "title": "diagnostic testing details", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101106", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", + "title": "prevalence_metrics", + "comments": [ + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + ], + "examples": [ + { + "value": "Number of total samples collected, Number of positive samples" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100480", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "description": "The details pertaining to the prevalence metrics from a surveillance project.", + "title": "prevalence_metrics_details", + "comments": [ + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + ], + "examples": [ + { + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100481", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "stage_of_production": { + "name": "stage_of_production", + "description": "The stage of food production.", + "title": "stage_of_production", + "comments": [ + "Provide the stage of food production as free text." + ], + "examples": [ + { + "value": "Abattoir [ENVO:01000925]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100482", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "stage_of_production menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_intervention": { + "name": "experimental_intervention", + "description": "The category of the experimental intervention applied in the food production system.", + "title": "experimental_intervention", + "comments": [ + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + ], + "examples": [ + { + "value": "Vaccination [NCIT:C15346]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100483", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "experimental_intervention menu" + }, + { + "range": "null value menu" + } + ] + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "description": "The details of the experimental intervention applied in the food production system.", + "title": "experiment_intervention_details", + "comments": [ + "If an experimental intervention was applied in the survey, provide details in this field as free text." + ], + "examples": [ + { + "value": "2% cranberry solution mixed in feed" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100484", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + } + }, + "classes": { + "dh_interface": { + "name": "dh_interface", + "description": "A DataHarmonizer interface", + "from_schema": "https://example.com/hpai" + }, + "HPAI": { + "name": "HPAI", + "annotations": { + "version": { + "tag": "version", + "value": "1.0.0" + } + }, + "title": "HPAI", + "from_schema": "https://example.com/hpai", + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database identifiers" + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "rank": 2, + "slot_group": "Database identifiers" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "rank": 3, + "slot_group": "Database identifiers" + }, + 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If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:sample_name" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen_collector_subsample_ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 2, + "slot_uri": "GENEPIO:0100752", + "alias": "specimen_collector_subsample_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled_sample_ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 3, + "slot_uri": "GENEPIO:0100996", + "alias": "pooled_sample_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "description": "The user-defined identifier assigned to a specific location from which samples are taken.", + "title": "sampling_site_ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 4, + "slot_uri": "GENEPIO:0100760", + "alias": "sampling_site_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sampling_event_id": { + "name": "sampling_event_id", + "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", + "title": "sampling_event_ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 5, + "slot_uri": "GENEPIO:0100761", + "alias": "sampling_event_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject_accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:bioproject_accession" + ], + "rank": 6, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample_accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMD00000001" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 7, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true, + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 8, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 9, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 10, + "slot_uri": "GENEPIO:0100762", + "alias": "sample_collection_data_steward_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "description": "The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_contact_email", + "comments": [ + "Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the \"sample collector contact email\"." + ], + "examples": [ + { + "value": "bloggsj@aglab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 11, + "slot_uri": "GENEPIO:0101107", + "alias": "sample_collection_data_steward_contact_email", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample_collected_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collected_by" + ], + "rank": 12, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 13, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo_loc_name_(country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 14, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "geo_loc_name_(country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory of origin of the sample.", + "title": "geo_loc_name_(state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 15, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_territory", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "description": "The county/region of origin of the sample.", + "title": "geo_loc_name_(county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 16, + "slot_uri": "GENEPIO:0100280", + "alias": "geo_loc_name_county_region", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "The city of origin of the sample.", + "title": "geo_loc_name_(city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 17, + "slot_uri": "GENEPIO:0001189", + "alias": "geo_loc_name_city", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo_loc_name_(site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 18, + "slot_uri": "GENEPIO:0100436", + "alias": "geo_loc_name_site__", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 19, + "slot_uri": "GENEPIO:0100309", + "alias": "geo_loc_latitude", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 20, + "slot_uri": "GENEPIO:0100310", + "alias": "geo_loc_longitude", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:organism" + ], + "rank": 21, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_subtype": { + "name": "influenza_subtype", + "title": "influenza_subtype", + "from_schema": "https://example.com/hpai", + "rank": 22, + "slot_uri": "GENEPIO:0101108", + "alias": "influenza_subtype", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subsubtype menu", + "required": true, + "multivalued": true + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "title": "influenza_subtyping_scheme_name", + "from_schema": "https://example.com/hpai", + "rank": 23, + "slot_uri": "GENEPIO:0101109", + "alias": "influenza_subtyping_scheme_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subtyping_scheme_name menu" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "title": "taxonomic_identification_process", + "from_schema": "https://example.com/hpai", + "rank": 24, + "slot_uri": "GENEPIO:0100583", + "alias": "taxonomic_identification_process", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "taxonomic_identification_process menu" + }, + "virus_identifier": { + "name": "virus_identifier", + "title": "virus_identifier", + "from_schema": "https://example.com/hpai", + "rank": 25, + "slot_uri": "GENEPIO:0101110", + "alias": "virus_identifier", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "who_oie_fao_h5_clade": { + "name": "who_oie_fao_h5_clade", + "title": "WHO/OIE/FAO_H5_clade", + "from_schema": "https://example.com/hpai", + "rank": 26, + "slot_uri": "GENEPIO:0101111", + "alias": "who_oie_fao_h5_clade", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected, or sampling began for a continuous sample.", + "title": "sample_collection_date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collection_date" + ], + "rank": 27, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "description": "The date on which sample collection ended for a continuous sample.", + "title": "sample_collection_end_date", + "comments": [ + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + ], + "examples": [ + { + "value": "2020-03-18" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 28, + "slot_uri": "GENEPIO:0101071", + "alias": "sample_collection_end_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "description": "The time at which sample collection began.", + "title": "sample_collection_start_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "17:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 29, + "slot_uri": "GENEPIO:0101072", + "alias": "sample_collection_start_time", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "description": "The time at which sample collection ended.", + "title": "sample_collection_end_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "19:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 30, + "slot_uri": "GENEPIO:0101073", + "alias": "sample_collection_end_time", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "description": "The descriptive time of day during which the sample was collected.", + "title": "sample_collection_time_of_day", + "comments": [ + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + ], + "examples": [ + { + "value": "Morning" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 31, + "slot_uri": "GENEPIO:0100765", + "alias": "sample_collection_time_of_day", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_collection_time_of_day menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "description": "The amount of time over which the sample was collected.", + "title": "sample_collection_time_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 32, + "slot_uri": "GENEPIO:0100766", + "alias": "sample_collection_time_duration_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "description": "The units of the time duration measurement of sample collection.", + "title": "sample_collection_time_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Hour" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 33, + "slot_uri": "GENEPIO:0100767", + "alias": "sample_collection_time_duration_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "sample_collection_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 34, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 35, + "slot_uri": "GENEPIO:0100763", + "alias": "sample_processing_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "host_origin_geo_loc_name_country": { + "name": "host_origin_geo_loc_name_country", + "description": "The country of origin of the host.", + "title": "host_origin_geo_loc_name (country)", + "comments": [ + "If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "South Africa [GAZ:00001094]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 36, + "slot_uri": "GENEPIO:0100438", + "alias": "host_origin_geo_loc_name_country", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product_origin_geo_loc_name_country": { + "name": "food_product_origin_geo_loc_name_country", + "description": "The country of origin of a food product.", + "title": "food_product_origin_geo_loc_name (country)", + "comments": [ + "If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "United States of America [GAZ:00002459]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:food_origin" + ], + "rank": 37, + "slot_uri": "GENEPIO:0100437", + "alias": "food_product_origin_geo_loc_name_country", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product": { + "name": "food_product", + "description": "A material consumed and digested for nutritional value or enjoyment.", + "title": "food_product", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feather meal [FOODON:00003927]" + }, + { + "value": "Bone meal [ENVO:02000054]" + }, + { + "value": "Chicken breast [FOODON:00002703]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_product", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:food_product_type" + ], + "rank": 38, + "slot_uri": "GENEPIO:0100444", + "alias": "food_product", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product_properties": { + "name": "food_product_properties", + "description": "Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers.", + "title": "food_product_properties", + "comments": [ + "Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free)." + ], + "examples": [ + { + "value": "Food (chopped) [FOODON:00002777]" + }, + { + "value": "Ready-to-eat (RTE) [FOODON:03316636]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_product_properties", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 39, + "slot_uri": "GENEPIO:0100445", + "alias": "food_product_properties", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product_properties menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_packaging": { + "name": "food_packaging", + "description": "The type of packaging used to contain a food product.", + "title": "food_packaging", + "comments": [ + "If known, provide information regarding how the food product was packaged." + ], + "examples": [ + { + "value": "Plastic tray or pan [FOODON:03490126]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_packaging", + "BIOSAMPLE_Enterics:food_contain_wrap" + ], + "rank": 40, + "slot_uri": "GENEPIO:0100447", + "alias": "food_packaging", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_packaging menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_quality_date": { + "name": "food_quality_date", + "description": "A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula.", + "title": "food_quality_date", + "comments": [ + "This date is typically labeled on a food product as \"best if used by\", best by\", \"use by\", or \"freeze by\" e.g. 5/24/2020. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:food_quality_date" + ], + "rank": 41, + "slot_uri": "GENEPIO:0100615", + "alias": "food_quality_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "range": "date" + }, + "food_packaging_date": { + "name": "food_packaging_date", + "description": "A food product's packaging date as marked by a food manufacturer or retailer.", + "title": "food_packaging_date", + "comments": [ + "The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 42, + "slot_uri": "GENEPIO:0100616", + "alias": "food_packaging_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "range": "date" + }, + "environmental_site": { + "name": "environmental_site", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "title": "environmental_site", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Poultry hatchery [ENVO:01001874]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_site", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:animal_env" + ], + "rank": 43, + "slot_uri": "GENEPIO:0001232", + "alias": "environmental_site", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_site menu" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "title": "environmental_material", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Soil [ENVO:00001998]" + }, + { + "value": "Water [CHEBI:15377]" + }, + { + "value": "Wastewater [ENVO:00002001]" + }, + { + "value": "Broom [ENVO:03501377]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_material", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 44, + "slot_uri": "GENEPIO:0001223", + "alias": "environmental_material", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "anatomical_material": { + "name": "anatomical_material", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "title": "anatomical_material", + "comments": [ + "An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Tissue [UBERON:0000479]" + }, + { + "value": "Blood [UBERON:0000178]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:anatomical_material", + "BIOSAMPLE_Enterics:host_tissue_sampled", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 45, + "slot_uri": "GENEPIO:0001211", + "alias": "anatomical_material", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "body_product": { + "name": "body_product", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "title": "body_product", + "comments": [ + "A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feces [UBERON:0001988]" + }, + { + "value": "Urine [UBERON:0001088]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:body_product", + "BIOSAMPLE_Enterics:host_body_product", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 46, + "slot_uri": "GENEPIO:0001216", + "alias": "body_product", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "body_product menu" + }, + { + "range": "null value menu" + } + ] + }, + "anatomical_part": { + "name": "anatomical_part", + "description": "An anatomical part of an organism e.g. oropharynx.", + "title": "anatomical_part", + "comments": [ + "An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Snout [UBERON:0006333]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:anatomical_part", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 47, + "slot_uri": "GENEPIO:0001214", + "alias": "anatomical_part", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_part menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection_device", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Drag swab [OBI:0002822]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_device", + "BIOSAMPLE_Enterics:samp_collect_device", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 48, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_device menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "title": "collection_method", + "comments": [ + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Rinsing for specimen collection [GENEPIO_0002116]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_method", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 49, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_method menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 50, + "slot_uri": "GENEPIO:0100768", + "alias": "sample_volume_measurement_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "milliliter (mL) [UO:0000098]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 51, + "slot_uri": "GENEPIO:0100769", + "alias": "sample_volume_measurement_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "sample_volume_measurement_unit menu" + }, + "residual_sample_status": { + "name": "residual_sample_status", + "description": "The status of the residual sample (whether any sample remains after its original use).", + "title": "residual_sample_status", + "comments": [ + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + ], + "examples": [ + { + "value": "No residual sample (sample all used) [GENEPIO:0101088]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 52, + "slot_uri": "GENEPIO:0101090", + "alias": "residual_sample_status", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "residual_sample_status menu" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:purpose_of_sampling" + ], + "rank": 53, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sampling menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity": { + "name": "presampling_activity", + "description": "The activities or variables upstream of sample collection that may affect the sample.", + "title": "presampling_activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 54, + "slot_uri": "GENEPIO:0100433", + "alias": "presampling_activity", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "presampling_activity menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the activities or variables that affected the sample collected.", + "title": "presampling_activity_details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 55, + "slot_uri": "GENEPIO:0100434", + "alias": "presampling_activity_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_storage_method": { + "name": "sample_storage_method", + "description": "The process used to store the sample.", + "title": "sample_storage_method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 56, + "slot_uri": "GENEPIO:0100448", + "alias": "sample_storage_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The medium in which a sample is stored.", + "title": "sample_storage_medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 57, + "slot_uri": "GENEPIO:0100449", + "alias": "sample_storage_medium", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 58, + "slot_uri": "GENEPIO:0101014", + "alias": "sample_storage_duration_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 59, + "slot_uri": "GENEPIO:0101015", + "alias": "sample_storage_duration_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_storage_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 60, + "slot_uri": "GENEPIO:0001253", + "alias": "specimen_processing", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "specimen_processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 61, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental_protocol", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "from_schema": "https://example.com/hpai", + "rank": 62, + "slot_uri": "GENEPIO:0101029", + "alias": "experimental_protocol", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 63, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "experimental_specimen_role_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "title": "experimental_specimen_details", + "from_schema": "https://example.com/hpai", + "rank": 64, + "slot_uri": "GENEPIO:0101112", + "alias": "experimental_specimen_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "available_data_types": { + "name": "available_data_types", + "description": "The type of data that is available, that may or may not require permission to access.", + "title": "available_data_types", + "comments": [ + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + ], + "examples": [ + { + "value": "Total coliform count [GENEPIO:0100729]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 65, + "slot_uri": "GENEPIO:0100690", + "alias": "available_data_types", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "available_data_types menu" + }, + { + "range": "null value menu" + } + ] + }, + "available_data_type_details": { + "name": "available_data_type_details", + "description": "Detailed information regarding other available data types.", + "title": "available_data_type_details", + "comments": [ + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + ], + "examples": [ + { + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 66, + "slot_uri": "GENEPIO:0101023", + "alias": "available_data_type_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "host_common_name": { + "name": "host_common_name", + "description": "The commonly used name of the host.", + "title": "host_(common_name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name." + ], + "examples": [ + { + "value": "Cow [NCBITaxon:9913]" + }, + { + "value": "Chicken [NCBITaxon:9913], Human [NCBITaxon:9606]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host" + ], + "rank": 67, + "slot_uri": "GENEPIO:0001386", + "alias": "host_common_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "recommended": true, + "any_of": [ + { + "range": "host (common name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_scientific_name": { + "name": "host_scientific_name", + "description": "The taxonomic, or scientific name of the host.", + "title": "host_(scientific_name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided." + ], + "examples": [ + { + "value": "Bos taurus [NCBITaxon:9913]" + }, + { + "value": "Homo sapiens [NCBITaxon:9103]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:host", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:host" + ], + "rank": 68, + "slot_uri": "GENEPIO:0001387", + "alias": "host_scientific_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "recommended": true, + "any_of": [ + { + "range": "host (scientific name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_ecotype": { + "name": "host_ecotype", + "description": "The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler.", + "title": "host_(ecotype)", + "comments": [ + "Provide the name of the ecotype of the host organism." + ], + "examples": [ + { + "value": "Sea ecotype" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_variety" + ], + "rank": 69, + "slot_uri": "GENEPIO:0100450", + "alias": "host_ecotype", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "range": "WhitespaceMinimizedString" + }, + "host_breed": { + "name": "host_breed", + "description": "A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding.", + "title": "host_(breed)", + "comments": [ + "Provide the name of the breed of the host organism." + ], + "examples": [ + { + "value": "Holstein" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:host_disease", + "BIOSAMPLE_Enterics:host_animal_breed" + ], + "rank": 70, + "slot_uri": "GENEPIO:0100451", + "alias": "host_breed", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "range": "WhitespaceMinimizedString" + }, + "host_food_production_name": { + "name": "host_food_production_name", + "description": "The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity.", + "title": "host_(food production name)", + "comments": [ + "Select the host's food production name from the pick list." + ], + "examples": [ + { + "value": "Calf [FOODON:03411349]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host" + ], + "rank": 71, + "slot_uri": "GENEPIO:0100452", + "alias": "host_food_production_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "any_of": [ + { + "range": "host (food production name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_age": { + "name": "host_age", + "description": "Age of host at the time of sampling.", + "title": "host_age", + "comments": [ + "If known, provide age. Age-binning is also acceptable." + ], + "examples": [ + { + "value": "79" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Patient%20age", + "CNPHI:host_age" + ], + "rank": 72, + "slot_uri": "GENEPIO:0001392", + "alias": "host_age", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "required": true, + "maximum_value": 130, + "any_of": [ + { + "range": "decimal" + }, + { + "range": "null value menu" + } + ] + }, + "host_age_unit": { + "name": "host_age_unit", + "description": "The units used to measure the host's age.", + "title": "host_age_unit", + "comments": [ + "If known, provide the age units used to measure the host's age from the pick list." + ], + "examples": [ + { + "value": "year [UO:0000036]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 73, + "slot_uri": "GENEPIO:0001393", + "alias": "host_age_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "required": true, + "any_of": [ + { + "range": "host_age_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_age_bin": { + "name": "host_age_bin", + "description": "Age of host at the time of sampling, expressed as an age group.", + "title": "host_age_bin", + "comments": [ + "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_age" + ], + "rank": 74, + "slot_uri": "GENEPIO:0001394", + "alias": "host_age_bin", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "any_of": [ + { + "range": "host_age_bin menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_disease": { + "name": "host_disease", + "description": "The name of the disease experienced by the host.", + "title": "host_disease", + "comments": [ + "This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”." + ], + "examples": [ + { + "value": "mastitis, gastroenteritis" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_disease" + ], + "rank": 75, + "slot_uri": "GENEPIO:0001391", + "alias": "host_disease", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "any_of": [ + { + "range": "host_disease menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_state": { + "name": "host_health_state", + "description": "Health status of the host at the time of sample collection.", + "title": "host_health_state", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Asymptomatic [NCIT:C3833]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Patient%20status", + "CNPHI:host_health_state" + ], + "rank": 76, + "slot_uri": "GENEPIO:0001388", + "alias": "host_health_state", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "host_health_state menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_status_details": { + "name": "host_health_status_details", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "title": "host_health_status_details", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Hospitalized (ICU) [GENEPIO:0100046]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 77, + "slot_uri": "GENEPIO:0001389", + "alias": "host_health_status_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "host_health_status_details menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_outcome": { + "name": "host_health_outcome", + "description": "Disease outcome in the host.", + "title": "host_health_outcome", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Recovered [NCIT:C49498]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:host_disease_outcome" + ], + "rank": 78, + "slot_uri": "GENEPIO:0001390", + "alias": "host_health_outcome", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "host_health_outcome menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_subject_id": { + "name": "host_subject_id", + "description": "A unique identifier by which each host can be referred to e.g. #131", + "title": "host_subject_ID", + "comments": [ + "Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward." + ], + "examples": [ + { + "value": "BCxy123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:host_subject_id" + ], + "rank": 79, + "slot_uri": "GENEPIO:0001398", + "alias": "host_subject_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "range": "WhitespaceMinimizedString" + }, + "case_id": { + "name": "case_id", + "description": "The identifier used to specify an epidemiologically detected case of disease.", + "title": "case_ID", + "comments": [ + "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing." + ], + "examples": [ + { + "value": "ABCD1234" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 80, + "slot_uri": "GENEPIO:0100281", + "alias": "case_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "range": "WhitespaceMinimizedString" + }, + "symptom_onset_date": { + "name": "symptom_onset_date", + "description": "The date on which the symptoms began or were first noted.", + "title": "symptom_onset_date", + "comments": [ + "If known, provide the symptom onset date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 81, + "slot_uri": "GENEPIO:0001399", + "alias": "symptom_onset_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "signs_and_symptoms": { + "name": "signs_and_symptoms", + "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", + "title": "signs_and_symptoms", + "comments": [ + "Select all of the symptoms experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 82, + "slot_uri": "GENEPIO:0001400", + "alias": "signs_and_symptoms", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "recommended": true, + "any_of": [ + { + "range": "signs_and_symptoms menu" + }, + { + "range": "null value menu" + } + ] + }, + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "description": "Patient pre-existing conditions and risk factors.\nPre-existing condition: A medical condition that existed prior to the current infection.\nRisk Factor: A variable associated with an increased risk of disease or infection.", + "title": "pre-existing_conditions_and_risk_factors", + "comments": [ + "Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Asthma [HP:0002099]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 83, + "slot_uri": "GENEPIO:0001401", + "alias": "preexisting_conditions_and_risk_factors", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "recommended": true, + "any_of": [ + { + "range": "pre-existing_conditions_and_risk_factors menu" + }, + { + "range": "null value menu" + } + ] + }, + "complications": { + "name": "complications", + "description": "Patient medical complications that are believed to have occurred as a result of host disease.", + "title": "complications", + "comments": [ + "Select all of the complications experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Acute respiratory failure [MONDO:0001208]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 84, + "slot_uri": "GENEPIO:0001402", + "alias": "complications", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "recommended": true, + "any_of": [ + { + "range": "complications menu" + }, + { + "range": "null value menu" + } + ] + }, + "exposure_event": { + "name": "exposure_event", + "description": "Event leading to exposure.", + "title": "exposure event", + "comments": [ + "Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Social Gathering" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Additional%20location%20information", + "CNPHI:Exposure%20Event", + "NML_LIMS:PH_EXPOSURE" + ], + "rank": 85, + "slot_uri": "GENEPIO:0001417", + "alias": "exposure_event", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure event menu" + }, + { + "range": "null value menu" + } + ] + }, + "exposure_contact_level": { + "name": "exposure_contact_level", + "description": "The exposure transmission contact type.", + "title": "exposure contact level", + "comments": [ + "Select direct or indirect exposure from the pick-list." + ], + "examples": [ + { + "value": "Direct" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:exposure%20contact%20level" + ], + "rank": 86, + "slot_uri": "GENEPIO:0001418", + "alias": "exposure_contact_level", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure contact level menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_role": { + "name": "host_role", + "description": "The role of the host in relation to the exposure setting.", + "title": "host role", + "comments": [ + "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Inpatient" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_HOST_ROLE" + ], + "rank": 87, + "slot_uri": "GENEPIO:0001419", + "alias": "host_role", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "range": "host role menu", + "multivalued": true + }, + "exposure_setting": { + "name": "exposure_setting", + "description": "The setting leading to exposure.", + "title": "exposure setting", + "comments": [ + "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Healthcare Setting" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE" + ], + "rank": 88, + "slot_uri": "GENEPIO:0001428", + "alias": "exposure_setting", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "range": "exposure setting menu", + "multivalued": true + }, + "exposure_details": { + "name": "exposure_details", + "description": "Additional host exposure information.", + "title": "exposure details", + "comments": [ + "Free text description of the exposure." + ], + "examples": [ + { + "value": "Case infected family at home" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_DETAILS" + ], + "rank": 89, + "slot_uri": "GENEPIO:0001431", + "alias": "exposure_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" + }, + "host_vaccination_status": { + "name": "host_vaccination_status", + "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", + "title": "host_vaccination_status", + "comments": [ + "Select the vaccination status of the host from the pick list." + ], + "examples": [ + { + "value": "Fully Vaccinated [GENEPIO:0100100]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:prior_sars_cov_2_vaccination" + ], + "rank": 90, + "slot_uri": "GENEPIO:0001404", + "alias": "host_vaccination_status", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "host_vaccination_status menu" + }, + { + "range": "null value menu" + } + ] + }, + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", + "description": "The number of doses of the vaccine recived by the host.", + "title": "number_of_vaccine_doses_received", + "comments": [ + "Record how many doses of the vaccine the host has received." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 91, + "slot_uri": "GENEPIO:0001406", + "alias": "number_of_vaccine_doses_received", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "integer", + "minimum_value": 0 + }, + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", + "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", + "title": "vaccination_dose_1_vaccine_name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 92, + "slot_uri": "GENEPIO:0100313", + "alias": "vaccination_dose_1_vaccine_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", + "description": "The date the first dose of a vaccine was administered.", + "title": "vaccination_dose_1_vaccination_date", + "comments": [ + "Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-03-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 93, + "slot_uri": "GENEPIO:0100314", + "alias": "vaccination_dose_1_vaccination_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "date" + }, + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", + "description": "The name of the vaccine administered as the second dose of a vaccine regimen.", + "title": "vaccination_dose_2_vaccine_name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 94, + "slot_uri": "GENEPIO:0100315", + "alias": "vaccination_dose_2_vaccine_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", + "description": "The date the second dose of a vaccine was administered.", + "title": "vaccination_dose_2_vaccination_date", + "comments": [ + "Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-09-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 95, + "slot_uri": "GENEPIO:0100316", + "alias": "vaccination_dose_2_vaccination_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "date" + }, + "vaccination_history": { + "name": "vaccination_history", + "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", + "title": "vaccination history", + "comments": [ + "Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons." + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2021-03-01" + }, + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2022-01-15" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Last%20vaccinated" + ], + "rank": 96, + "slot_uri": "GENEPIO:0100321", + "alias": "vaccination_history", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "influenza_antiviral_treatment_administration": { + "name": "influenza_antiviral_treatment_administration", + "description": "An action of giving or applying an influenza antiviral agent to a patient as part of a treatment regimen.", + "title": "influenza_antiviral_treatment_administration", + "examples": [ + { + "value": "Influenza antiviral treatment administered [GENEPIO:0101194]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 97, + "slot_uri": "GENEPIO:0101113", + "alias": "influenza_antiviral_treatment_administration", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host treatment information", + "any_of": [ + { + "range": "influenza_antiviral_treatment_administration menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_antiviral_agent__": { + "name": "influenza_antiviral_agent__", + "description": "A substance that destroys or inhibits replication of viruses.", + "title": "influenza_antiviral_agent", + "from_schema": "https://example.com/hpai", + "rank": 98, + "slot_uri": "GENEPIO:0101114", + "alias": "influenza_antiviral_agent__", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host treatment information", + "range": "WhitespaceMinimizedString" + }, + "influenza_antiviral_treatment_date": { + "name": "influenza_antiviral_treatment_date", + "description": "The date on which the influenza antiviral agent was administered to a patient as part of treatment", + "title": "influenza_antiviral_treatment_date", + "comments": [ + "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given." + ], + "from_schema": "https://example.com/hpai", + "rank": 99, + "slot_uri": "GENEPIO:0101115", + "alias": "influenza_antiviral_treatment_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host treatment information", + "range": "date" + }, + "water_catchment_area_human_population_measurement_value": { + "name": "water_catchment_area_human_population_measurement_value", + "description": "The numerical value of the human population measurement that contributes to the composition of water in a catchment area.", + "title": "water_catchment_area_human_population_measurement_value", + "comments": [ + "Where known, provide the numerical value of population size, i.e. the number of people." + ], + "examples": [ + { + "value": "10,500" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 100, + "slot_uri": "GENEPIO:0100773", + "alias": "water_catchment_area_human_population_measurement_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "integer" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_range": { + "name": "water_catchment_area_human_population_range", + "description": "The human population range of the water catchment that contributes effluent to a wastewater site.", + "title": "water_catchment_area_human_population_range", + "comments": [ + "Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist." + ], + "examples": [ + { + "value": "1,000 - 10,000 people" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 101, + "slot_uri": "GENEPIO:0100774", + "alias": "water_catchment_area_human_population_range", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water catchment area human population range menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_measurement_method": { + "name": "water_catchment_area_human_population_measurement_method", + "description": "The method by which a water catchment 's human population size was measured or estimated", + "title": "water_catchment_area_human_population_measurement_method", + "comments": [ + "Provide a brief description of how catchment population size was measured or estimated." + ], + "examples": [ + { + "value": "population of jurisdiction encompassing the wastewater service area" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 102, + "slot_uri": "GENEPIO:0100775", + "alias": "water_catchment_area_human_population_measurement_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_value": { + "name": "water_catchment_area_human_population_density_value", + "description": "The numerical value describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density value", + "comments": [ + "Provide the numerical value of the population density in the catchement area." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 103, + "slot_uri": "GENEPIO:0100776", + "alias": "water_catchment_area_human_population_density_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_unit": { + "name": "water_catchment_area_human_population_density_unit", + "description": "The unit describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density unit", + "comments": [ + "Provide the unit of the population density in the catchement area." + ], + "examples": [ + { + "value": "persons per Km^2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 104, + "slot_uri": "GENEPIO:0100777", + "alias": "water_catchment_area_human_population_density_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water catchment area human population density unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "populated_area_type": { + "name": "populated_area_type", + "description": "A type of area that is populated by humans to different degrees.", + "title": "populated area type", + "comments": [ + "Provide the populated area type from the pick list." + ], + "examples": [ + { + "value": "Urban area" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 105, + "slot_uri": "GENEPIO:0100778", + "alias": "populated_area_type", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "populated area type menu" + }, + { + "range": "null value menu" + } + ] + }, + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "sampling weather conditions", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 106, + "slot_uri": "GENEPIO:0100779", + "alias": "sampling_weather_conditions", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "sampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", + "description": "Weather conditions prior to collection that may affect the sample.", + "title": "presampling weather conditions", + "comments": [ + "Provide the weather conditions prior to sample collection." + ], + "examples": [ + { + "value": "Drizzle" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 107, + "slot_uri": "GENEPIO:0100780", + "alias": "presampling_weather_conditions", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "presampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", + "comments": [ + "Provide the quantity of precipitation in the area leading up to the time of sample collection." + ], + "examples": [ + { + "value": "12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 108, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "water_depth": { + "name": "water_depth", + "description": "The depth of some water.", + "title": "water_depth", + "comments": [ + "Provide the numerical depth only of water only (without units)." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 109, + "slot_uri": "GENEPIO:0100440", + "alias": "water_depth", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_depth_units": { + "name": "water_depth_units", + "description": "The units of measurement for water depth.", + "title": "water_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 110, + "slot_uri": "GENEPIO:0101025", + "alias": "water_depth_units", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "sediment_depth": { + "name": "sediment_depth", + "description": "The depth of some sediment.", + "title": "sediment_depth", + "comments": [ + "Provide the numerical depth only of the sediment (without units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 111, + "slot_uri": "GENEPIO:0100697", + "alias": "sediment_depth", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sediment_depth_units": { + "name": "sediment_depth_units", + "description": "The units of measurement for sediment depth.", + "title": "sediment_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 112, + "slot_uri": "GENEPIO:0101026", + "alias": "sediment_depth_units", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sediment_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "air_temperature": { + "name": "air_temperature", + "description": "The temperature of some air.", + "title": "air_temperature", + "comments": [ + "Provide the numerical value for the temperature of the air (without units)." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 113, + "slot_uri": "GENEPIO:0100441", + "alias": "air_temperature", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "air_temperature_units": { + "name": "air_temperature_units", + "description": "The units of measurement for air temperature.", + "title": "air_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 114, + "slot_uri": "GENEPIO:0101027", + "alias": "air_temperature_units", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "air_temperature_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_temperature": { + "name": "water_temperature", + "description": "The temperature of some water.", + "title": "water_temperature", + "comments": [ + "Provide the numerical value for the temperature of the water (without units)." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 115, + "slot_uri": "GENEPIO:0100698", + "alias": "water_temperature", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_temperature_units": { + "name": "water_temperature_units", + "description": "The units of measurement for water temperature.", + "title": "water_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 116, + "slot_uri": "GENEPIO:0101028", + "alias": "water_temperature_units", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_temperature_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "weather_type": { + "name": "weather_type", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "weather_type", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain [ENVO:01001564]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 117, + "slot_uri": "GENEPIO:0100442", + "alias": "weather_type", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "weather_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_unit": { + "name": "precipitation_measurement_unit", + "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement unit", + "comments": [ + "Provide the units of precipitation by selecting a value from the pick list." + ], + "examples": [ + { + "value": "inch" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 118, + "slot_uri": "GENEPIO:0100912", + "alias": "precipitation_measurement_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "precipitation measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", + "description": "The process used to measure the amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement method", + "comments": [ + "Provide the name of the procedure or method used to measure precipitation." + ], + "examples": [ + { + "value": "Rain gauge over a 12 hour period 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"sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", + "description": "The numerical value of a measurement of temperature of a sample upon receipt.", + "title": "sample temperature value (when received)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 182, + "slot_uri": "GENEPIO:0100823", + "alias": "sample_temperature_value_when_received", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_unit_when_received": { + "name": "sample_temperature_unit_when_received", + "description": "The units of a measurement of temperature of a sample at the time upon receipt.", + "title": "sample temperature unit (when received)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 183, + "slot_uri": "GENEPIO:0100824", + "alias": "sample_temperature_unit_when_received", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sample temperature unit (when received) menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library_ID", + "comments": [ + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "LS_2010_NP_123446" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 184, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing_assay_type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 185, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "sequencing_assay_type menu" + }, + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 186, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "date" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "description": "The reason that the sample was sequenced.", + "title": "purpose_of_sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 187, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing__", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sequencing menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose_of_sequencing_details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 188, + "slot_uri": "GENEPIO:0001446", + "alias": "purpose_of_sequencing_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:sequenced_by", + "BIOSAMPLE_Enterics:sequenced_by" + ], + "rank": 189, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 190, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 191, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 192, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence_submitted_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 193, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequence_submitter_contact_email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 194, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic_acid_extraction_method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 195, + "slot_uri": "GENEPIO:0100939", + "alias": "nucleic_acid_extraction_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic_acid_extraction_kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 196, + "slot_uri": "GENEPIO:0100772", + "alias": "nucleic_acid_extraction_kit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "description": "The description of the endogenous controls included when extracting a sample.", + "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], + "from_schema": "https://example.com/hpai", + "rank": 197, + "slot_uri": "GENEPIO:0100923", + "alias": "endogenous_control_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "AMR-GRDI (PA-1356)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 198, + "slot_uri": "GENEPIO:0100472", + "alias": "sequencing_project_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing_platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 199, + "slot_uri": "GENEPIO:0100473", + "alias": "sequencing_platform", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_platform menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing_instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 200, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_instrument menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library_preparation_kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 201, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA_fragment_length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 202, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 203, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "genomic_target_enrichment_method menu" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method_details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ + { + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 204, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon_pcr_primer_scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 205, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon_size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 206, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing_flow_cell_version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 207, + "slot_uri": "GENEPIO:0101102", + "alias": "sequencing_flow_cell_version", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing_protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 208, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1_fastq_filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 209, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2_fastq_filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 210, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5_filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "batch1a_sequences.fast5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 211, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 212, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "assembly_filename": { + "name": "assembly_filename", + "description": "The user-defined filename of the FASTA file.", + "title": "assembly_filename", + "comments": [ + "Provide the FASTA filename." + ], + "examples": [ + { + "value": "pathogenassembly123.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 213, + "slot_uri": "GENEPIO:0001461", + "alias": "assembly_filename", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 214, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 215, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 216, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_determination menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 217, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_issues menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 218, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 219, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 220, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 221, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 222, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 223, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 224, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 225, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 226, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 227, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 228, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 229, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 230, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 231, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 232, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 233, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 234, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 235, + "slot_uri": "GENEPIO:0001484", + "alias": "ns_per_100_kbp", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 236, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 237, + "slot_uri": "GENEPIO:0100845", + "alias": "percent_read_contamination_", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 238, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "The length of the genome defined by the most common nucleotides at each position.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 239, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 240, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 241, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 242, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 243, + "slot_uri": "GENEPIO:0100832", + "alias": "read_mapping_software_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 244, + "slot_uri": "GENEPIO:0100833", + "alias": "read_mapping_software_version", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 245, + "slot_uri": "GENEPIO:0100834", + "alias": "taxonomic_reference_database_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 246, + "slot_uri": "GENEPIO:0100835", + "alias": "taxonomic_reference_database_version", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 247, + "slot_uri": "GENEPIO:0101074", + "alias": "taxonomic_analysis_report_filename", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 248, + "slot_uri": "GENEPIO:0101075", + "alias": "taxonomic_analysis_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "date" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 249, + "slot_uri": "GENEPIO:0100836", + "alias": "read_mapping_criteria", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "description": "The name of the genetic marker used for testing.", + "title": "genetic target name", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 250, + "slot_uri": "GENEPIO:0101116", + "alias": "genetic_target_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "genetic_target_region": { + "name": "genetic_target_region", + "description": "The specific region or segment of a genetic sequence used for testing or analysis.", + "title": "genetic target region", + "from_schema": "https://example.com/hpai", + "rank": 251, + "slot_uri": "GENEPIO:0101117", + "alias": "genetic_target_region", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", + "title": "genetic target region reference genome", + "from_schema": "https://example.com/hpai", + "rank": 252, + "slot_uri": "GENEPIO:0101118", + "alias": "genetic_target_region_reference_genome", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 253, + "slot_uri": "GENEPIO:0100962", + "alias": "diagnostic_target_presence", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic target presence menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 254, + "slot_uri": "GENEPIO:0100963", + "alias": "diagnostic_measurement_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 255, + "slot_uri": "GENEPIO:0100964", + "alias": "diagnostic_measurement_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 256, + "slot_uri": "GENEPIO:0100965", + "alias": "diagnostic_measurement_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement method menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold value", + "from_schema": "https://example.com/hpai", + "rank": 257, + "slot_uri": "GENEPIO:0101104", + "alias": "diagnostic_testing_threshold_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "integer" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold units", + "from_schema": "https://example.com/hpai", + "rank": 258, + "slot_uri": "GENEPIO:0101105", + "alias": "diagnostic_testing_threshold_units", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "description": "Describe any details of the diagnsotic testing.", + "title": "diagnostic testing details", + "from_schema": "https://example.com/hpai", + "rank": 259, + "slot_uri": "GENEPIO:0101106", + "alias": "diagnostic_testing_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", + "title": "prevalence_metrics", + "comments": [ + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + ], + "examples": [ + { + "value": "Number of total samples collected, Number of positive samples" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 260, + "slot_uri": "GENEPIO:0100480", + "alias": "prevalence_metrics", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "description": "The details pertaining to the prevalence metrics from a surveillance project.", + "title": "prevalence_metrics_details", + "comments": [ + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + ], + "examples": [ + { + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 261, + "slot_uri": "GENEPIO:0100481", + "alias": "prevalence_metrics_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "stage_of_production": { + "name": "stage_of_production", + "description": "The stage of food production.", + "title": "stage_of_production", + "comments": [ + "Provide the stage of food production as free text." + ], + "examples": [ + { + "value": "Abattoir [ENVO:01000925]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 262, + "slot_uri": "GENEPIO:0100482", + "alias": "stage_of_production", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "any_of": [ + { + "range": "stage_of_production menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_intervention": { + "name": "experimental_intervention", + "description": "The category of the experimental intervention applied in the food production system.", + "title": "experimental_intervention", + "comments": [ + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + ], + "examples": [ + { + "value": "Vaccination [NCIT:C15346]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 263, + "slot_uri": "GENEPIO:0100483", + "alias": "experimental_intervention", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "experimental_intervention menu" + }, + { + "range": "null value menu" + } + ] + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "description": "The details of the experimental intervention applied in the food production system.", + "title": "experiment_intervention_details", + "comments": [ + "If an experimental intervention was applied in the survey, provide details in this field as free text." + ], + "examples": [ + { + "value": "2% cranberry solution mixed in feed" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 264, + "slot_uri": "GENEPIO:0100484", + "alias": "experiment_intervention_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + } + } + }, + "HPAIFood": { + "name": "HPAIFood", + "annotations": { + "version": { + "tag": "version", + "value": "1.0.0" + } + }, + "title": "HPAI Food", + "from_schema": "https://example.com/hpai", + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database identifiers" + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "rank": 2, + "slot_group": "Database identifiers" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "rank": 3, + "slot_group": "Database identifiers" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "rank": 4, + "slot_group": "Database identifiers" + }, + "sampling_event_id": { + "name": "sampling_event_id", + "rank": 5, + "slot_group": "Database identifiers" + }, + "bioproject_accession": { + "name": "bioproject_accession", + "rank": 6, + "slot_group": "Database identifiers" + }, + "biosample_accession": { + "name": "biosample_accession", + "rank": 7, + "slot_group": "Database identifiers" + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "rank": 8, + "slot_group": "Database identifiers" + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "rank": 9, + "slot_group": "Database identifiers" + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "rank": 10, + "slot_group": "Sample collection and processing" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "rank": 11, + "slot_group": "Sample collection and processing" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "rank": 12, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "rank": 13, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "rank": 14, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "rank": 15, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "rank": 16, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "rank": 17, + "slot_group": "Sample 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If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:sample_name" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen_collector_subsample_ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 2, + "slot_uri": "GENEPIO:0100752", + "alias": "specimen_collector_subsample_id", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled_sample_ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 3, + "slot_uri": "GENEPIO:0100996", + "alias": "pooled_sample_id", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "description": "The user-defined identifier assigned to a specific location from which samples are taken.", + "title": "sampling_site_ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 4, + "slot_uri": "GENEPIO:0100760", + "alias": "sampling_site_id", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sampling_event_id": { + "name": "sampling_event_id", + "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", + "title": "sampling_event_ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 5, + "slot_uri": "GENEPIO:0100761", + "alias": "sampling_event_id", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject_accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:bioproject_accession" + ], + "rank": 6, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample_accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMD00000001" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 7, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true, + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 8, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 9, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 10, + "slot_uri": "GENEPIO:0100762", + "alias": "sample_collection_data_steward_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "description": "The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_contact_email", + "comments": [ + "Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the \"sample collector contact email\"." + ], + "examples": [ + { + "value": "bloggsj@aglab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 11, + "slot_uri": "GENEPIO:0101107", + "alias": "sample_collection_data_steward_contact_email", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample_collected_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collected_by" + ], + "rank": 12, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 13, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo_loc_name_(country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 14, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "geo_loc_name_(country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory of origin of the sample.", + "title": "geo_loc_name_(state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 15, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_territory", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "description": "The county/region of origin of the sample.", + "title": "geo_loc_name_(county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 16, + "slot_uri": "GENEPIO:0100280", + "alias": "geo_loc_name_county_region", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "The city of origin of the sample.", + "title": "geo_loc_name_(city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 17, + "slot_uri": "GENEPIO:0001189", + "alias": "geo_loc_name_city", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo_loc_name_(site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 18, + "slot_uri": "GENEPIO:0100436", + "alias": "geo_loc_name_site__", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 19, + "slot_uri": "GENEPIO:0100309", + "alias": "geo_loc_latitude", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 20, + "slot_uri": "GENEPIO:0100310", + "alias": "geo_loc_longitude", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:organism" + ], + "rank": 21, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_subtype": { + "name": "influenza_subtype", + "title": "influenza_subtype", + "from_schema": "https://example.com/hpai", + "rank": 22, + "slot_uri": "GENEPIO:0101108", + "alias": "influenza_subtype", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subsubtype menu", + "required": true, + "multivalued": true + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "title": "influenza_subtyping_scheme_name", + "from_schema": "https://example.com/hpai", + "rank": 23, + "slot_uri": "GENEPIO:0101109", + "alias": "influenza_subtyping_scheme_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subtyping_scheme_name menu" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "title": "taxonomic_identification_process", + "from_schema": "https://example.com/hpai", + "rank": 24, + "slot_uri": "GENEPIO:0100583", + "alias": "taxonomic_identification_process", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "taxonomic_identification_process menu" + }, + "virus_identifier": { + "name": "virus_identifier", + "title": "virus_identifier", + "from_schema": "https://example.com/hpai", + "rank": 25, + "slot_uri": "GENEPIO:0101110", + "alias": "virus_identifier", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "who_oie_fao_h5_clade": { + "name": "who_oie_fao_h5_clade", + "title": "WHO/OIE/FAO_H5_clade", + "from_schema": "https://example.com/hpai", + "rank": 26, + "slot_uri": "GENEPIO:0101111", + "alias": "who_oie_fao_h5_clade", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected, or sampling began for a continuous sample.", + "title": "sample_collection_date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collection_date" + ], + "rank": 27, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 28, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 29, + "slot_uri": "GENEPIO:0100763", + "alias": "sample_processing_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "food_product_origin_geo_loc_name_country": { + "name": "food_product_origin_geo_loc_name_country", + "description": "The country of origin of a food product.", + "title": "food_product_origin_geo_loc_name (country)", + "comments": [ + "If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "United States of America [GAZ:00002459]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:food_origin" + ], + "rank": 30, + "slot_uri": "GENEPIO:0100437", + "alias": "food_product_origin_geo_loc_name_country", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product": { + "name": "food_product", + "description": "A material consumed and digested for nutritional value or enjoyment.", + "title": "food_product", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feather meal [FOODON:00003927]" + }, + { + "value": "Bone meal [ENVO:02000054]" + }, + { + "value": "Chicken breast [FOODON:00002703]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_product", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:food_product_type" + ], + "rank": 31, + "slot_uri": "GENEPIO:0100444", + "alias": "food_product", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product_properties": { + "name": "food_product_properties", + "description": "Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers.", + "title": "food_product_properties", + "comments": [ + "Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free)." + ], + "examples": [ + { + "value": "Food (chopped) [FOODON:00002777]" + }, + { + "value": "Ready-to-eat (RTE) [FOODON:03316636]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_product_properties", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 32, + "slot_uri": "GENEPIO:0100445", + "alias": "food_product_properties", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product_properties menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_packaging": { + "name": "food_packaging", + "description": "The type of packaging used to contain a food product.", + "title": "food_packaging", + "comments": [ + "If known, provide information regarding how the food product was packaged." + ], + "examples": [ + { + "value": "Plastic tray or pan [FOODON:03490126]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_packaging", + "BIOSAMPLE_Enterics:food_contain_wrap" + ], + "rank": 33, + "slot_uri": "GENEPIO:0100447", + "alias": "food_packaging", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_packaging menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_quality_date": { + "name": "food_quality_date", + "description": "A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula.", + "title": "food_quality_date", + "comments": [ + "This date is typically labeled on a food product as \"best if used by\", best by\", \"use by\", or \"freeze by\" e.g. 5/24/2020. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:food_quality_date" + ], + "rank": 34, + "slot_uri": "GENEPIO:0100615", + "alias": "food_quality_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "range": "date" + }, + "food_packaging_date": { + "name": "food_packaging_date", + "description": "A food product's packaging date as marked by a food manufacturer or retailer.", + "title": "food_packaging_date", + "comments": [ + "The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 35, + "slot_uri": "GENEPIO:0100616", + "alias": "food_packaging_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "range": "date" + }, + "environmental_site": { + "name": "environmental_site", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "title": "environmental_site", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Poultry hatchery [ENVO:01001874]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_site", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:animal_env" + ], + "rank": 36, + "slot_uri": "GENEPIO:0001232", + "alias": "environmental_site", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_site menu" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "title": "environmental_material", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Soil [ENVO:00001998]" + }, + { + "value": "Water [CHEBI:15377]" + }, + { + "value": "Wastewater [ENVO:00002001]" + }, + { + "value": "Broom [ENVO:03501377]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_material", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 37, + "slot_uri": "GENEPIO:0001223", + "alias": "environmental_material", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection_device", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Drag swab [OBI:0002822]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_device", + "BIOSAMPLE_Enterics:samp_collect_device", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 38, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_device menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "title": "collection_method", + "comments": [ + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Rinsing for specimen collection [GENEPIO_0002116]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_method", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 39, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_method menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 40, + "slot_uri": "GENEPIO:0100768", + "alias": "sample_volume_measurement_value", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "milliliter (mL) [UO:0000098]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 41, + "slot_uri": "GENEPIO:0100769", + "alias": "sample_volume_measurement_unit", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "sample_volume_measurement_unit menu" + }, + "residual_sample_status": { + "name": "residual_sample_status", + "description": "The status of the residual sample (whether any sample remains after its original use).", + "title": "residual_sample_status", + "comments": [ + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + ], + "examples": [ + { + "value": "No residual sample (sample all used) [GENEPIO:0101088]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 42, + "slot_uri": "GENEPIO:0101090", + "alias": "residual_sample_status", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "residual_sample_status menu" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:purpose_of_sampling" + ], + "rank": 43, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sampling menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity": { + "name": "presampling_activity", + "description": "The activities or variables upstream of sample collection that may affect the sample.", + "title": "presampling_activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 44, + "slot_uri": "GENEPIO:0100433", + "alias": "presampling_activity", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "presampling_activity menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the activities or variables that affected the sample collected.", + "title": "presampling_activity_details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 45, + "slot_uri": "GENEPIO:0100434", + "alias": "presampling_activity_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_storage_method": { + "name": "sample_storage_method", + "description": "The process used to store the sample.", + "title": "sample_storage_method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 46, + "slot_uri": "GENEPIO:0100448", + "alias": "sample_storage_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The medium in which a sample is stored.", + "title": "sample_storage_medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 47, + "slot_uri": "GENEPIO:0100449", + "alias": "sample_storage_medium", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 48, + "slot_uri": "GENEPIO:0101014", + "alias": "sample_storage_duration_value", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 49, + "slot_uri": "GENEPIO:0101015", + "alias": "sample_storage_duration_unit", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_storage_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 50, + "slot_uri": "GENEPIO:0001253", + "alias": "specimen_processing", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "specimen_processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 51, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental_protocol", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "from_schema": "https://example.com/hpai", + "rank": 52, + "slot_uri": "GENEPIO:0101029", + "alias": "experimental_protocol", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 53, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "experimental_specimen_role_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "title": "experimental_specimen_details", + "from_schema": "https://example.com/hpai", + "rank": 54, + "slot_uri": "GENEPIO:0101112", + "alias": "experimental_specimen_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "available_data_types": { + "name": "available_data_types", + "description": "The type of data that is available, that may or may not require permission to access.", + "title": "available_data_types", + "comments": [ + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + ], + "examples": [ + { + "value": "Total coliform count [GENEPIO:0100729]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 55, + "slot_uri": "GENEPIO:0100690", + "alias": "available_data_types", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "available_data_types menu" + }, + { + "range": "null value menu" + } + ] + }, + "available_data_type_details": { + "name": "available_data_type_details", + "description": "Detailed information regarding other available data types.", + "title": "available_data_type_details", + "comments": [ + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + ], + "examples": [ + { + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 56, + "slot_uri": "GENEPIO:0101023", + "alias": "available_data_type_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library_ID", + "comments": [ + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "LS_2010_NP_123446" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 57, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing_assay_type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 58, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "sequencing_assay_type menu" + }, + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 59, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "date" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "description": "The reason that the sample was sequenced.", + "title": "purpose_of_sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 60, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing__", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sequencing menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose_of_sequencing_details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 61, + "slot_uri": "GENEPIO:0001446", + "alias": "purpose_of_sequencing_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:sequenced_by", + "BIOSAMPLE_Enterics:sequenced_by" + ], + "rank": 62, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 63, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 64, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 65, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence_submitted_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 66, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequence_submitter_contact_email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 67, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic_acid_extraction_method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 68, + "slot_uri": "GENEPIO:0100939", + "alias": "nucleic_acid_extraction_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic_acid_extraction_kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 69, + "slot_uri": "GENEPIO:0100772", + "alias": "nucleic_acid_extraction_kit", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "description": "The description of the endogenous controls included when extracting a sample.", + "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], + "from_schema": "https://example.com/hpai", + "rank": 70, + "slot_uri": "GENEPIO:0100923", + "alias": "endogenous_control_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "AMR-GRDI (PA-1356)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 71, + "slot_uri": "GENEPIO:0100472", + "alias": "sequencing_project_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing_platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 72, + "slot_uri": "GENEPIO:0100473", + "alias": "sequencing_platform", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_platform menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing_instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 73, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_instrument menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library_preparation_kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 74, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA_fragment_length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 75, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 76, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "genomic_target_enrichment_method menu" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method_details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ + { + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 77, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon_pcr_primer_scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 78, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon_size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 79, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing_flow_cell_version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 80, + "slot_uri": "GENEPIO:0101102", + "alias": "sequencing_flow_cell_version", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing_protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 81, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1_fastq_filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 82, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2_fastq_filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 83, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5_filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "batch1a_sequences.fast5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 84, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 85, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "assembly_filename": { + "name": "assembly_filename", + "description": "The user-defined filename of the FASTA file.", + "title": "assembly_filename", + "comments": [ + "Provide the FASTA filename." + ], + "examples": [ + { + "value": "pathogenassembly123.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 86, + "slot_uri": "GENEPIO:0001461", + "alias": "assembly_filename", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 87, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 88, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 89, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_determination menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 90, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_issues menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 91, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 92, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 93, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 94, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 95, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 96, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 97, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 98, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 99, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 100, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 101, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 102, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 103, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 104, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 105, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 106, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 107, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 108, + "slot_uri": "GENEPIO:0001484", + "alias": "ns_per_100_kbp", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 109, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 110, + "slot_uri": "GENEPIO:0100845", + "alias": "percent_read_contamination_", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 111, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "The length of the genome defined by the most common nucleotides at each position.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 112, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 113, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 114, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 115, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 116, + "slot_uri": "GENEPIO:0100832", + "alias": "read_mapping_software_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 117, + "slot_uri": "GENEPIO:0100833", + "alias": "read_mapping_software_version", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 118, + "slot_uri": "GENEPIO:0100834", + "alias": "taxonomic_reference_database_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 119, + "slot_uri": "GENEPIO:0100835", + "alias": "taxonomic_reference_database_version", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 120, + "slot_uri": "GENEPIO:0101074", + "alias": "taxonomic_analysis_report_filename", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 121, + "slot_uri": "GENEPIO:0101075", + "alias": "taxonomic_analysis_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "date" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 122, + "slot_uri": "GENEPIO:0100836", + "alias": "read_mapping_criteria", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "description": "The name of the genetic marker used for testing.", + "title": "genetic target name", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 123, + "slot_uri": "GENEPIO:0101116", + "alias": "genetic_target_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "genetic_target_region": { + "name": "genetic_target_region", + "description": "The specific region or segment of a genetic sequence used for testing or analysis.", + "title": "genetic target region", + "from_schema": "https://example.com/hpai", + "rank": 124, + "slot_uri": "GENEPIO:0101117", + "alias": "genetic_target_region", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", + "title": "genetic target region reference genome", + "from_schema": "https://example.com/hpai", + "rank": 125, + "slot_uri": "GENEPIO:0101118", + "alias": "genetic_target_region_reference_genome", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 126, + "slot_uri": "GENEPIO:0100962", + "alias": "diagnostic_target_presence", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic target presence menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 127, + "slot_uri": "GENEPIO:0100963", + "alias": "diagnostic_measurement_value", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 128, + "slot_uri": "GENEPIO:0100964", + "alias": "diagnostic_measurement_unit", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 129, + "slot_uri": "GENEPIO:0100965", + "alias": "diagnostic_measurement_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement method menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold value", + "from_schema": "https://example.com/hpai", + "rank": 130, + "slot_uri": "GENEPIO:0101104", + "alias": "diagnostic_testing_threshold_value", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "integer" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold units", + "from_schema": "https://example.com/hpai", + "rank": 131, + "slot_uri": "GENEPIO:0101105", + "alias": "diagnostic_testing_threshold_units", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "description": "Describe any details of the diagnsotic testing.", + "title": "diagnostic testing details", + "from_schema": "https://example.com/hpai", + "rank": 132, + "slot_uri": "GENEPIO:0101106", + "alias": "diagnostic_testing_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", + "title": "prevalence_metrics", + "comments": [ + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + ], + "examples": [ + { + "value": "Number of total samples collected, Number of positive samples" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 133, + "slot_uri": "GENEPIO:0100480", + "alias": "prevalence_metrics", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "description": "The details pertaining to the prevalence metrics from a surveillance project.", + "title": "prevalence_metrics_details", + "comments": [ + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + ], + "examples": [ + { + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 134, + "slot_uri": "GENEPIO:0100481", + "alias": "prevalence_metrics_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "stage_of_production": { + "name": "stage_of_production", + "description": "The stage of food production.", + "title": "stage_of_production", + "comments": [ + "Provide the stage of food production as free text." + ], + "examples": [ + { + "value": "Abattoir [ENVO:01000925]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 135, + "slot_uri": "GENEPIO:0100482", + "alias": "stage_of_production", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "any_of": [ + { + "range": "stage_of_production menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_intervention": { + "name": "experimental_intervention", + "description": "The category of the experimental intervention applied in the food production system.", + "title": "experimental_intervention", + "comments": [ + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + ], + "examples": [ + { + "value": "Vaccination [NCIT:C15346]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 136, + "slot_uri": "GENEPIO:0100483", + "alias": "experimental_intervention", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "experimental_intervention menu" + }, + { + "range": "null value menu" + } + ] + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "description": "The details of the experimental intervention applied in the food production system.", + "title": "experiment_intervention_details", + "comments": [ + "If an experimental intervention was applied in the survey, provide details in this field as free text." + ], + "examples": [ + { + "value": "2% cranberry solution mixed in feed" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 137, + "slot_uri": "GENEPIO:0100484", + "alias": "experiment_intervention_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + } + } + }, + "HPAIWW": { + "name": "HPAIWW", + "annotations": { + "version": { + "tag": "version", + "value": "1.0.0" + } + }, + "title": "HPAI Wastewater", + "from_schema": "https://example.com/hpai", + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database identifiers" + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "rank": 2, + "slot_group": "Database identifiers" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "rank": 3, + "slot_group": "Database identifiers" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "rank": 4, + "slot_group": "Database identifiers" + }, + "sampling_event_id": { + "name": "sampling_event_id", + "rank": 5, + "slot_group": "Database identifiers" + }, + "bioproject_accession": { + "name": "bioproject_accession", + "rank": 6, + "slot_group": "Database identifiers" + }, + "biosample_accession": { + "name": "biosample_accession", + "rank": 7, + "slot_group": "Database identifiers" + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "rank": 8, + "slot_group": "Database identifiers" + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "rank": 9, + "slot_group": "Database identifiers" + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "rank": 10, + "slot_group": "Sample collection and processing" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "rank": 11, + "slot_group": "Sample collection and processing" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "rank": 12, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "rank": 13, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "rank": 14, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "rank": 15, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "rank": 16, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "rank": 17, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "rank": 18, + "slot_group": "Sample collection and processing" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "rank": 19, + "slot_group": "Sample collection and processing" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "rank": 20, + "slot_group": "Sample collection and processing" + }, + "organism": { + "name": "organism", + "rank": 21, + "slot_group": "Sample collection and processing" + }, + "influenza_subtype": { + "name": "influenza_subtype", + "rank": 22, + "slot_group": "Sample collection and processing" + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "rank": 23, + "slot_group": "Sample collection and processing" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "rank": 24, + "slot_group": "Sample collection and processing" + }, + "virus_identifier": { + "name": 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"percent_read_contamination_", + "rank": 194, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "rank": 195, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "rank": 196, + "slot_group": "Bioinformatics and QC metrics" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "rank": 197, + "slot_group": "Bioinformatics and QC metrics" + }, + "deduplication_method": { + "name": "deduplication_method", + "rank": 198, + "slot_group": "Bioinformatics and QC metrics" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "rank": 199, + "slot_group": "Bioinformatics and QC metrics" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "rank": 200, + "slot_group": "Taxonomic identification information" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "rank": 201, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "rank": 202, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "rank": 203, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "rank": 204, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "rank": 205, + "slot_group": "Taxonomic identification information" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "rank": 206, + "slot_group": "Taxonomic identification information" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "rank": 207, + "slot_group": "Pathogen diagnostic testing" + }, + "genetic_target_region": { + "name": "genetic_target_region", + "rank": 208, + "slot_group": "Pathogen diagnostic testing" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "rank": 209, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "rank": 210, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "rank": 211, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "rank": 212, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "rank": 213, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "rank": 214, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "rank": 215, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "rank": 216, + "slot_group": "Pathogen diagnostic testing" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "rank": 217, + "slot_group": "Risk assessment information" + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "rank": 218, + "slot_group": "Risk assessment information" + }, + "stage_of_production": { + "name": "stage_of_production", + "rank": 219, + "slot_group": "Risk assessment information" + }, + "experimental_intervention": { + "name": "experimental_intervention", + "rank": 220, + "slot_group": "Risk assessment information" + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "rank": 221, + "slot_group": "Risk assessment information" + } + }, + "attributes": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen_collector_sample_ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:sample_name" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen_collector_subsample_ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 2, + "slot_uri": "GENEPIO:0100752", + "alias": "specimen_collector_subsample_id", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled_sample_ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 3, + "slot_uri": "GENEPIO:0100996", + "alias": "pooled_sample_id", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "description": "The user-defined identifier assigned to a specific location from which samples are taken.", + "title": "sampling_site_ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 4, + "slot_uri": "GENEPIO:0100760", + "alias": "sampling_site_id", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sampling_event_id": { + "name": "sampling_event_id", + "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", + "title": "sampling_event_ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 5, + "slot_uri": "GENEPIO:0100761", + "alias": "sampling_event_id", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject_accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:bioproject_accession" + ], + "rank": 6, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample_accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMD00000001" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 7, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true, + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 8, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 9, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 10, + "slot_uri": "GENEPIO:0100762", + "alias": "sample_collection_data_steward_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "description": "The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_contact_email", + "comments": [ + "Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the \"sample collector contact email\"." + ], + "examples": [ + { + "value": "bloggsj@aglab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 11, + "slot_uri": "GENEPIO:0101107", + "alias": "sample_collection_data_steward_contact_email", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample_collected_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collected_by" + ], + "rank": 12, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 13, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo_loc_name_(country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 14, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "geo_loc_name_(country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory of origin of the sample.", + "title": "geo_loc_name_(state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 15, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_territory", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "description": "The county/region of origin of the sample.", + "title": "geo_loc_name_(county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 16, + "slot_uri": "GENEPIO:0100280", + "alias": "geo_loc_name_county_region", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "The city of origin of the sample.", + "title": "geo_loc_name_(city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 17, + "slot_uri": "GENEPIO:0001189", + "alias": "geo_loc_name_city", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo_loc_name_(site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 18, + "slot_uri": "GENEPIO:0100436", + "alias": "geo_loc_name_site__", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 19, + "slot_uri": "GENEPIO:0100309", + "alias": "geo_loc_latitude", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 20, + "slot_uri": "GENEPIO:0100310", + "alias": "geo_loc_longitude", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:organism" + ], + "rank": 21, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_subtype": { + "name": "influenza_subtype", + "title": "influenza_subtype", + "from_schema": "https://example.com/hpai", + "rank": 22, + "slot_uri": "GENEPIO:0101108", + "alias": "influenza_subtype", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subsubtype menu", + "required": true, + "multivalued": true + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "title": "influenza_subtyping_scheme_name", + "from_schema": "https://example.com/hpai", + "rank": 23, + "slot_uri": "GENEPIO:0101109", + "alias": "influenza_subtyping_scheme_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subtyping_scheme_name menu" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "title": "taxonomic_identification_process", + "from_schema": "https://example.com/hpai", + "rank": 24, + "slot_uri": "GENEPIO:0100583", + "alias": "taxonomic_identification_process", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "taxonomic_identification_process menu" + }, + "virus_identifier": { + "name": "virus_identifier", + "title": "virus_identifier", + "from_schema": "https://example.com/hpai", + "rank": 25, + "slot_uri": "GENEPIO:0101110", + "alias": "virus_identifier", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "who_oie_fao_h5_clade": { + "name": "who_oie_fao_h5_clade", + "title": "WHO/OIE/FAO_H5_clade", + "from_schema": "https://example.com/hpai", + "rank": 26, + "slot_uri": "GENEPIO:0101111", + "alias": "who_oie_fao_h5_clade", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected, or sampling began for a continuous sample.", + "title": "sample_collection_date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collection_date" + ], + "rank": 27, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "description": "The date on which sample collection ended for a continuous sample.", + "title": "sample_collection_end_date", + "comments": [ + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + ], + "examples": [ + { + "value": "2020-03-18" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 28, + "slot_uri": "GENEPIO:0101071", + "alias": "sample_collection_end_date", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "description": "The time at which sample collection began.", + "title": "sample_collection_start_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "17:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 29, + "slot_uri": "GENEPIO:0101072", + "alias": "sample_collection_start_time", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "description": "The time at which sample collection ended.", + "title": "sample_collection_end_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "19:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 30, + "slot_uri": "GENEPIO:0101073", + "alias": "sample_collection_end_time", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "description": "The descriptive time of day during which the sample was collected.", + "title": "sample_collection_time_of_day", + "comments": [ + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + ], + "examples": [ + { + "value": "Morning" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 31, + "slot_uri": "GENEPIO:0100765", + "alias": "sample_collection_time_of_day", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_collection_time_of_day menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "description": "The amount of time over which the sample was collected.", + "title": "sample_collection_time_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 32, + "slot_uri": "GENEPIO:0100766", + "alias": "sample_collection_time_duration_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "description": "The units of the time duration measurement of sample collection.", + "title": "sample_collection_time_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Hour" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 33, + "slot_uri": "GENEPIO:0100767", + "alias": "sample_collection_time_duration_unit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "sample_collection_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 34, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 35, + "slot_uri": "GENEPIO:0100763", + "alias": "sample_processing_date", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_site": { + "name": "environmental_site", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "title": "environmental_site", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Poultry hatchery [ENVO:01001874]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_site", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:animal_env" + ], + "rank": 36, + "slot_uri": "GENEPIO:0001232", + "alias": "environmental_site", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_site menu" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "title": "environmental_material", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Soil [ENVO:00001998]" + }, + { + "value": "Water [CHEBI:15377]" + }, + { + "value": "Wastewater [ENVO:00002001]" + }, + { + "value": "Broom [ENVO:03501377]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_material", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 37, + "slot_uri": "GENEPIO:0001223", + "alias": "environmental_material", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection_device", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Drag swab [OBI:0002822]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_device", + "BIOSAMPLE_Enterics:samp_collect_device", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 38, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_device menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "title": "collection_method", + "comments": [ + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Rinsing for specimen collection [GENEPIO_0002116]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_method", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 39, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_method menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 40, + "slot_uri": "GENEPIO:0100768", + "alias": "sample_volume_measurement_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "milliliter (mL) [UO:0000098]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 41, + "slot_uri": "GENEPIO:0100769", + "alias": "sample_volume_measurement_unit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "sample_volume_measurement_unit menu" + }, + "residual_sample_status": { + "name": "residual_sample_status", + "description": "The status of the residual sample (whether any sample remains after its original use).", + "title": "residual_sample_status", + "comments": [ + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + ], + "examples": [ + { + "value": "No residual sample (sample all used) [GENEPIO:0101088]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 42, + "slot_uri": "GENEPIO:0101090", + "alias": "residual_sample_status", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "residual_sample_status menu" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:purpose_of_sampling" + ], + "rank": 43, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sampling menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity": { + "name": "presampling_activity", + "description": "The activities or variables upstream of sample collection that may affect the sample.", + "title": "presampling_activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 44, + "slot_uri": "GENEPIO:0100433", + "alias": "presampling_activity", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "presampling_activity menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the activities or variables that affected the sample collected.", + "title": "presampling_activity_details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 45, + "slot_uri": "GENEPIO:0100434", + "alias": "presampling_activity_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_storage_method": { + "name": "sample_storage_method", + "description": "The process used to store the sample.", + "title": "sample_storage_method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 46, + "slot_uri": "GENEPIO:0100448", + "alias": "sample_storage_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The medium in which a sample is stored.", + "title": "sample_storage_medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 47, + "slot_uri": "GENEPIO:0100449", + "alias": "sample_storage_medium", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 48, + "slot_uri": "GENEPIO:0101014", + "alias": "sample_storage_duration_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 49, + "slot_uri": "GENEPIO:0101015", + "alias": "sample_storage_duration_unit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_storage_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 50, + "slot_uri": "GENEPIO:0001253", + "alias": "specimen_processing", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "specimen_processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 51, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental_protocol", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "from_schema": "https://example.com/hpai", + "rank": 52, + "slot_uri": "GENEPIO:0101029", + "alias": "experimental_protocol", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 53, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "experimental_specimen_role_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "title": "experimental_specimen_details", + "from_schema": "https://example.com/hpai", + "rank": 54, + "slot_uri": "GENEPIO:0101112", + "alias": "experimental_specimen_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "available_data_types": { + "name": "available_data_types", + "description": "The type of data that is available, that may or may not require permission to access.", + "title": "available_data_types", + "comments": [ + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + ], + "examples": [ + { + "value": "Total coliform count [GENEPIO:0100729]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 55, + "slot_uri": "GENEPIO:0100690", + "alias": "available_data_types", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "available_data_types menu" + }, + { + "range": "null value menu" + } + ] + }, + "available_data_type_details": { + "name": "available_data_type_details", + "description": "Detailed information regarding other available data types.", + "title": "available_data_type_details", + "comments": [ + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + ], + "examples": [ + { + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 56, + "slot_uri": "GENEPIO:0101023", + "alias": "available_data_type_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_measurement_value": { + "name": "water_catchment_area_human_population_measurement_value", + "description": "The numerical value of the human population measurement that contributes to the composition of water in a catchment area.", + "title": "water_catchment_area_human_population_measurement_value", + "comments": [ + "Where known, provide the numerical value of population size, i.e. the number of people." + ], + "examples": [ + { + "value": "10,500" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 57, + "slot_uri": "GENEPIO:0100773", + "alias": "water_catchment_area_human_population_measurement_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "integer" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_range": { + "name": "water_catchment_area_human_population_range", + "description": "The human population range of the water catchment that contributes effluent to a wastewater site.", + "title": "water_catchment_area_human_population_range", + "comments": [ + "Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist." + ], + "examples": [ + { + "value": "1,000 - 10,000 people" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 58, + "slot_uri": "GENEPIO:0100774", + "alias": "water_catchment_area_human_population_range", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water catchment area human population range menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_measurement_method": { + "name": "water_catchment_area_human_population_measurement_method", + "description": "The method by which a water catchment 's human population size was measured or estimated", + "title": "water_catchment_area_human_population_measurement_method", + "comments": [ + "Provide a brief description of how catchment population size was measured or estimated." + ], + "examples": [ + { + "value": "population of jurisdiction encompassing the wastewater service area" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 59, + "slot_uri": "GENEPIO:0100775", + "alias": "water_catchment_area_human_population_measurement_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_value": { + "name": "water_catchment_area_human_population_density_value", + "description": "The numerical value describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density value", + "comments": [ + "Provide the numerical value of the population density in the catchement area." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 60, + "slot_uri": "GENEPIO:0100776", + "alias": "water_catchment_area_human_population_density_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_unit": { + "name": "water_catchment_area_human_population_density_unit", + "description": "The unit describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density unit", + "comments": [ + "Provide the unit of the population density in the catchement area." + ], + "examples": [ + { + "value": "persons per Km^2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 61, + "slot_uri": "GENEPIO:0100777", + "alias": "water_catchment_area_human_population_density_unit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water catchment area human population density unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "populated_area_type": { + "name": "populated_area_type", + "description": "A type of area that is populated by humans to different degrees.", + "title": "populated area type", + "comments": [ + "Provide the populated area type from the pick list." + ], + "examples": [ + { + "value": "Urban area" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 62, + "slot_uri": "GENEPIO:0100778", + "alias": "populated_area_type", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "populated area type menu" + }, + { + "range": "null value menu" + } + ] + }, + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "sampling weather conditions", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 63, + "slot_uri": "GENEPIO:0100779", + "alias": "sampling_weather_conditions", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "sampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", + "description": "Weather conditions prior to collection that may affect the sample.", + "title": "presampling weather conditions", + "comments": [ + "Provide the weather conditions prior to sample collection." + ], + "examples": [ + { + "value": "Drizzle" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 64, + "slot_uri": "GENEPIO:0100780", + "alias": "presampling_weather_conditions", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "presampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", + "comments": [ + "Provide the quantity of precipitation in the area leading up to the time of sample collection." + ], + "examples": [ + { + "value": "12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 65, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "water_depth": { + "name": "water_depth", + "description": "The depth of some water.", + "title": "water_depth", + "comments": [ + "Provide the numerical depth only of water only (without units)." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 66, + "slot_uri": "GENEPIO:0100440", + "alias": "water_depth", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_depth_units": { + "name": "water_depth_units", + "description": "The units of measurement for water depth.", + "title": "water_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 67, + "slot_uri": "GENEPIO:0101025", + "alias": "water_depth_units", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "sediment_depth": { + "name": "sediment_depth", + "description": "The depth of some sediment.", + "title": "sediment_depth", + "comments": [ + "Provide the numerical depth only of the sediment (without units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 68, + "slot_uri": "GENEPIO:0100697", + "alias": "sediment_depth", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sediment_depth_units": { + "name": "sediment_depth_units", + "description": "The units of measurement for sediment depth.", + "title": "sediment_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 69, + "slot_uri": "GENEPIO:0101026", + "alias": "sediment_depth_units", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sediment_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "air_temperature": { + "name": "air_temperature", + "description": "The temperature of some air.", + "title": "air_temperature", + "comments": [ + "Provide the numerical value for the temperature of the air (without units)." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 70, + "slot_uri": "GENEPIO:0100441", + "alias": "air_temperature", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "air_temperature_units": { + "name": "air_temperature_units", + "description": "The units of measurement for air temperature.", + "title": "air_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 71, + "slot_uri": "GENEPIO:0101027", + "alias": "air_temperature_units", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "air_temperature_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_temperature": { + "name": "water_temperature", + "description": "The temperature of some water.", + "title": "water_temperature", + "comments": [ + "Provide the numerical value for the temperature of the water (without units)." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 72, + "slot_uri": "GENEPIO:0100698", + "alias": "water_temperature", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_temperature_units": { + "name": "water_temperature_units", + "description": "The units of measurement for water temperature.", + "title": "water_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 73, + "slot_uri": "GENEPIO:0101028", + "alias": "water_temperature_units", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_temperature_units menu" + }, + { + "range": "null value 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"comments": [ + "Provide the units of precipitation by selecting a value from the pick list." + ], + "examples": [ + { + "value": "inch" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 75, + "slot_uri": "GENEPIO:0100912", + "alias": "precipitation_measurement_unit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "precipitation measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", + "description": "The process used to measure the amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement method", + "comments": [ + "Provide the name of the procedure or method used to measure precipitation." + ], + "examples": [ + { + "value": "Rain gauge over a 12 hour period prior to sample 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value menu" + } + ] + }, + "sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", + "description": "The numerical value of a measurement of temperature of a sample upon receipt.", + "title": "sample temperature value (when received)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 139, + "slot_uri": "GENEPIO:0100823", + "alias": "sample_temperature_value_when_received", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_unit_when_received": { + "name": "sample_temperature_unit_when_received", + "description": "The units of a measurement of temperature of a sample at the time upon receipt.", + "title": "sample temperature unit (when received)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 140, + "slot_uri": "GENEPIO:0100824", + "alias": "sample_temperature_unit_when_received", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sample temperature unit (when received) menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library_ID", + "comments": [ + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "LS_2010_NP_123446" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 141, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing_assay_type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 142, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "sequencing_assay_type menu" + }, + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 143, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "date" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "description": "The reason that the sample was sequenced.", + "title": "purpose_of_sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 144, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing__", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sequencing menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose_of_sequencing_details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 145, + "slot_uri": "GENEPIO:0001446", + "alias": "purpose_of_sequencing_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:sequenced_by", + "BIOSAMPLE_Enterics:sequenced_by" + ], + "rank": 146, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 147, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 148, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 149, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence_submitted_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 150, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequence_submitter_contact_email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 151, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic_acid_extraction_method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 152, + "slot_uri": "GENEPIO:0100939", + "alias": "nucleic_acid_extraction_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic_acid_extraction_kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 153, + "slot_uri": "GENEPIO:0100772", + "alias": "nucleic_acid_extraction_kit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "description": "The description of the endogenous controls included when extracting a sample.", + "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], + "from_schema": "https://example.com/hpai", + "rank": 154, + "slot_uri": "GENEPIO:0100923", + "alias": "endogenous_control_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "AMR-GRDI (PA-1356)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 155, + "slot_uri": "GENEPIO:0100472", + "alias": "sequencing_project_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing_platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 156, + "slot_uri": "GENEPIO:0100473", + "alias": "sequencing_platform", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_platform menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing_instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 157, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_instrument menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library_preparation_kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 158, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA_fragment_length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 159, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 160, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "genomic_target_enrichment_method menu" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method_details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ + { + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 161, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon_pcr_primer_scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 162, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon_size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 163, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing_flow_cell_version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 164, + "slot_uri": "GENEPIO:0101102", + "alias": "sequencing_flow_cell_version", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing_protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 165, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1_fastq_filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 166, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2_fastq_filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 167, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5_filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "batch1a_sequences.fast5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 168, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 169, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "assembly_filename": { + "name": "assembly_filename", + "description": "The user-defined filename of the FASTA file.", + "title": "assembly_filename", + "comments": [ + "Provide the FASTA filename." + ], + "examples": [ + { + "value": "pathogenassembly123.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 170, + "slot_uri": "GENEPIO:0001461", + "alias": "assembly_filename", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 171, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 172, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 173, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_determination menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 174, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_issues menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 175, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 176, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 177, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 178, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 179, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 180, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 181, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 182, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 183, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 184, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 185, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 186, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 187, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 188, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 189, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 190, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 191, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 192, + "slot_uri": "GENEPIO:0001484", + "alias": "ns_per_100_kbp", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 193, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 194, + "slot_uri": "GENEPIO:0100845", + "alias": "percent_read_contamination_", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 195, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "The length of the genome defined by the most common nucleotides at each position.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 196, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 197, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 198, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 199, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 200, + "slot_uri": "GENEPIO:0100832", + "alias": "read_mapping_software_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 201, + "slot_uri": "GENEPIO:0100833", + "alias": "read_mapping_software_version", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 202, + "slot_uri": "GENEPIO:0100834", + "alias": "taxonomic_reference_database_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 203, + "slot_uri": "GENEPIO:0100835", + "alias": "taxonomic_reference_database_version", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 204, + "slot_uri": "GENEPIO:0101074", + "alias": "taxonomic_analysis_report_filename", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 205, + "slot_uri": "GENEPIO:0101075", + "alias": "taxonomic_analysis_date", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "date" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 206, + "slot_uri": "GENEPIO:0100836", + "alias": "read_mapping_criteria", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "description": "The name of the genetic marker used for testing.", + "title": "genetic target name", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 207, + "slot_uri": "GENEPIO:0101116", + "alias": "genetic_target_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "genetic_target_region": { + "name": "genetic_target_region", + "description": "The specific region or segment of a genetic sequence used for testing or analysis.", + "title": "genetic target region", + "from_schema": "https://example.com/hpai", + "rank": 208, + "slot_uri": "GENEPIO:0101117", + "alias": "genetic_target_region", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", + "title": "genetic target region reference genome", + "from_schema": "https://example.com/hpai", + "rank": 209, + "slot_uri": "GENEPIO:0101118", + "alias": "genetic_target_region_reference_genome", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 210, + "slot_uri": "GENEPIO:0100962", + "alias": "diagnostic_target_presence", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic target presence menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 211, + "slot_uri": "GENEPIO:0100963", + "alias": "diagnostic_measurement_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 212, + "slot_uri": "GENEPIO:0100964", + "alias": "diagnostic_measurement_unit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 213, + "slot_uri": "GENEPIO:0100965", + "alias": "diagnostic_measurement_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement method menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold value", + "from_schema": "https://example.com/hpai", + "rank": 214, + "slot_uri": "GENEPIO:0101104", + "alias": "diagnostic_testing_threshold_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "integer" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold units", + "from_schema": "https://example.com/hpai", + "rank": 215, + "slot_uri": "GENEPIO:0101105", + "alias": "diagnostic_testing_threshold_units", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "description": "Describe any details of the diagnsotic testing.", + "title": "diagnostic testing details", + "from_schema": "https://example.com/hpai", + "rank": 216, + "slot_uri": "GENEPIO:0101106", + "alias": "diagnostic_testing_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", + "title": "prevalence_metrics", + "comments": [ + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + ], + "examples": [ + { + "value": "Number of total samples collected, Number of positive samples" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 217, + "slot_uri": "GENEPIO:0100480", + "alias": "prevalence_metrics", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "description": "The details pertaining to the prevalence metrics from a surveillance project.", + "title": "prevalence_metrics_details", + "comments": [ + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + ], + "examples": [ + { + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 218, + "slot_uri": "GENEPIO:0100481", + "alias": "prevalence_metrics_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "stage_of_production": { + "name": "stage_of_production", + "description": "The stage of food production.", + "title": "stage_of_production", + "comments": [ + "Provide the stage of food production as free text." + ], + "examples": [ + { + "value": "Abattoir [ENVO:01000925]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 219, + "slot_uri": "GENEPIO:0100482", + "alias": "stage_of_production", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "any_of": [ + { + "range": "stage_of_production menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_intervention": { + "name": "experimental_intervention", + "description": "The category of the experimental intervention applied in the food production system.", + "title": "experimental_intervention", + "comments": [ + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + ], + "examples": [ + { + "value": "Vaccination [NCIT:C15346]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 220, + "slot_uri": "GENEPIO:0100483", + "alias": "experimental_intervention", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "experimental_intervention menu" + }, + { + "range": "null value menu" + } + ] + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "description": "The details of the experimental intervention applied in the food production system.", + "title": "experiment_intervention_details", + "comments": [ + "If an experimental intervention was applied in the survey, provide details in this field as free text." + ], + "examples": [ + { + "value": "2% cranberry solution mixed in feed" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 221, + "slot_uri": "GENEPIO:0100484", + "alias": "experiment_intervention_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + } + } + }, + "HPAIEnviro": { + "name": "HPAIEnviro", + "annotations": { + "version": { + "tag": "version", + "value": "1.0.0" + } + }, + "title": "HPAI Environmental", + "from_schema": "https://example.com/hpai", + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database identifiers" + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "rank": 2, + "slot_group": "Database identifiers" + }, + "pooled_sample_id": { + 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"name": "quality_control_determination", + "rank": 173, + "slot_group": "Bioinformatics and QC metrics" + }, + "quality_control_issues": { + "name": "quality_control_issues", + "rank": 174, + "slot_group": "Bioinformatics and QC metrics" + }, + "quality_control_details": { + "name": "quality_control_details", + "rank": 175, + "slot_group": "Bioinformatics and QC metrics" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "rank": 176, + "slot_group": "Bioinformatics and QC metrics" + }, + "dehosting_method": { + "name": "dehosting_method", + "rank": 177, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "rank": 178, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "rank": 179, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "rank": 180, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "rank": 181, + "slot_group": "Bioinformatics and QC metrics" + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "rank": 182, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "rank": 183, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "rank": 184, + "slot_group": "Bioinformatics and QC metrics" + }, + "genome_completeness": { + "name": "genome_completeness", + "rank": 185, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "rank": 186, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "rank": 187, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "rank": 188, + "slot_group": "Bioinformatics and QC metrics" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "rank": 189, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "rank": 190, + "slot_group": "Bioinformatics and QC metrics" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "rank": 191, + "slot_group": "Bioinformatics and QC metrics" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "rank": 192, + "slot_group": "Bioinformatics and QC metrics" + }, + "n50": { + "name": "n50", + "rank": 193, + "slot_group": "Bioinformatics and QC metrics" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "rank": 194, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "rank": 195, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "rank": 196, + "slot_group": "Bioinformatics and QC metrics" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "rank": 197, + "slot_group": "Bioinformatics and QC metrics" + }, + "deduplication_method": { + "name": "deduplication_method", + "rank": 198, + "slot_group": "Bioinformatics and QC metrics" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "rank": 199, + "slot_group": "Bioinformatics and QC metrics" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "rank": 200, + "slot_group": "Taxonomic identification information" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "rank": 201, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "rank": 202, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "rank": 203, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "rank": 204, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "rank": 205, + "slot_group": "Taxonomic identification information" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "rank": 206, + "slot_group": "Taxonomic identification information" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "rank": 207, + "slot_group": "Pathogen diagnostic testing" + }, + "genetic_target_region": { + "name": "genetic_target_region", + "rank": 208, + "slot_group": "Pathogen diagnostic testing" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "rank": 209, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "rank": 210, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "rank": 211, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "rank": 212, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "rank": 213, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "rank": 214, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "rank": 215, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "rank": 216, + "slot_group": "Pathogen diagnostic testing" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "rank": 217, + "slot_group": "Risk assessment information" + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "rank": 218, + "slot_group": "Risk assessment information" + }, + "stage_of_production": { + "name": "stage_of_production", + "rank": 219, + "slot_group": "Risk assessment information" + }, + "experimental_intervention": { + "name": "experimental_intervention", + "rank": 220, + "slot_group": "Risk assessment information" + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "rank": 221, + "slot_group": "Risk assessment information" + } + }, + "attributes": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen_collector_sample_ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:sample_name" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen_collector_subsample_ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 2, + "slot_uri": "GENEPIO:0100752", + "alias": "specimen_collector_subsample_id", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled_sample_ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 3, + "slot_uri": "GENEPIO:0100996", + "alias": "pooled_sample_id", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "description": "The user-defined identifier assigned to a specific location from which samples are taken.", + "title": "sampling_site_ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 4, + "slot_uri": "GENEPIO:0100760", + "alias": "sampling_site_id", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sampling_event_id": { + "name": "sampling_event_id", + "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", + "title": "sampling_event_ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 5, + "slot_uri": "GENEPIO:0100761", + "alias": "sampling_event_id", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject_accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:bioproject_accession" + ], + "rank": 6, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample_accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMD00000001" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 7, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true, + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 8, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 9, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 10, + "slot_uri": "GENEPIO:0100762", + "alias": "sample_collection_data_steward_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "description": "The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_contact_email", + "comments": [ + "Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the \"sample collector contact email\"." + ], + "examples": [ + { + "value": "bloggsj@aglab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 11, + "slot_uri": "GENEPIO:0101107", + "alias": "sample_collection_data_steward_contact_email", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample_collected_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collected_by" + ], + "rank": 12, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 13, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo_loc_name_(country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 14, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "geo_loc_name_(country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory of origin of the sample.", + "title": "geo_loc_name_(state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 15, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_territory", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "description": "The county/region of origin of the sample.", + "title": "geo_loc_name_(county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 16, + "slot_uri": "GENEPIO:0100280", + "alias": "geo_loc_name_county_region", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "The city of origin of the sample.", + "title": "geo_loc_name_(city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 17, + "slot_uri": "GENEPIO:0001189", + "alias": "geo_loc_name_city", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo_loc_name_(site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 18, + "slot_uri": "GENEPIO:0100436", + "alias": "geo_loc_name_site__", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 19, + "slot_uri": "GENEPIO:0100309", + "alias": "geo_loc_latitude", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 20, + "slot_uri": "GENEPIO:0100310", + "alias": "geo_loc_longitude", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:organism" + ], + "rank": 21, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_subtype": { + "name": "influenza_subtype", + "title": "influenza_subtype", + "from_schema": "https://example.com/hpai", + "rank": 22, + "slot_uri": "GENEPIO:0101108", + "alias": "influenza_subtype", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subsubtype menu", + "required": true, + "multivalued": true + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "title": "influenza_subtyping_scheme_name", + "from_schema": "https://example.com/hpai", + "rank": 23, + "slot_uri": "GENEPIO:0101109", + "alias": "influenza_subtyping_scheme_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subtyping_scheme_name menu" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "title": "taxonomic_identification_process", + "from_schema": "https://example.com/hpai", + "rank": 24, + "slot_uri": "GENEPIO:0100583", + "alias": "taxonomic_identification_process", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "taxonomic_identification_process menu" + }, + "virus_identifier": { + "name": "virus_identifier", + "title": "virus_identifier", + "from_schema": "https://example.com/hpai", + "rank": 25, + "slot_uri": "GENEPIO:0101110", + "alias": "virus_identifier", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "who_oie_fao_h5_clade": { + "name": "who_oie_fao_h5_clade", + "title": "WHO/OIE/FAO_H5_clade", + "from_schema": "https://example.com/hpai", + "rank": 26, + "slot_uri": "GENEPIO:0101111", + "alias": "who_oie_fao_h5_clade", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected, or sampling began for a continuous sample.", + "title": "sample_collection_date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collection_date" + ], + "rank": 27, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "description": "The date on which sample collection ended for a continuous sample.", + "title": "sample_collection_end_date", + "comments": [ + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + ], + "examples": [ + { + "value": "2020-03-18" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 28, + "slot_uri": "GENEPIO:0101071", + "alias": "sample_collection_end_date", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "description": "The time at which sample collection began.", + "title": "sample_collection_start_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "17:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 29, + "slot_uri": "GENEPIO:0101072", + "alias": "sample_collection_start_time", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "description": "The time at which sample collection ended.", + "title": "sample_collection_end_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "19:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 30, + "slot_uri": "GENEPIO:0101073", + "alias": "sample_collection_end_time", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "description": "The descriptive time of day during which the sample was collected.", + "title": "sample_collection_time_of_day", + "comments": [ + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + ], + "examples": [ + { + "value": "Morning" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 31, + "slot_uri": "GENEPIO:0100765", + "alias": "sample_collection_time_of_day", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_collection_time_of_day menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "description": "The amount of time over which the sample was collected.", + "title": "sample_collection_time_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 32, + "slot_uri": "GENEPIO:0100766", + "alias": "sample_collection_time_duration_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "description": "The units of the time duration measurement of sample collection.", + "title": "sample_collection_time_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Hour" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 33, + "slot_uri": "GENEPIO:0100767", + "alias": "sample_collection_time_duration_unit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "sample_collection_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 34, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 35, + "slot_uri": "GENEPIO:0100763", + "alias": "sample_processing_date", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_site": { + "name": "environmental_site", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "title": "environmental_site", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Poultry hatchery [ENVO:01001874]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_site", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:animal_env" + ], + "rank": 36, + "slot_uri": "GENEPIO:0001232", + "alias": "environmental_site", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_site menu" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "title": "environmental_material", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Soil [ENVO:00001998]" + }, + { + "value": "Water [CHEBI:15377]" + }, + { + "value": "Wastewater [ENVO:00002001]" + }, + { + "value": "Broom [ENVO:03501377]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_material", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 37, + "slot_uri": "GENEPIO:0001223", + "alias": "environmental_material", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection_device", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Drag swab [OBI:0002822]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_device", + "BIOSAMPLE_Enterics:samp_collect_device", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 38, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_device menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "title": "collection_method", + "comments": [ + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Rinsing for specimen collection [GENEPIO_0002116]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_method", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 39, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_method menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 40, + "slot_uri": "GENEPIO:0100768", + "alias": "sample_volume_measurement_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "milliliter (mL) [UO:0000098]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 41, + "slot_uri": "GENEPIO:0100769", + "alias": "sample_volume_measurement_unit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "sample_volume_measurement_unit menu" + }, + "residual_sample_status": { + "name": "residual_sample_status", + "description": "The status of the residual sample (whether any sample remains after its original use).", + "title": "residual_sample_status", + "comments": [ + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + ], + "examples": [ + { + "value": "No residual sample (sample all used) [GENEPIO:0101088]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 42, + "slot_uri": "GENEPIO:0101090", + "alias": "residual_sample_status", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "residual_sample_status menu" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:purpose_of_sampling" + ], + "rank": 43, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sampling menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity": { + "name": "presampling_activity", + "description": "The activities or variables upstream of sample collection that may affect the sample.", + "title": "presampling_activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 44, + "slot_uri": "GENEPIO:0100433", + "alias": "presampling_activity", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "presampling_activity menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the activities or variables that affected the sample collected.", + "title": "presampling_activity_details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 45, + "slot_uri": "GENEPIO:0100434", + "alias": "presampling_activity_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_storage_method": { + "name": "sample_storage_method", + "description": "The process used to store the sample.", + "title": "sample_storage_method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 46, + "slot_uri": "GENEPIO:0100448", + "alias": "sample_storage_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The medium in which a sample is stored.", + "title": "sample_storage_medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 47, + "slot_uri": "GENEPIO:0100449", + "alias": "sample_storage_medium", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 48, + "slot_uri": "GENEPIO:0101014", + "alias": "sample_storage_duration_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 49, + "slot_uri": "GENEPIO:0101015", + "alias": "sample_storage_duration_unit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_storage_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 50, + "slot_uri": "GENEPIO:0001253", + "alias": "specimen_processing", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "specimen_processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 51, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental_protocol", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "from_schema": "https://example.com/hpai", + "rank": 52, + "slot_uri": "GENEPIO:0101029", + "alias": "experimental_protocol", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 53, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "experimental_specimen_role_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "title": "experimental_specimen_details", + "from_schema": "https://example.com/hpai", + "rank": 54, + "slot_uri": "GENEPIO:0101112", + "alias": "experimental_specimen_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "available_data_types": { + "name": "available_data_types", + "description": "The type of data that is available, that may or may not require permission to access.", + "title": "available_data_types", + "comments": [ + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + ], + "examples": [ + { + "value": "Total coliform count [GENEPIO:0100729]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 55, + "slot_uri": "GENEPIO:0100690", + "alias": "available_data_types", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "available_data_types menu" + }, + { + "range": "null value menu" + } + ] + }, + "available_data_type_details": { + "name": "available_data_type_details", + "description": "Detailed information regarding other available data types.", + "title": "available_data_type_details", + "comments": [ + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + ], + "examples": [ + { + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 56, + "slot_uri": "GENEPIO:0101023", + "alias": "available_data_type_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_measurement_value": { + "name": "water_catchment_area_human_population_measurement_value", + "description": "The numerical value of the human population measurement that contributes to the composition of water in a catchment area.", + "title": "water_catchment_area_human_population_measurement_value", + "comments": [ + "Where known, provide the numerical value of population size, i.e. the number of people." + ], + "examples": [ + { + "value": "10,500" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 57, + "slot_uri": "GENEPIO:0100773", + "alias": "water_catchment_area_human_population_measurement_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "integer" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_range": { + "name": "water_catchment_area_human_population_range", + "description": "The human population range of the water catchment that contributes effluent to a wastewater site.", + "title": "water_catchment_area_human_population_range", + "comments": [ + "Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist." + ], + "examples": [ + { + "value": "1,000 - 10,000 people" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 58, + "slot_uri": "GENEPIO:0100774", + "alias": "water_catchment_area_human_population_range", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water catchment area human population range menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_measurement_method": { + "name": "water_catchment_area_human_population_measurement_method", + "description": "The method by which a water catchment 's human population size was measured or estimated", + "title": "water_catchment_area_human_population_measurement_method", + "comments": [ + "Provide a brief description of how catchment population size was measured or estimated." + ], + "examples": [ + { + "value": "population of jurisdiction encompassing the wastewater service area" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 59, + "slot_uri": "GENEPIO:0100775", + "alias": "water_catchment_area_human_population_measurement_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_value": { + "name": "water_catchment_area_human_population_density_value", + "description": "The numerical value describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density value", + "comments": [ + "Provide the numerical value of the population density in the catchement area." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 60, + "slot_uri": "GENEPIO:0100776", + "alias": "water_catchment_area_human_population_density_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_unit": { + "name": "water_catchment_area_human_population_density_unit", + "description": "The unit describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density unit", + "comments": [ + "Provide the unit of the population density in the catchement area." + ], + "examples": [ + { + "value": "persons per Km^2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 61, + "slot_uri": "GENEPIO:0100777", + "alias": "water_catchment_area_human_population_density_unit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water catchment area human population density unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "populated_area_type": { + "name": "populated_area_type", + "description": "A type of area that is populated by humans to different degrees.", + "title": "populated area type", + "comments": [ + "Provide the populated area type from the pick list." + ], + "examples": [ + { + "value": "Urban area" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 62, + "slot_uri": "GENEPIO:0100778", + "alias": "populated_area_type", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "populated area type menu" + }, + { + "range": "null value menu" + } + ] + }, + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "sampling weather conditions", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 63, + "slot_uri": "GENEPIO:0100779", + "alias": "sampling_weather_conditions", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "sampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", + "description": "Weather conditions prior to collection that may affect the sample.", + "title": "presampling weather conditions", + "comments": [ + "Provide the weather conditions prior to sample collection." + ], + "examples": [ + { + "value": "Drizzle" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 64, + "slot_uri": "GENEPIO:0100780", + "alias": "presampling_weather_conditions", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "presampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", + "comments": [ + "Provide the quantity of precipitation in the area leading up to the time of sample collection." + ], + "examples": [ + { + "value": "12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 65, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "water_depth": { + "name": "water_depth", + "description": "The depth of some water.", + "title": "water_depth", + "comments": [ + "Provide the numerical depth only of water only (without units)." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 66, + "slot_uri": "GENEPIO:0100440", + "alias": "water_depth", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_depth_units": { + "name": "water_depth_units", + "description": "The units of measurement for water depth.", + "title": "water_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 67, + "slot_uri": "GENEPIO:0101025", + "alias": "water_depth_units", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "sediment_depth": { + "name": "sediment_depth", + "description": "The depth of some sediment.", + "title": "sediment_depth", + "comments": [ + "Provide the numerical depth only of the sediment (without units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 68, + "slot_uri": "GENEPIO:0100697", + "alias": "sediment_depth", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sediment_depth_units": { + "name": "sediment_depth_units", + "description": "The units of measurement for sediment depth.", + "title": "sediment_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 69, + "slot_uri": "GENEPIO:0101026", + "alias": "sediment_depth_units", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sediment_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "air_temperature": { + "name": "air_temperature", + "description": "The temperature of some air.", + "title": "air_temperature", + "comments": [ + "Provide the numerical value for the temperature of the air (without units)." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 70, + "slot_uri": "GENEPIO:0100441", + "alias": "air_temperature", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "air_temperature_units": { + "name": "air_temperature_units", + "description": "The units of measurement for air temperature.", + "title": "air_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 71, + "slot_uri": "GENEPIO:0101027", + "alias": "air_temperature_units", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "air_temperature_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_temperature": { + "name": "water_temperature", + "description": "The temperature of some water.", + "title": "water_temperature", + "comments": [ + "Provide the numerical value for the temperature of the water (without units)." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 72, + "slot_uri": "GENEPIO:0100698", + "alias": "water_temperature", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_temperature_units": { + "name": "water_temperature_units", + "description": "The units of measurement for water temperature.", + "title": "water_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 73, + "slot_uri": "GENEPIO:0101028", + "alias": "water_temperature_units", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_temperature_units menu" + 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collection.", + "title": "sample temperature value (at collection)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "20" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 137, + "slot_uri": "GENEPIO:0100821", + "alias": "sample_temperature_value_at_collection", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_unit_at_collection": { + "name": "sample_temperature_unit_at_collection", + "description": "The units of a measurement of temperature of a sample at the time of collection.", + "title": "sample temperature unit (at collection)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 138, + "slot_uri": "GENEPIO:0100822", + "alias": "sample_temperature_unit_at_collection", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sample temperature unit (at collection) menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", + "description": "The numerical value of a measurement of temperature of a sample upon receipt.", + "title": "sample temperature value (when received)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 139, + "slot_uri": "GENEPIO:0100823", + "alias": "sample_temperature_value_when_received", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_unit_when_received": { + "name": "sample_temperature_unit_when_received", + "description": "The units of a measurement of temperature of a sample at the time upon receipt.", + "title": "sample temperature unit (when received)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 140, + "slot_uri": "GENEPIO:0100824", + "alias": "sample_temperature_unit_when_received", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sample temperature unit (when received) menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library_ID", + "comments": [ + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "LS_2010_NP_123446" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 141, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing_assay_type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 142, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "sequencing_assay_type menu" + }, + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 143, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "date" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "description": "The reason that the sample was sequenced.", + "title": "purpose_of_sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 144, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing__", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sequencing menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose_of_sequencing_details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 145, + "slot_uri": "GENEPIO:0001446", + "alias": "purpose_of_sequencing_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:sequenced_by", + "BIOSAMPLE_Enterics:sequenced_by" + ], + "rank": 146, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 147, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 148, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 149, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence_submitted_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 150, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequence_submitter_contact_email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 151, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic_acid_extraction_method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 152, + "slot_uri": "GENEPIO:0100939", + "alias": "nucleic_acid_extraction_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic_acid_extraction_kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 153, + "slot_uri": "GENEPIO:0100772", + "alias": "nucleic_acid_extraction_kit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "description": "The description of the endogenous controls included when extracting a sample.", + "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], + "from_schema": "https://example.com/hpai", + "rank": 154, + "slot_uri": "GENEPIO:0100923", + "alias": "endogenous_control_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "AMR-GRDI (PA-1356)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 155, + "slot_uri": "GENEPIO:0100472", + "alias": "sequencing_project_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing_platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 156, + "slot_uri": "GENEPIO:0100473", + "alias": "sequencing_platform", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_platform menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing_instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 157, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_instrument menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library_preparation_kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 158, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA_fragment_length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 159, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 160, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "genomic_target_enrichment_method menu" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method_details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ + { + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 161, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon_pcr_primer_scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 162, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon_size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 163, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing_flow_cell_version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 164, + "slot_uri": "GENEPIO:0101102", + "alias": "sequencing_flow_cell_version", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing_protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 165, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1_fastq_filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 166, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2_fastq_filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 167, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5_filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "batch1a_sequences.fast5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 168, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 169, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "assembly_filename": { + "name": "assembly_filename", + "description": "The user-defined filename of the FASTA file.", + "title": "assembly_filename", + "comments": [ + "Provide the FASTA filename." + ], + "examples": [ + { + "value": "pathogenassembly123.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 170, + "slot_uri": "GENEPIO:0001461", + "alias": "assembly_filename", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 171, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 172, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 173, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_determination menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 174, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_issues menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 175, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 176, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 177, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 178, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 179, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 180, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 181, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 182, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 183, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 184, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 185, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 186, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 187, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 188, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 189, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 190, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 191, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 192, + "slot_uri": "GENEPIO:0001484", + "alias": "ns_per_100_kbp", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 193, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 194, + "slot_uri": "GENEPIO:0100845", + "alias": "percent_read_contamination_", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 195, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "The length of the genome defined by the most common nucleotides at each position.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 196, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 197, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 198, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 199, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 200, + "slot_uri": "GENEPIO:0100832", + "alias": "read_mapping_software_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 201, + "slot_uri": "GENEPIO:0100833", + "alias": "read_mapping_software_version", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 202, + "slot_uri": "GENEPIO:0100834", + "alias": "taxonomic_reference_database_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 203, + "slot_uri": "GENEPIO:0100835", + "alias": "taxonomic_reference_database_version", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 204, + "slot_uri": "GENEPIO:0101074", + "alias": "taxonomic_analysis_report_filename", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 205, + "slot_uri": "GENEPIO:0101075", + "alias": "taxonomic_analysis_date", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "date" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 206, + "slot_uri": "GENEPIO:0100836", + "alias": "read_mapping_criteria", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "description": "The name of the genetic marker used for testing.", + "title": "genetic target name", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 207, + "slot_uri": "GENEPIO:0101116", + "alias": "genetic_target_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "genetic_target_region": { + "name": "genetic_target_region", + "description": "The specific region or segment of a genetic sequence used for testing or analysis.", + "title": "genetic target region", + "from_schema": "https://example.com/hpai", + "rank": 208, + "slot_uri": "GENEPIO:0101117", + "alias": "genetic_target_region", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", + "title": "genetic target region reference genome", + "from_schema": "https://example.com/hpai", + "rank": 209, + "slot_uri": "GENEPIO:0101118", + "alias": "genetic_target_region_reference_genome", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 210, + "slot_uri": "GENEPIO:0100962", + "alias": "diagnostic_target_presence", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic target presence menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 211, + "slot_uri": "GENEPIO:0100963", + "alias": "diagnostic_measurement_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 212, + "slot_uri": "GENEPIO:0100964", + "alias": "diagnostic_measurement_unit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 213, + "slot_uri": "GENEPIO:0100965", + "alias": "diagnostic_measurement_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement method menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold value", + "from_schema": "https://example.com/hpai", + "rank": 214, + "slot_uri": "GENEPIO:0101104", + "alias": "diagnostic_testing_threshold_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "integer" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold units", + "from_schema": "https://example.com/hpai", + "rank": 215, + "slot_uri": "GENEPIO:0101105", + "alias": "diagnostic_testing_threshold_units", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "description": "Describe any details of the diagnsotic testing.", + "title": "diagnostic testing details", + "from_schema": "https://example.com/hpai", + "rank": 216, + "slot_uri": "GENEPIO:0101106", + "alias": "diagnostic_testing_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", + "title": "prevalence_metrics", + "comments": [ + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + ], + "examples": [ + { + "value": "Number of total samples collected, Number of positive samples" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 217, + "slot_uri": "GENEPIO:0100480", + "alias": "prevalence_metrics", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "description": "The details pertaining to the prevalence metrics from a surveillance project.", + "title": "prevalence_metrics_details", + "comments": [ + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + ], + "examples": [ + { + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 218, + "slot_uri": "GENEPIO:0100481", + "alias": "prevalence_metrics_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "stage_of_production": { + "name": "stage_of_production", + "description": "The stage of food production.", + "title": "stage_of_production", + "comments": [ + "Provide the stage of food production as free text." + ], + "examples": [ + { + "value": "Abattoir [ENVO:01000925]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 219, + "slot_uri": "GENEPIO:0100482", + "alias": "stage_of_production", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "any_of": [ + { + "range": "stage_of_production menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_intervention": { + "name": "experimental_intervention", + "description": "The category of the experimental intervention applied in the food production system.", + "title": "experimental_intervention", + "comments": [ + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + ], + "examples": [ + { + "value": "Vaccination [NCIT:C15346]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 220, + "slot_uri": "GENEPIO:0100483", + "alias": "experimental_intervention", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "experimental_intervention menu" + }, + { + "range": "null value menu" + } + ] + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "description": "The details of the experimental intervention applied in the food production system.", + "title": "experiment_intervention_details", + "comments": [ + "If an experimental intervention was applied in the survey, provide details in this field as free text." + ], + "examples": [ + { + "value": "2% cranberry solution mixed in feed" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 221, + "slot_uri": "GENEPIO:0100484", + "alias": "experiment_intervention_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + } + } + }, + "HPAIHost": { + "name": "HPAIHost", + "annotations": { + "version": { + "tag": "version", + "value": "1.0.0" + } + }, + "title": "HPAI Host", + "from_schema": "https://example.com/hpai", + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database identifiers" + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "rank": 2, + "slot_group": "Database identifiers" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "rank": 3, + "slot_group": "Database identifiers" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "rank": 4, + "slot_group": "Database identifiers" + }, + "sampling_event_id": { + "name": "sampling_event_id", + "rank": 5, + "slot_group": "Database identifiers" + }, + "bioproject_accession": { + "name": "bioproject_accession", + "rank": 6, + "slot_group": "Database identifiers" + }, + "biosample_accession": { + "name": "biosample_accession", + "rank": 7, + "slot_group": "Database identifiers" + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "rank": 8, + "slot_group": "Database identifiers" + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "rank": 9, + "slot_group": "Database identifiers" + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "rank": 10, + "slot_group": "Sample collection and processing" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "rank": 11, + "slot_group": "Sample collection and processing" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "rank": 12, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "rank": 13, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "rank": 14, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "rank": 15, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "rank": 16, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "rank": 17, + "slot_group": "Sample 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"presampling_activity": { + "name": "presampling_activity", + "rank": 40, + "slot_group": "Sample collection and processing" + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "rank": 41, + "slot_group": "Sample collection and processing" + }, + "sample_storage_method": { + "name": "sample_storage_method", + "rank": 42, + "slot_group": "Sample collection and processing" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "rank": 43, + "slot_group": "Sample collection and processing" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "rank": 44, + "slot_group": "Sample collection and processing" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "rank": 45, + "slot_group": "Sample collection and processing" + }, + "specimen_processing": { + "name": "specimen_processing", + "rank": 46, + "slot_group": "Sample collection and processing" + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "rank": 47, + "slot_group": "Sample collection and processing" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "rank": 48, + "slot_group": "Sample collection and processing" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "rank": 49, + "slot_group": "Sample collection and processing" + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "rank": 50, + "slot_group": "Sample collection and processing" + }, + "available_data_types": { + "name": "available_data_types", + "rank": 51, + "slot_group": "Sample collection and processing" + }, + "available_data_type_details": { + "name": "available_data_type_details", + "rank": 52, + "slot_group": "Sample collection and processing" + }, + "host_common_name": { + "name": "host_common_name", + "rank": 53, + "slot_group": "Host information" + }, + "host_scientific_name": { + "name": "host_scientific_name", + "rank": 54, + "slot_group": "Host information" + }, + "host_ecotype": { + "name": "host_ecotype", + "rank": 55, + "slot_group": "Host information" + }, + "host_breed": { + "name": "host_breed", + "rank": 56, + "slot_group": "Host information" + }, + "host_food_production_name": { + "name": "host_food_production_name", + "rank": 57, + "slot_group": "Host information" + }, + "host_age": { + "name": "host_age", + "rank": 58, + "slot_group": "Host Information" + }, + "host_age_unit": { + "name": "host_age_unit", + "rank": 59, + "slot_group": "Host Information" + }, + "host_age_bin": { + "name": "host_age_bin", + "rank": 60, + "slot_group": "Host information" + }, + "host_disease": { + "name": "host_disease", + "rank": 61, + "slot_group": "Host information" + }, + "host_health_state": { + "name": "host_health_state", + "rank": 62, + "slot_group": "Host Information" + }, + "host_health_status_details": { + "name": "host_health_status_details", + "rank": 63, + "slot_group": "Host Information" + }, + "host_health_outcome": { + "name": "host_health_outcome", + "rank": 64, + "slot_group": "Host Information" + }, + "host_subject_id": { + "name": "host_subject_id", + "rank": 65, + "slot_group": "Host Information" + }, + "case_id": { + "name": "case_id", + "rank": 66, + "slot_group": "Host Information" + }, + "symptom_onset_date": { + "name": "symptom_onset_date", + "rank": 67, + "slot_group": "Host Information" + }, + "signs_and_symptoms": { + "name": "signs_and_symptoms", + "rank": 68, + "slot_group": "Host Information" + }, + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "rank": 69, + "slot_group": "Host Information" + }, + "complications": { + "name": "complications", + "rank": 70, + "slot_group": "Host Information" + }, + "exposure_event": { + "name": "exposure_event", + "rank": 71, + "slot_group": "Host exposure information" + }, + "exposure_contact_level": { + "name": 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"slot_group": "Sequence information" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "rank": 87, + "slot_group": "Sequence information" + }, + "sequencing_date": { + "name": "sequencing_date", + "rank": 88, + "slot_group": "Sequence information" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "rank": 89, + "slot_group": "Sequence information" + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "rank": 90, + "slot_group": "Sequence information" + }, + "sequenced_by": { + "name": "sequenced_by", + "rank": 91, + "slot_group": "Sequence information" + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "rank": 92, + "slot_group": "Sequence information" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "rank": 93, + "slot_group": "Sequence information" + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "rank": 94, + "slot_group": "Sequence information" + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "rank": 95, + "slot_group": "Sequence information" + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "rank": 96, + "slot_group": "Sequence information" + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "rank": 97, + "slot_group": "Sample collection and processing" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "rank": 98, + "slot_group": "Sample collection and processing" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "rank": 99, + "slot_group": "Sample collection and processing" + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "rank": 100, + "slot_group": "Sequence information" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "rank": 101, + "slot_group": "Sequence information" + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "rank": 102, + "slot_group": "Sequence information" + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "rank": 103, + "slot_group": "Sequence information" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "rank": 104, + "slot_group": "Sequence information" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "rank": 105, + "slot_group": "Sequence information" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "rank": 106, + "slot_group": "Sequence information" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "rank": 107, + "slot_group": "Sequence information" + }, + "amplicon_size": { + "name": "amplicon_size", + "rank": 108, + "slot_group": "Sequence information" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "rank": 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"slot_group": "Bioinformatics and QC metrics" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "rank": 118, + "slot_group": "Bioinformatics and QC metrics" + }, + "quality_control_issues": { + "name": "quality_control_issues", + "rank": 119, + "slot_group": "Bioinformatics and QC metrics" + }, + "quality_control_details": { + "name": "quality_control_details", + "rank": 120, + "slot_group": "Bioinformatics and QC metrics" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "rank": 121, + "slot_group": "Bioinformatics and QC metrics" + }, + "dehosting_method": { + "name": "dehosting_method", + "rank": 122, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "rank": 123, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "rank": 124, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "rank": 125, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "rank": 126, + "slot_group": "Bioinformatics and QC metrics" + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "rank": 127, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "rank": 128, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "rank": 129, + "slot_group": "Bioinformatics and QC metrics" + }, + "genome_completeness": { + "name": "genome_completeness", + "rank": 130, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_base_pairs_sequenced": { + "name": 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"genetic_target_name", + "rank": 152, + "slot_group": "Pathogen diagnostic testing" + }, + "genetic_target_region": { + "name": "genetic_target_region", + "rank": 153, + "slot_group": "Pathogen diagnostic testing" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "rank": 154, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "rank": 155, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "rank": 156, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "rank": 157, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "rank": 158, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "rank": 159, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "rank": 160, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "rank": 161, + "slot_group": "Pathogen diagnostic testing" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "rank": 162, + "slot_group": "Risk assessment information" + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "rank": 163, + "slot_group": "Risk assessment information" + }, + "stage_of_production": { + "name": "stage_of_production", + "rank": 164, + "slot_group": "Risk assessment information" + }, + "experimental_intervention": { + "name": "experimental_intervention", + "rank": 165, + "slot_group": "Risk assessment information" + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "rank": 166, + "slot_group": "Risk assessment information" + } + }, + "attributes": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen_collector_sample_ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:sample_name" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen_collector_subsample_ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 2, + "slot_uri": "GENEPIO:0100752", + "alias": "specimen_collector_subsample_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled_sample_ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 3, + "slot_uri": "GENEPIO:0100996", + "alias": "pooled_sample_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "description": "The user-defined identifier assigned to a specific location from which samples are taken.", + "title": "sampling_site_ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 4, + "slot_uri": "GENEPIO:0100760", + "alias": "sampling_site_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sampling_event_id": { + "name": "sampling_event_id", + "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", + "title": "sampling_event_ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 5, + "slot_uri": "GENEPIO:0100761", + "alias": "sampling_event_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject_accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:bioproject_accession" + ], + "rank": 6, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample_accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMD00000001" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 7, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true, + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 8, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 9, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 10, + "slot_uri": "GENEPIO:0100762", + "alias": "sample_collection_data_steward_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "description": "The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_contact_email", + "comments": [ + "Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the \"sample collector contact email\"." + ], + "examples": [ + { + "value": "bloggsj@aglab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 11, + "slot_uri": "GENEPIO:0101107", + "alias": "sample_collection_data_steward_contact_email", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample_collected_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collected_by" + ], + "rank": 12, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 13, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo_loc_name_(country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 14, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "geo_loc_name_(country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory of origin of the sample.", + "title": "geo_loc_name_(state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 15, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_territory", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "description": "The county/region of origin of the sample.", + "title": "geo_loc_name_(county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 16, + "slot_uri": "GENEPIO:0100280", + "alias": "geo_loc_name_county_region", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "The city of origin of the sample.", + "title": "geo_loc_name_(city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 17, + "slot_uri": "GENEPIO:0001189", + "alias": "geo_loc_name_city", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo_loc_name_(site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 18, + "slot_uri": "GENEPIO:0100436", + "alias": "geo_loc_name_site__", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 19, + "slot_uri": "GENEPIO:0100309", + "alias": "geo_loc_latitude", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 20, + "slot_uri": "GENEPIO:0100310", + "alias": "geo_loc_longitude", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:organism" + ], + "rank": 21, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_subtype": { + "name": "influenza_subtype", + "title": "influenza_subtype", + "from_schema": "https://example.com/hpai", + "rank": 22, + "slot_uri": "GENEPIO:0101108", + "alias": "influenza_subtype", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subsubtype menu", + "required": true, + "multivalued": true + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "title": "influenza_subtyping_scheme_name", + "from_schema": "https://example.com/hpai", + "rank": 23, + "slot_uri": "GENEPIO:0101109", + "alias": "influenza_subtyping_scheme_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subtyping_scheme_name menu" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "title": "taxonomic_identification_process", + "from_schema": "https://example.com/hpai", + "rank": 24, + "slot_uri": "GENEPIO:0100583", + "alias": "taxonomic_identification_process", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "taxonomic_identification_process menu" + }, + "virus_identifier": { + "name": "virus_identifier", + "title": "virus_identifier", + "from_schema": "https://example.com/hpai", + "rank": 25, + "slot_uri": "GENEPIO:0101110", + "alias": "virus_identifier", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "who_oie_fao_h5_clade": { + "name": "who_oie_fao_h5_clade", + "title": "WHO/OIE/FAO_H5_clade", + "from_schema": "https://example.com/hpai", + "rank": 26, + "slot_uri": "GENEPIO:0101111", + "alias": "who_oie_fao_h5_clade", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected, or sampling began for a continuous sample.", + "title": "sample_collection_date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collection_date" + ], + "rank": 27, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 28, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 29, + "slot_uri": "GENEPIO:0100763", + "alias": "sample_processing_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "host_origin_geo_loc_name_country": { + "name": "host_origin_geo_loc_name_country", + "description": "The country of origin of the host.", + "title": "host_origin_geo_loc_name (country)", + "comments": [ + "If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "South Africa [GAZ:00001094]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 30, + "slot_uri": "GENEPIO:0100438", + "alias": "host_origin_geo_loc_name_country", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "anatomical_material": { + "name": "anatomical_material", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "title": "anatomical_material", + "comments": [ + "An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Tissue [UBERON:0000479]" + }, + { + "value": "Blood [UBERON:0000178]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:anatomical_material", + "BIOSAMPLE_Enterics:host_tissue_sampled", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 31, + "slot_uri": "GENEPIO:0001211", + "alias": "anatomical_material", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "body_product": { + "name": "body_product", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "title": "body_product", + "comments": [ + "A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feces [UBERON:0001988]" + }, + { + "value": "Urine [UBERON:0001088]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:body_product", + "BIOSAMPLE_Enterics:host_body_product", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 32, + "slot_uri": "GENEPIO:0001216", + "alias": "body_product", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "body_product menu" + }, + { + "range": "null value menu" + } + ] + }, + "anatomical_part": { + "name": "anatomical_part", + "description": "An anatomical part of an organism e.g. oropharynx.", + "title": "anatomical_part", + "comments": [ + "An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Snout [UBERON:0006333]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:anatomical_part", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 33, + "slot_uri": "GENEPIO:0001214", + "alias": "anatomical_part", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_part menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection_device", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Drag swab [OBI:0002822]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_device", + "BIOSAMPLE_Enterics:samp_collect_device", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 34, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_device menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "title": "collection_method", + "comments": [ + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Rinsing for specimen collection [GENEPIO_0002116]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_method", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 35, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_method menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 36, + "slot_uri": "GENEPIO:0100768", + "alias": "sample_volume_measurement_value", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "milliliter (mL) [UO:0000098]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 37, + "slot_uri": "GENEPIO:0100769", + "alias": "sample_volume_measurement_unit", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "sample_volume_measurement_unit menu" + }, + "residual_sample_status": { + "name": "residual_sample_status", + "description": "The status of the residual sample (whether any sample remains after its original use).", + "title": "residual_sample_status", + "comments": [ + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + ], + "examples": [ + { + "value": "No residual sample (sample all used) [GENEPIO:0101088]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 38, + "slot_uri": "GENEPIO:0101090", + "alias": "residual_sample_status", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "residual_sample_status menu" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:purpose_of_sampling" + ], + "rank": 39, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sampling menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity": { + "name": "presampling_activity", + "description": "The activities or variables upstream of sample collection that may affect the sample.", + "title": "presampling_activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 40, + "slot_uri": "GENEPIO:0100433", + "alias": "presampling_activity", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "presampling_activity menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the activities or variables that affected the sample collected.", + "title": "presampling_activity_details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 41, + "slot_uri": "GENEPIO:0100434", + "alias": "presampling_activity_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_storage_method": { + "name": "sample_storage_method", + "description": "The process used to store the sample.", + "title": "sample_storage_method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 42, + "slot_uri": "GENEPIO:0100448", + "alias": "sample_storage_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The medium in which a sample is stored.", + "title": "sample_storage_medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 43, + "slot_uri": "GENEPIO:0100449", + "alias": "sample_storage_medium", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 44, + "slot_uri": "GENEPIO:0101014", + "alias": "sample_storage_duration_value", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 45, + "slot_uri": "GENEPIO:0101015", + "alias": "sample_storage_duration_unit", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_storage_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 46, + "slot_uri": "GENEPIO:0001253", + "alias": "specimen_processing", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "specimen_processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 47, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental_protocol", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "from_schema": "https://example.com/hpai", + "rank": 48, + "slot_uri": "GENEPIO:0101029", + "alias": "experimental_protocol", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 49, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "experimental_specimen_role_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "title": "experimental_specimen_details", + "from_schema": "https://example.com/hpai", + "rank": 50, + "slot_uri": "GENEPIO:0101112", + "alias": "experimental_specimen_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "available_data_types": { + "name": "available_data_types", + "description": "The type of data that is available, that may or may not require permission to access.", + "title": "available_data_types", + "comments": [ + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + ], + "examples": [ + { + "value": "Total coliform count [GENEPIO:0100729]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 51, + "slot_uri": "GENEPIO:0100690", + "alias": "available_data_types", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "available_data_types menu" + }, + { + "range": "null value menu" + } + ] + }, + "available_data_type_details": { + "name": "available_data_type_details", + "description": "Detailed information regarding other available data types.", + "title": "available_data_type_details", + "comments": [ + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + ], + "examples": [ + { + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 52, + "slot_uri": "GENEPIO:0101023", + "alias": "available_data_type_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "host_common_name": { + "name": "host_common_name", + "description": "The commonly used name of the host.", + "title": "host_(common_name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name." + ], + "examples": [ + { + "value": "Cow [NCBITaxon:9913]" + }, + { + "value": "Chicken [NCBITaxon:9913], Human [NCBITaxon:9606]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host" + ], + "rank": 53, + "slot_uri": "GENEPIO:0001386", + "alias": "host_common_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "recommended": true, + "any_of": [ + { + "range": "host (common name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_scientific_name": { + "name": "host_scientific_name", + "description": "The taxonomic, or scientific name of the host.", + "title": "host_(scientific_name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided." + ], + "examples": [ + { + "value": "Bos taurus [NCBITaxon:9913]" + }, + { + "value": "Homo sapiens [NCBITaxon:9103]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:host", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:host" + ], + "rank": 54, + "slot_uri": "GENEPIO:0001387", + "alias": "host_scientific_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "recommended": true, + "any_of": [ + { + "range": "host (scientific name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_ecotype": { + "name": "host_ecotype", + "description": "The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler.", + "title": "host_(ecotype)", + "comments": [ + "Provide the name of the ecotype of the host organism." + ], + "examples": [ + { + "value": "Sea ecotype" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_variety" + ], + "rank": 55, + "slot_uri": "GENEPIO:0100450", + "alias": "host_ecotype", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "range": "WhitespaceMinimizedString" + }, + "host_breed": { + "name": "host_breed", + "description": "A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding.", + "title": "host_(breed)", + "comments": [ + "Provide the name of the breed of the host organism." + ], + "examples": [ + { + "value": "Holstein" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:host_disease", + "BIOSAMPLE_Enterics:host_animal_breed" + ], + "rank": 56, + "slot_uri": "GENEPIO:0100451", + "alias": "host_breed", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "range": "WhitespaceMinimizedString" + }, + "host_food_production_name": { + "name": "host_food_production_name", + "description": "The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity.", + "title": "host_(food production name)", + "comments": [ + "Select the host's food production name from the pick list." + ], + "examples": [ + { + "value": "Calf [FOODON:03411349]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host" + ], + "rank": 57, + "slot_uri": "GENEPIO:0100452", + "alias": "host_food_production_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "any_of": [ + { + "range": "host (food production name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_age": { + "name": "host_age", + "description": "Age of host at the time of sampling.", + "title": "host_age", + "comments": [ + "If known, provide age. Age-binning is also acceptable." + ], + "examples": [ + { + "value": "79" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Patient%20age", + "CNPHI:host_age" + ], + "rank": 58, + "slot_uri": "GENEPIO:0001392", + "alias": "host_age", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "required": true, + "maximum_value": 130, + "any_of": [ + { + "range": "decimal" + }, + { + "range": "null value menu" + } + ] + }, + "host_age_unit": { + "name": "host_age_unit", + "description": "The units used to measure the host's age.", + "title": "host_age_unit", + "comments": [ + "If known, provide the age units used to measure the host's age from the pick list." + ], + "examples": [ + { + "value": "year [UO:0000036]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 59, + "slot_uri": "GENEPIO:0001393", + "alias": "host_age_unit", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "required": true, + "any_of": [ + { + "range": "host_age_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_age_bin": { + "name": "host_age_bin", + "description": "Age of host at the time of sampling, expressed as an age group.", + "title": "host_age_bin", + "comments": [ + "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_age" + ], + "rank": 60, + "slot_uri": "GENEPIO:0001394", + "alias": "host_age_bin", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "any_of": [ + { + "range": "host_age_bin menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_disease": { + "name": "host_disease", + "description": "The name of the disease experienced by the host.", + "title": "host_disease", + "comments": [ + "This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”." + ], + "examples": [ + { + "value": "mastitis, gastroenteritis" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_disease" + ], + "rank": 61, + "slot_uri": "GENEPIO:0001391", + "alias": "host_disease", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "any_of": [ + { + "range": "host_disease menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_state": { + "name": "host_health_state", + "description": "Health status of the host at the time of sample collection.", + "title": "host_health_state", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Asymptomatic [NCIT:C3833]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Patient%20status", + "CNPHI:host_health_state" + ], + "rank": 62, + "slot_uri": "GENEPIO:0001388", + "alias": "host_health_state", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "host_health_state menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_status_details": { + "name": "host_health_status_details", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "title": "host_health_status_details", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Hospitalized (ICU) [GENEPIO:0100046]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 63, + "slot_uri": "GENEPIO:0001389", + "alias": "host_health_status_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "host_health_status_details menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_outcome": { + "name": "host_health_outcome", + "description": "Disease outcome in the host.", + "title": "host_health_outcome", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Recovered [NCIT:C49498]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:host_disease_outcome" + ], + "rank": 64, + "slot_uri": "GENEPIO:0001390", + "alias": "host_health_outcome", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "host_health_outcome menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_subject_id": { + "name": "host_subject_id", + "description": "A unique identifier by which each host can be referred to e.g. #131", + "title": "host_subject_ID", + "comments": [ + "Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward." + ], + "examples": [ + { + "value": "BCxy123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:host_subject_id" + ], + "rank": 65, + "slot_uri": "GENEPIO:0001398", + "alias": "host_subject_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "range": "WhitespaceMinimizedString" + }, + "case_id": { + "name": "case_id", + "description": "The identifier used to specify an epidemiologically detected case of disease.", + "title": "case_ID", + "comments": [ + "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing." + ], + "examples": [ + { + "value": "ABCD1234" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 66, + "slot_uri": "GENEPIO:0100281", + "alias": "case_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "range": "WhitespaceMinimizedString" + }, + "symptom_onset_date": { + "name": "symptom_onset_date", + "description": "The date on which the symptoms began or were first noted.", + "title": "symptom_onset_date", + "comments": [ + "If known, provide the symptom onset date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 67, + "slot_uri": "GENEPIO:0001399", + "alias": "symptom_onset_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "signs_and_symptoms": { + "name": "signs_and_symptoms", + "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", + "title": "signs_and_symptoms", + "comments": [ + "Select all of the symptoms experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 68, + "slot_uri": "GENEPIO:0001400", + "alias": "signs_and_symptoms", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "recommended": true, + "any_of": [ + { + "range": "signs_and_symptoms menu" + }, + { + "range": "null value menu" + } + ] + }, + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "description": "Patient pre-existing conditions and risk factors.\nPre-existing condition: A medical condition that existed prior to the current infection.\nRisk Factor: A variable associated with an increased risk of disease or infection.", + "title": "pre-existing_conditions_and_risk_factors", + "comments": [ + "Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Asthma [HP:0002099]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 69, + "slot_uri": "GENEPIO:0001401", + "alias": "preexisting_conditions_and_risk_factors", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "recommended": true, + "any_of": [ + { + "range": "pre-existing_conditions_and_risk_factors menu" + }, + { + "range": "null value menu" + } + ] + }, + "complications": { + "name": "complications", + "description": "Patient medical complications that are believed to have occurred as a result of host disease.", + "title": "complications", + "comments": [ + "Select all of the complications experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Acute respiratory failure [MONDO:0001208]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 70, + "slot_uri": "GENEPIO:0001402", + "alias": "complications", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "recommended": true, + "any_of": [ + { + "range": "complications menu" + }, + { + "range": "null value menu" + } + ] + }, + "exposure_event": { + "name": "exposure_event", + "description": "Event leading to exposure.", + "title": "exposure event", + "comments": [ + "Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Social Gathering" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Additional%20location%20information", + "CNPHI:Exposure%20Event", + "NML_LIMS:PH_EXPOSURE" + ], + "rank": 71, + "slot_uri": "GENEPIO:0001417", + "alias": "exposure_event", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure event menu" + }, + { + "range": "null value menu" + } + ] + }, + "exposure_contact_level": { + "name": "exposure_contact_level", + "description": "The exposure transmission contact type.", + "title": "exposure contact level", + "comments": [ + "Select direct or indirect exposure from the pick-list." + ], + "examples": [ + { + "value": "Direct" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:exposure%20contact%20level" + ], + "rank": 72, + "slot_uri": "GENEPIO:0001418", + "alias": "exposure_contact_level", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure contact level menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_role": { + "name": "host_role", + "description": "The role of the host in relation to the exposure setting.", + "title": "host role", + "comments": [ + "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Inpatient" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_HOST_ROLE" + ], + "rank": 73, + "slot_uri": "GENEPIO:0001419", + "alias": "host_role", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "range": "host role menu", + "multivalued": true + }, + "exposure_setting": { + "name": "exposure_setting", + "description": "The setting leading to exposure.", + "title": "exposure setting", + "comments": [ + "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Healthcare Setting" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE" + ], + "rank": 74, + "slot_uri": "GENEPIO:0001428", + "alias": "exposure_setting", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "range": "exposure setting menu", + "multivalued": true + }, + "exposure_details": { + "name": "exposure_details", + "description": "Additional host exposure information.", + "title": "exposure details", + "comments": [ + "Free text description of the exposure." + ], + "examples": [ + { + "value": "Case infected family at home" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_DETAILS" + ], + "rank": 75, + "slot_uri": "GENEPIO:0001431", + "alias": "exposure_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" + }, + "host_vaccination_status": { + "name": "host_vaccination_status", + "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", + "title": "host_vaccination_status", + "comments": [ + "Select the vaccination status of the host from the pick list." + ], + "examples": [ + { + "value": "Fully Vaccinated [GENEPIO:0100100]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:prior_sars_cov_2_vaccination" + ], + "rank": 76, + "slot_uri": "GENEPIO:0001404", + "alias": "host_vaccination_status", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "host_vaccination_status menu" + }, + { + "range": "null value menu" + } + ] + }, + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", + "description": "The number of doses of the vaccine recived by the host.", + "title": "number_of_vaccine_doses_received", + "comments": [ + "Record how many doses of the vaccine the host has received." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 77, + "slot_uri": "GENEPIO:0001406", + "alias": "number_of_vaccine_doses_received", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "integer", + "minimum_value": 0 + }, + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", + "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", + "title": "vaccination_dose_1_vaccine_name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 78, + "slot_uri": "GENEPIO:0100313", + "alias": "vaccination_dose_1_vaccine_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", + "description": "The date the first dose of a vaccine was administered.", + "title": "vaccination_dose_1_vaccination_date", + "comments": [ + "Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-03-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 79, + "slot_uri": "GENEPIO:0100314", + "alias": "vaccination_dose_1_vaccination_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "date" + }, + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", + "description": "The name of the vaccine administered as the second dose of a vaccine regimen.", + "title": "vaccination_dose_2_vaccine_name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 80, + "slot_uri": "GENEPIO:0100315", + "alias": "vaccination_dose_2_vaccine_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", + "description": "The date the second dose of a vaccine was administered.", + "title": "vaccination_dose_2_vaccination_date", + "comments": [ + "Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-09-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 81, + "slot_uri": "GENEPIO:0100316", + "alias": "vaccination_dose_2_vaccination_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "date" + }, + "vaccination_history": { + "name": "vaccination_history", + "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", + "title": "vaccination history", + "comments": [ + "Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons." + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2021-03-01" + }, + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2022-01-15" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Last%20vaccinated" + ], + "rank": 82, + "slot_uri": "GENEPIO:0100321", + "alias": "vaccination_history", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "influenza_antiviral_treatment_administration": { + "name": "influenza_antiviral_treatment_administration", + "description": "An action of giving or applying an influenza antiviral agent to a patient as part of a treatment regimen.", + "title": "influenza_antiviral_treatment_administration", + "examples": [ + { + "value": "Influenza antiviral treatment administered [GENEPIO:0101194]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 83, + "slot_uri": "GENEPIO:0101113", + "alias": "influenza_antiviral_treatment_administration", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host treatment information", + "any_of": [ + { + "range": "influenza_antiviral_treatment_administration menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_antiviral_agent__": { + "name": "influenza_antiviral_agent__", + "description": "A substance that destroys or inhibits replication of viruses.", + "title": "influenza_antiviral_agent", + "from_schema": "https://example.com/hpai", + "rank": 84, + "slot_uri": "GENEPIO:0101114", + "alias": "influenza_antiviral_agent__", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host treatment information", + "range": "WhitespaceMinimizedString" + }, + "influenza_antiviral_treatment_date": { + "name": "influenza_antiviral_treatment_date", + "description": "The date on which the influenza antiviral agent was administered to a patient as part of treatment", + "title": "influenza_antiviral_treatment_date", + "comments": [ + "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given." + ], + "from_schema": "https://example.com/hpai", + "rank": 85, + "slot_uri": "GENEPIO:0101115", + "alias": "influenza_antiviral_treatment_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host treatment information", + "range": "date" + }, + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library_ID", + "comments": [ + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "LS_2010_NP_123446" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 86, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing_assay_type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 87, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "sequencing_assay_type menu" + }, + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 88, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "date" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "description": "The reason that the sample was sequenced.", + "title": "purpose_of_sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 89, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing__", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sequencing menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose_of_sequencing_details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 90, + "slot_uri": "GENEPIO:0001446", + "alias": "purpose_of_sequencing_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:sequenced_by", + "BIOSAMPLE_Enterics:sequenced_by" + ], + "rank": 91, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 92, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 93, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 94, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence_submitted_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 95, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequence_submitter_contact_email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 96, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic_acid_extraction_method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 97, + "slot_uri": "GENEPIO:0100939", + "alias": "nucleic_acid_extraction_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic_acid_extraction_kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 98, + "slot_uri": "GENEPIO:0100772", + "alias": "nucleic_acid_extraction_kit", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "description": "The description of the endogenous controls included when extracting a sample.", + "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], + "from_schema": "https://example.com/hpai", + "rank": 99, + "slot_uri": "GENEPIO:0100923", + "alias": "endogenous_control_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "AMR-GRDI (PA-1356)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 100, + "slot_uri": "GENEPIO:0100472", + "alias": "sequencing_project_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing_platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 101, + "slot_uri": "GENEPIO:0100473", + "alias": "sequencing_platform", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_platform menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing_instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 102, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_instrument menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library_preparation_kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 103, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA_fragment_length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 104, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 105, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "genomic_target_enrichment_method menu" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method_details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ + { + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 106, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon_pcr_primer_scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 107, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon_size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 108, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing_flow_cell_version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 109, + "slot_uri": "GENEPIO:0101102", + "alias": "sequencing_flow_cell_version", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing_protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 110, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1_fastq_filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 111, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2_fastq_filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 112, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5_filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "batch1a_sequences.fast5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 113, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 114, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "assembly_filename": { + "name": "assembly_filename", + "description": "The user-defined filename of the FASTA file.", + "title": "assembly_filename", + "comments": [ + "Provide the FASTA filename." + ], + "examples": [ + { + "value": "pathogenassembly123.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 115, + "slot_uri": "GENEPIO:0001461", + "alias": "assembly_filename", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 116, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 117, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 118, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_determination menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 119, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_issues menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 120, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 121, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 122, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 123, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 124, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 125, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 126, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 127, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 128, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 129, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 130, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 131, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 132, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 133, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 134, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 135, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 136, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 137, + "slot_uri": "GENEPIO:0001484", + "alias": "ns_per_100_kbp", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 138, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 139, + "slot_uri": "GENEPIO:0100845", + "alias": "percent_read_contamination_", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 140, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "The length of the genome defined by the most common nucleotides at each position.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 141, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 142, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 143, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 144, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 145, + "slot_uri": "GENEPIO:0100832", + "alias": "read_mapping_software_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 146, + "slot_uri": "GENEPIO:0100833", + "alias": "read_mapping_software_version", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 147, + "slot_uri": "GENEPIO:0100834", + "alias": "taxonomic_reference_database_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 148, + "slot_uri": "GENEPIO:0100835", + "alias": "taxonomic_reference_database_version", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 149, + "slot_uri": "GENEPIO:0101074", + "alias": "taxonomic_analysis_report_filename", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 150, + "slot_uri": "GENEPIO:0101075", + "alias": "taxonomic_analysis_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "date" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 151, + "slot_uri": "GENEPIO:0100836", + "alias": "read_mapping_criteria", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "description": "The name of the genetic marker used for testing.", + "title": "genetic target name", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 152, + "slot_uri": "GENEPIO:0101116", + "alias": "genetic_target_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "genetic_target_region": { + "name": "genetic_target_region", + "description": "The specific region or segment of a genetic sequence used for testing or analysis.", + "title": "genetic target region", + "from_schema": "https://example.com/hpai", + "rank": 153, + "slot_uri": "GENEPIO:0101117", + "alias": "genetic_target_region", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", + "title": "genetic target region reference genome", + "from_schema": "https://example.com/hpai", + "rank": 154, + "slot_uri": "GENEPIO:0101118", + "alias": "genetic_target_region_reference_genome", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 155, + "slot_uri": "GENEPIO:0100962", + "alias": "diagnostic_target_presence", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic target presence menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 156, + "slot_uri": "GENEPIO:0100963", + "alias": "diagnostic_measurement_value", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 157, + "slot_uri": "GENEPIO:0100964", + "alias": "diagnostic_measurement_unit", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 158, + "slot_uri": "GENEPIO:0100965", + "alias": "diagnostic_measurement_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement method menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold value", + "from_schema": "https://example.com/hpai", + "rank": 159, + "slot_uri": "GENEPIO:0101104", + "alias": "diagnostic_testing_threshold_value", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "integer" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold units", + "from_schema": "https://example.com/hpai", + "rank": 160, + "slot_uri": "GENEPIO:0101105", + "alias": "diagnostic_testing_threshold_units", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "description": "Describe any details of the diagnsotic testing.", + "title": "diagnostic testing details", + "from_schema": "https://example.com/hpai", + "rank": 161, + "slot_uri": "GENEPIO:0101106", + "alias": "diagnostic_testing_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", + "title": "prevalence_metrics", + "comments": [ + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + ], + "examples": [ + { + "value": "Number of total samples collected, Number of positive samples" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 162, + "slot_uri": "GENEPIO:0100480", + "alias": "prevalence_metrics", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "description": "The details pertaining to the prevalence metrics from a surveillance project.", + "title": "prevalence_metrics_details", + "comments": [ + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + ], + "examples": [ + { + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 163, + "slot_uri": "GENEPIO:0100481", + "alias": "prevalence_metrics_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "stage_of_production": { + "name": "stage_of_production", + "description": "The stage of food production.", + "title": "stage_of_production", + "comments": [ + "Provide the stage of food production as free text." + ], + "examples": [ + { + "value": "Abattoir [ENVO:01000925]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 164, + "slot_uri": "GENEPIO:0100482", + "alias": "stage_of_production", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "any_of": [ + { + "range": "stage_of_production menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_intervention": { + "name": "experimental_intervention", + "description": "The category of the experimental intervention applied in the food production system.", + "title": "experimental_intervention", + "comments": [ + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + ], + "examples": [ + { + "value": "Vaccination [NCIT:C15346]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 165, + "slot_uri": "GENEPIO:0100483", + "alias": "experimental_intervention", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "experimental_intervention menu" + }, + { + "range": "null value menu" + } + ] + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "description": "The details of the experimental intervention applied in the food production system.", + "title": "experiment_intervention_details", + "comments": [ + "If an experimental intervention was applied in the survey, provide details in this field as free text." + ], + "examples": [ + { + "value": "2% cranberry solution mixed in feed" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 166, + "slot_uri": "GENEPIO:0100484", + "alias": "experiment_intervention_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + } + } + } + }, + "settings": { + "Title_Case": { + "setting_key": "Title_Case", + "setting_value": "(((?<=\\b)[^a-z\\W]\\w*?|[\\W])+)" + }, + "UPPER_CASE": { + "setting_key": "UPPER_CASE", + "setting_value": "[A-Z\\W\\d_]*" + }, + "lower_case": { + "setting_key": "lower_case", + "setting_value": "[a-z\\W\\d_]*" + } + }, + "@type": "SchemaDefinition" +} \ No newline at end of file diff --git a/web/templates/hpai/schema.yaml b/web/templates/hpai/schema.yaml new file mode 100644 index 00000000..83dafead --- /dev/null +++ b/web/templates/hpai/schema.yaml @@ -0,0 +1,15257 @@ +id: https://example.com/hpai +name: Mpox +version: 4.3.3 +description: The HPAI specification was developed by the Public Health Alliance for + Genomic Epidemiology (PHA4GE) to better enable harmonization of highly pathogenic + avian influenza genomic surveillance contextual data. The specification is intended + to support H5N1 monitoring, and provides standardized, ontology-based fields and + terms for samples, sequences, and bioinformatics analysis. +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + GENEPIO: http://purl.obolibrary.org/obo/GENEPIO_ +classes: + dh_interface: + name: dh_interface + description: A DataHarmonizer interface + from_schema: https://example.com/hpai + HPAI: + name: HPAI + title: HPAI + description: null + is_a: dh_interface + see_also: null + annotations: + version: 1.0.0 + slots: + - specimen_collector_sample_id + - specimen_collector_subsample_id + - pooled_sample_id + - sampling_site_id + - sampling_event_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - insdc_assembly_accession + - sample_collection_data_steward_name + - sample_collection_data_steward_contact_email + - sample_collected_by + - sample_collector_contact_email + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_name_site__ + - geo_loc_latitude + - geo_loc_longitude + - organism + - influenza_subtype + - influenza_subtyping_scheme_name + - taxonomic_identification_process + - virus_identifier + - who_oie_fao_h5_clade + - sample_collection_date + - sample_collection_end_date + - sample_collection_start_time + - sample_collection_end_time + - sample_collection_time_of_day + - sample_collection_time_duration_value + - sample_collection_time_duration_unit + - sample_received_date + - sample_processing_date + - host_origin_geo_loc_name_country + - food_product_origin_geo_loc_name_country + - food_product + - food_product_properties + - food_packaging + - food_quality_date + - food_packaging_date + - environmental_site + - environmental_material + - anatomical_material + - body_product + - anatomical_part + - collection_device + - collection_method + - sample_volume_measurement_value + - sample_volume_measurement_unit + - residual_sample_status + - purpose_of_sampling + - presampling_activity + - presampling_activity_details + - sample_storage_method + - sample_storage_medium + - sample_storage_duration_value + - sample_storage_duration_unit + - specimen_processing + - specimen_processing_details + - experimental_protocol + - experimental_specimen_role_type + - experimental_specimen_details + - available_data_types + - available_data_type_details + - host_common_name + - host_scientific_name + - host_ecotype + - host_breed + - host_food_production_name + - host_age + - host_age_unit + - host_age_bin + - host_disease + - host_health_state + - host_health_status_details + - host_health_outcome + - host_subject_id + - case_id + - symptom_onset_date + - signs_and_symptoms + - preexisting_conditions_and_risk_factors + - complications + - exposure_event + - exposure_contact_level + - host_role + - exposure_setting + - exposure_details + - host_vaccination_status + - number_of_vaccine_doses_received + - vaccination_dose_1_vaccine_name + - vaccination_dose_1_vaccination_date + - vaccination_dose_2_vaccine_name + - vaccination_dose_2_vaccination_date + - vaccination_history + - influenza_antiviral_treatment_administration + - influenza_antiviral_agent__ + - influenza_antiviral_treatment_date + - water_catchment_area_human_population_measurement_value + - water_catchment_area_human_population_range + - water_catchment_area_human_population_measurement_method + - water_catchment_area_human_population_density_value + - water_catchment_area_human_population_density_unit + - populated_area_type + - sampling_weather_conditions + - presampling_weather_conditions + - precipitation_measurement_value + - water_depth + - water_depth_units + - sediment_depth + - sediment_depth_units + - air_temperature + - air_temperature_units + - water_temperature + - water_temperature_units + - weather_type + - precipitation_measurement_unit + - precipitation_measurement_method + - ambient_temperature_measurement_value + - ambient_temperature_measurement_unit + - ph_measurement_value + - ph_measurement_method + - total_daily_flow_rate_measurement_value + - total_daily_flow_rate_measurement_unit + - total_daily_flow_rate_measurement_method + - instantaneous_flow_rate_measurement_value + - instantaneous_flow_rate_measurement_unit + - instantaneous_flow_rate_measurement_method + - turbidity_measurement_value + - turbidity_measurement_unit + - turbidity_measurement_method + - dissolved_oxygen_measurement_value + - dissolved_oxygen_measurement_unit + - dissolved_oxygen_measurement_method + - oxygen_reduction_potential_orp_measurement_value + - oxygen_reduction_potential_orp_measurement_unit + - oxygen_reduction_potential_orp_measurement_method + - chemical_oxygen_demand_cod_measurement_value + - chemical_oxygen_demand_cod_measurement_unit + - chemical_oxygen_demand_cod_measurement_method + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_value + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_method + - total_suspended_solids_tss_measurement_value + - total_suspended_solids_tss_measurement_unit + - total_suspended_solids_tss_measurement_method + - total_dissolved_solids_tds_measurement_value + - total_dissolved_solids_tds_measurement_unit + - total_dissolved_solids_tds_measurement_method + - total_solids_ts_measurement_value + - total_solids_ts_measurement_unit + - total_solids_ts_measurement_method + - alkalinity_measurement_value + - alkalinity_measurement_unit + - alkalinity_measurement_method + - conductivity_measurement_value + - conductivity_measurement_unit + - conductivity_measurement_method + - salinity_measurement_value + - salinity_measurement_unit + - salinity_measurement_method + - total_nitrogen_tn_measurement_value + - total_nitrogen_tn_measurement_unit + - total_nitrogen_tn_measurement_method + - total_phosphorus_tp_measurement_value + - total_phosphorus_tp_measurement_unit + - total_phosphorus_tp_measurement_method + - fecal_contamination_indicator_ + - fecal_contamination_value + - fecal_contamination_unit + - fecal_contamination_method + - fecal_coliform_count_value + - fecal_coliform_count_unit + - fecal_coliform_count_method + - urinary_contamination_indicator + - urinary_contamination_value + - urinary_contamination_unit + - urinary_contamination_method + - sample_temperature_value_at_collection + - sample_temperature_unit_at_collection + - sample_temperature_value_when_received + - sample_temperature_unit_when_received + - library_id + - sequencing_assay_type + - sequencing_date + - purpose_of_sequencing__ + - purpose_of_sequencing_details + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequence_submitted_by + - sequence_submitter_contact_email + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - endogenous_control_details + - sequencing_project_name + - sequencing_platform + - sequencing_instrument + - library_preparation_kit + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - sequencing_flow_cell_version + - sequencing_protocol + - r1_fastq_filename + - r2_fastq_filename + - fast5_filename + - genome_sequence_file_name + - assembly_filename + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - sequence_assembly_software_name + - sequence_assembly_software_version + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - genome_completeness + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - number_of_contigs + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - n50 + - percent_read_contamination_ + - sequence_assembly_length + - consensus_genome_length + - reference_genome_accession + - deduplication_method + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria + - genetic_target_name + - genetic_target_region + - genetic_target_region_reference_genome + - diagnostic_target_presence + - diagnostic_measurement_value + - diagnostic_measurement_unit + - diagnostic_measurement_method + - diagnostic_testing_threshold_value + - diagnostic_testing_threshold_units + - diagnostic_testing_details + - prevalence_metrics + - prevalence_metrics_details + - stage_of_production + - experimental_intervention + - experiment_intervention_details + slot_usage: + specimen_collector_sample_id: + rank: 1 + slot_group: Database identifiers + specimen_collector_subsample_id: + rank: 2 + slot_group: Database identifiers + pooled_sample_id: + rank: 3 + slot_group: Database identifiers + sampling_site_id: + rank: 4 + slot_group: Database identifiers + sampling_event_id: + rank: 5 + slot_group: Database identifiers + bioproject_accession: + rank: 6 + slot_group: Database identifiers + biosample_accession: + rank: 7 + slot_group: Database identifiers + insdc_sequence_read_accession: + rank: 8 + slot_group: Database identifiers + insdc_assembly_accession: + rank: 9 + slot_group: Database identifiers + sample_collection_data_steward_name: + rank: 10 + slot_group: Sample collection and processing + sample_collection_data_steward_contact_email: + rank: 11 + slot_group: Sample collection and processing + sample_collected_by: + rank: 12 + slot_group: Sample collection and processing + sample_collector_contact_email: + rank: 13 + slot_group: Sample collection and processing + geo_loc_name_country: + rank: 14 + slot_group: Sample collection and processing + geo_loc_name_state_province_territory: + rank: 15 + slot_group: Sample collection and processing + geo_loc_name_county_region: + rank: 16 + slot_group: Sample collection and processing + geo_loc_name_city: + rank: 17 + slot_group: Sample collection and processing + geo_loc_name_site__: + rank: 18 + slot_group: Sample collection and processing + geo_loc_latitude: + rank: 19 + slot_group: Sample collection and processing + geo_loc_longitude: + rank: 20 + slot_group: Sample collection and processing + organism: + rank: 21 + slot_group: Sample collection and processing + influenza_subtype: + rank: 22 + slot_group: Sample collection and processing + influenza_subtyping_scheme_name: + rank: 23 + slot_group: Sample collection and processing + taxonomic_identification_process: + rank: 24 + slot_group: Sample collection and processing + virus_identifier: + rank: 25 + slot_group: Sample collection and processing + who_oie_fao_h5_clade: + rank: 26 + slot_group: Sample collection and processing + sample_collection_date: + rank: 27 + slot_group: Sample collection and processing + sample_collection_end_date: + rank: 28 + slot_group: Sample collection and processing + sample_collection_start_time: + rank: 29 + slot_group: Sample collection and processing + sample_collection_end_time: + rank: 30 + slot_group: Sample collection and processing + sample_collection_time_of_day: + rank: 31 + slot_group: Sample collection and processing + sample_collection_time_duration_value: + rank: 32 + slot_group: Sample collection and processing + sample_collection_time_duration_unit: + rank: 33 + slot_group: Sample collection and processing + sample_received_date: + rank: 34 + slot_group: Sample collection and processing + sample_processing_date: + rank: 35 + slot_group: Sample collection and processing + host_origin_geo_loc_name_country: + rank: 36 + slot_group: Sample collection and processing + food_product_origin_geo_loc_name_country: + rank: 37 + slot_group: Sample collection and processing + food_product: + rank: 38 + slot_group: Sample collection and processing + food_product_properties: + rank: 39 + slot_group: Sample collection and processing + food_packaging: + rank: 40 + slot_group: Sample collection and processing + food_quality_date: + rank: 41 + slot_group: Sample collection and processing + food_packaging_date: + rank: 42 + slot_group: Sample collection and processing + environmental_site: + rank: 43 + slot_group: Sample collection and processing + environmental_material: + rank: 44 + slot_group: Sample collection and processing + anatomical_material: + rank: 45 + slot_group: Sample collection and processing + body_product: + rank: 46 + slot_group: Sample collection and processing + anatomical_part: + rank: 47 + slot_group: Sample collection and processing + collection_device: + rank: 48 + slot_group: Sample collection and processing + collection_method: + rank: 49 + slot_group: Sample collection and processing + sample_volume_measurement_value: + rank: 50 + slot_group: Sample collection and processing + sample_volume_measurement_unit: + rank: 51 + slot_group: Sample collection and processing + residual_sample_status: + rank: 52 + slot_group: Sample collection and processing + purpose_of_sampling: + rank: 53 + slot_group: Sample collection and processing + presampling_activity: + rank: 54 + slot_group: Sample collection and processing + presampling_activity_details: + rank: 55 + slot_group: Sample collection and processing + sample_storage_method: + rank: 56 + slot_group: Sample collection and processing + sample_storage_medium: + rank: 57 + slot_group: Sample collection and processing + sample_storage_duration_value: + rank: 58 + slot_group: Sample collection and processing + sample_storage_duration_unit: + rank: 59 + slot_group: Sample collection and processing + specimen_processing: + rank: 60 + slot_group: Sample collection and processing + specimen_processing_details: + rank: 61 + slot_group: Sample collection and processing + experimental_protocol: + rank: 62 + slot_group: Sample collection and processing + experimental_specimen_role_type: + rank: 63 + slot_group: Sample collection and processing + experimental_specimen_details: + rank: 64 + slot_group: Sample collection and processing + available_data_types: + rank: 65 + slot_group: Sample collection and processing + available_data_type_details: + rank: 66 + slot_group: Sample collection and processing + host_common_name: + rank: 67 + slot_group: Host information + host_scientific_name: + rank: 68 + slot_group: Host information + host_ecotype: + rank: 69 + slot_group: Host information + host_breed: + rank: 70 + slot_group: Host information + host_food_production_name: + rank: 71 + slot_group: Host information + host_age: + rank: 72 + slot_group: Host Information + host_age_unit: + rank: 73 + slot_group: Host Information + host_age_bin: + rank: 74 + slot_group: Host information + host_disease: + rank: 75 + slot_group: Host information + host_health_state: + rank: 76 + slot_group: Host Information + host_health_status_details: + rank: 77 + slot_group: Host Information + host_health_outcome: + rank: 78 + slot_group: Host Information + host_subject_id: + rank: 79 + slot_group: Host Information + case_id: + rank: 80 + slot_group: Host Information + symptom_onset_date: + rank: 81 + slot_group: Host Information + signs_and_symptoms: + rank: 82 + slot_group: Host Information + preexisting_conditions_and_risk_factors: + rank: 83 + slot_group: Host Information + complications: + rank: 84 + slot_group: Host Information + exposure_event: + rank: 85 + slot_group: Host exposure information + exposure_contact_level: + rank: 86 + slot_group: Host exposure information + host_role: + rank: 87 + slot_group: Host exposure information + exposure_setting: + rank: 88 + slot_group: Host exposure information + exposure_details: + rank: 89 + slot_group: Host exposure information + host_vaccination_status: + rank: 90 + slot_group: Host vaccination information + number_of_vaccine_doses_received: + rank: 91 + slot_group: Host vaccination information + vaccination_dose_1_vaccine_name: + rank: 92 + slot_group: Host vaccination information + vaccination_dose_1_vaccination_date: + rank: 93 + slot_group: Host vaccination information + vaccination_dose_2_vaccine_name: + rank: 94 + slot_group: Host vaccination information + vaccination_dose_2_vaccination_date: + rank: 95 + slot_group: Host vaccination information + vaccination_history: + rank: 96 + slot_group: Host vaccination information + influenza_antiviral_treatment_administration: + rank: 97 + slot_group: Host treatment information + influenza_antiviral_agent__: + rank: 98 + slot_group: Host treatment information + influenza_antiviral_treatment_date: + rank: 99 + slot_group: Host treatment information + water_catchment_area_human_population_measurement_value: + rank: 100 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_range: + rank: 101 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_measurement_method: + rank: 102 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_density_value: + rank: 103 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_density_unit: + rank: 104 + slot_group: Environmental conditions and measurements + populated_area_type: + rank: 105 + slot_group: Environmental conditions and measurements + sampling_weather_conditions: + rank: 106 + slot_group: Environmental conditions and measurements + presampling_weather_conditions: + rank: 107 + slot_group: Environmental conditions and measurements + precipitation_measurement_value: + rank: 108 + slot_group: Environmental conditions and measurements + water_depth: + rank: 109 + slot_group: Environmental conditions and measurements + water_depth_units: + rank: 110 + slot_group: Environmental conditions and measurements + sediment_depth: + rank: 111 + slot_group: Environmental conditions and measurements + sediment_depth_units: + rank: 112 + slot_group: Environmental conditions and measurements + air_temperature: + rank: 113 + slot_group: Environmental conditions and measurements + air_temperature_units: + rank: 114 + slot_group: Environmental conditions and measurements + water_temperature: + rank: 115 + slot_group: Environmental conditions and measurements + water_temperature_units: + rank: 116 + slot_group: Environmental conditions and measurements + weather_type: + rank: 117 + slot_group: Environmental conditions and measurements + precipitation_measurement_unit: + rank: 118 + slot_group: Environmental conditions and measurements + precipitation_measurement_method: + rank: 119 + slot_group: Environmental conditions and measurements + ambient_temperature_measurement_value: + rank: 120 + slot_group: Environmental conditions and measurements + ambient_temperature_measurement_unit: + rank: 121 + slot_group: Environmental conditions and measurements + ph_measurement_value: + rank: 122 + slot_group: Environmental conditions and measurements + ph_measurement_method: + rank: 123 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_value: + rank: 124 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_unit: + rank: 125 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_method: + rank: 126 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_value: + rank: 127 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_unit: + rank: 128 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_method: + rank: 129 + slot_group: Environmental conditions and measurements + turbidity_measurement_value: + rank: 130 + slot_group: Environmental conditions and measurements + turbidity_measurement_unit: + rank: 131 + slot_group: Environmental conditions and measurements + turbidity_measurement_method: + rank: 132 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_value: + rank: 133 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_unit: + rank: 134 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_method: + rank: 135 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_value: + rank: 136 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_unit: + rank: 137 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_method: + rank: 138 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_value: + rank: 139 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_unit: + rank: 140 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_method: + rank: 141 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: + rank: 142 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: + rank: 143 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: + rank: 144 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_value: + rank: 145 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_unit: + rank: 146 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_method: + rank: 147 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_value: + rank: 148 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_unit: + rank: 149 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_method: + rank: 150 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_value: + rank: 151 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_unit: + rank: 152 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_method: + rank: 153 + slot_group: Environmental conditions and measurements + alkalinity_measurement_value: + rank: 154 + slot_group: Environmental conditions and measurements + alkalinity_measurement_unit: + rank: 155 + slot_group: Environmental conditions and measurements + alkalinity_measurement_method: + rank: 156 + slot_group: Environmental conditions and measurements + conductivity_measurement_value: + rank: 157 + slot_group: Environmental conditions and measurements + conductivity_measurement_unit: + rank: 158 + slot_group: Environmental conditions and measurements + conductivity_measurement_method: + rank: 159 + slot_group: Environmental conditions and measurements + salinity_measurement_value: + rank: 160 + slot_group: Environmental conditions and measurements + salinity_measurement_unit: + rank: 161 + slot_group: Environmental conditions and measurements + salinity_measurement_method: + rank: 162 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_value: + rank: 163 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_unit: + rank: 164 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_method: + rank: 165 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_value: + rank: 166 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_unit: + rank: 167 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_method: + rank: 168 + slot_group: Environmental conditions and measurements + fecal_contamination_indicator_: + rank: 169 + slot_group: Environmental conditions and measurements + fecal_contamination_value: + rank: 170 + slot_group: Environmental conditions and measurements + fecal_contamination_unit: + rank: 171 + slot_group: Environmental conditions and measurements + fecal_contamination_method: + rank: 172 + slot_group: Environmental conditions and measurements + fecal_coliform_count_value: + rank: 173 + slot_group: Environmental conditions and measurements + fecal_coliform_count_unit: + rank: 174 + slot_group: Environmental conditions and measurements + fecal_coliform_count_method: + rank: 175 + slot_group: Environmental conditions and measurements + urinary_contamination_indicator: + rank: 176 + slot_group: Environmental conditions and measurements + urinary_contamination_value: + rank: 177 + slot_group: Environmental conditions and measurements + urinary_contamination_unit: + rank: 178 + slot_group: Environmental conditions and measurements + urinary_contamination_method: + rank: 179 + slot_group: Environmental conditions and measurements + sample_temperature_value_at_collection: + rank: 180 + slot_group: Environmental conditions and measurements + sample_temperature_unit_at_collection: + rank: 181 + slot_group: Environmental conditions and measurements + sample_temperature_value_when_received: + rank: 182 + slot_group: Environmental conditions and measurements + sample_temperature_unit_when_received: + rank: 183 + slot_group: Environmental conditions and measurements + library_id: + rank: 184 + slot_group: Sequence information + sequencing_assay_type: + rank: 185 + slot_group: Sequence information + sequencing_date: + rank: 186 + slot_group: Sequence information + purpose_of_sequencing__: + rank: 187 + slot_group: Sequence information + purpose_of_sequencing_details: + rank: 188 + slot_group: Sequence information + sequenced_by: + rank: 189 + slot_group: Sequence information + sequenced_by_laboratory_name: + rank: 190 + slot_group: Sequence information + sequenced_by_contact_name: + rank: 191 + slot_group: Sequence information + sequenced_by_contact_email: + rank: 192 + slot_group: Sequence information + sequence_submitted_by: + rank: 193 + slot_group: Sequence information + sequence_submitter_contact_email: + rank: 194 + slot_group: Sequence information + nucleic_acid_extraction_method: + rank: 195 + slot_group: Sample collection and processing + nucleic_acid_extraction_kit: + rank: 196 + slot_group: Sample collection and processing + endogenous_control_details: + rank: 197 + slot_group: Sample collection and processing + sequencing_project_name: + rank: 198 + slot_group: Sequence information + sequencing_platform: + rank: 199 + slot_group: Sequence information + sequencing_instrument: + rank: 200 + slot_group: Sequence information + library_preparation_kit: + rank: 201 + slot_group: Sequence information + dna_fragment_length: + rank: 202 + slot_group: Sequence information + genomic_target_enrichment_method: + rank: 203 + slot_group: Sequence information + genomic_target_enrichment_method_details: + rank: 204 + slot_group: Sequence information + amplicon_pcr_primer_scheme: + rank: 205 + slot_group: Sequence information + amplicon_size: + rank: 206 + slot_group: Sequence information + sequencing_flow_cell_version: + rank: 207 + slot_group: Sequence information + sequencing_protocol: + rank: 208 + slot_group: Sequence information + r1_fastq_filename: + rank: 209 + slot_group: Sequence information + r2_fastq_filename: + rank: 210 + slot_group: Sequence information + fast5_filename: + rank: 211 + slot_group: Sequence information + genome_sequence_file_name: + rank: 212 + slot_group: Sequence information + assembly_filename: + rank: 213 + slot_group: Sequence information + quality_control_method_name: + rank: 214 + slot_group: Bioinformatics and QC metrics + quality_control_method_version: + rank: 215 + slot_group: Bioinformatics and QC metrics + quality_control_determination: + rank: 216 + slot_group: Bioinformatics and QC metrics + quality_control_issues: + rank: 217 + slot_group: Bioinformatics and QC metrics + quality_control_details: + rank: 218 + slot_group: Bioinformatics and QC metrics + raw_sequence_data_processing_method: + rank: 219 + slot_group: Bioinformatics and QC metrics + dehosting_method: + rank: 220 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_name: + rank: 221 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_version: + rank: 222 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_name: + rank: 223 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_version: + rank: 224 + slot_group: Bioinformatics and QC metrics + breadth_of_coverage_value: + rank: 225 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_value: + rank: 226 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_threshold: + rank: 227 + slot_group: Bioinformatics and QC metrics + genome_completeness: + rank: 228 + slot_group: Bioinformatics and QC metrics + number_of_base_pairs_sequenced: + rank: 229 + slot_group: Bioinformatics and QC metrics + number_of_total_reads: + rank: 230 + slot_group: Bioinformatics and QC metrics + number_of_unique_reads: + rank: 231 + slot_group: Bioinformatics and QC metrics + minimum_posttrimming_read_length: + rank: 232 + slot_group: Bioinformatics and QC metrics + number_of_contigs: + rank: 233 + slot_group: Bioinformatics and QC metrics + percent_ns_across_total_genome_length: + rank: 234 + slot_group: Bioinformatics and QC metrics + ns_per_100_kbp: + rank: 235 + slot_group: Bioinformatics and QC metrics + n50: + rank: 236 + slot_group: Bioinformatics and QC metrics + percent_read_contamination_: + rank: 237 + slot_group: Bioinformatics and QC metrics + sequence_assembly_length: + rank: 238 + slot_group: Bioinformatics and QC metrics + consensus_genome_length: + rank: 239 + slot_group: Bioinformatics and QC metrics + reference_genome_accession: + rank: 240 + slot_group: Bioinformatics and QC metrics + deduplication_method: + rank: 241 + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: + rank: 242 + slot_group: Bioinformatics and QC metrics + read_mapping_software_name: + rank: 243 + slot_group: Taxonomic identification information + read_mapping_software_version: + rank: 244 + slot_group: Taxonomic identification information + taxonomic_reference_database_name: + rank: 245 + slot_group: Taxonomic identification information + taxonomic_reference_database_version: + rank: 246 + slot_group: Taxonomic identification information + taxonomic_analysis_report_filename: + rank: 247 + slot_group: Taxonomic identification information + taxonomic_analysis_date: + rank: 248 + slot_group: Taxonomic identification information + read_mapping_criteria: + rank: 249 + slot_group: Taxonomic identification information + genetic_target_name: + rank: 250 + slot_group: Pathogen diagnostic testing + genetic_target_region: + rank: 251 + slot_group: Pathogen diagnostic testing + genetic_target_region_reference_genome: + rank: 252 + slot_group: Pathogen diagnostic testing + diagnostic_target_presence: + rank: 253 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value: + rank: 254 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit: + rank: 255 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method: + rank: 256 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_value: + rank: 257 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_units: + rank: 258 + slot_group: Pathogen diagnostic testing + diagnostic_testing_details: + rank: 259 + slot_group: Pathogen diagnostic testing + prevalence_metrics: + rank: 260 + slot_group: Risk assessment information + prevalence_metrics_details: + rank: 261 + slot_group: Risk assessment information + stage_of_production: + rank: 262 + slot_group: Risk assessment information + experimental_intervention: + rank: 263 + slot_group: Risk assessment information + experiment_intervention_details: + rank: 264 + slot_group: Risk assessment information + HPAIFood: + name: HPAIFood + title: HPAI Food + description: null + is_a: dh_interface + see_also: null + annotations: + version: 1.0.0 + slots: + - specimen_collector_sample_id + - specimen_collector_subsample_id + - pooled_sample_id + - sampling_site_id + - sampling_event_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - insdc_assembly_accession + - sample_collection_data_steward_name + - sample_collection_data_steward_contact_email + - sample_collected_by + - sample_collector_contact_email + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_name_site__ + - geo_loc_latitude + - geo_loc_longitude + - organism + - influenza_subtype + - influenza_subtyping_scheme_name + - taxonomic_identification_process + - virus_identifier + - who_oie_fao_h5_clade + - sample_collection_date + - sample_received_date + - sample_processing_date + - food_product_origin_geo_loc_name_country + - food_product + - food_product_properties + - food_packaging + - food_quality_date + - food_packaging_date + - environmental_site + - environmental_material + - collection_device + - collection_method + - sample_volume_measurement_value + - sample_volume_measurement_unit + - residual_sample_status + - purpose_of_sampling + - presampling_activity + - presampling_activity_details + - sample_storage_method + - sample_storage_medium + - sample_storage_duration_value + - sample_storage_duration_unit + - specimen_processing + - specimen_processing_details + - experimental_protocol + - experimental_specimen_role_type + - experimental_specimen_details + - available_data_types + - available_data_type_details + - library_id + - sequencing_assay_type + - sequencing_date + - purpose_of_sequencing__ + - purpose_of_sequencing_details + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequence_submitted_by + - sequence_submitter_contact_email + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - endogenous_control_details + - sequencing_project_name + - sequencing_platform + - sequencing_instrument + - library_preparation_kit + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - sequencing_flow_cell_version + - sequencing_protocol + - r1_fastq_filename + - r2_fastq_filename + - fast5_filename + - genome_sequence_file_name + - assembly_filename + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - sequence_assembly_software_name + - sequence_assembly_software_version + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - genome_completeness + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - number_of_contigs + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - n50 + - percent_read_contamination_ + - sequence_assembly_length + - consensus_genome_length + - reference_genome_accession + - deduplication_method + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria + - genetic_target_name + - genetic_target_region + - genetic_target_region_reference_genome + - diagnostic_target_presence + - diagnostic_measurement_value + - diagnostic_measurement_unit + - diagnostic_measurement_method + - diagnostic_testing_threshold_value + - diagnostic_testing_threshold_units + - diagnostic_testing_details + - prevalence_metrics + - prevalence_metrics_details + - stage_of_production + - experimental_intervention + - experiment_intervention_details + slot_usage: + specimen_collector_sample_id: + rank: 1 + slot_group: Database identifiers + specimen_collector_subsample_id: + rank: 2 + slot_group: Database identifiers + pooled_sample_id: + rank: 3 + slot_group: Database identifiers + sampling_site_id: + rank: 4 + slot_group: Database identifiers + sampling_event_id: + rank: 5 + slot_group: Database identifiers + bioproject_accession: + rank: 6 + slot_group: Database identifiers + biosample_accession: + rank: 7 + slot_group: Database identifiers + insdc_sequence_read_accession: + rank: 8 + slot_group: Database identifiers + insdc_assembly_accession: + rank: 9 + slot_group: Database identifiers + sample_collection_data_steward_name: + rank: 10 + slot_group: Sample collection and processing + sample_collection_data_steward_contact_email: + rank: 11 + slot_group: Sample collection and processing + sample_collected_by: + rank: 12 + slot_group: Sample collection and processing + sample_collector_contact_email: + rank: 13 + slot_group: Sample collection and processing + geo_loc_name_country: + rank: 14 + slot_group: Sample collection and processing + geo_loc_name_state_province_territory: + rank: 15 + slot_group: Sample collection and processing + geo_loc_name_county_region: + rank: 16 + slot_group: Sample collection and processing + geo_loc_name_city: + rank: 17 + slot_group: Sample collection and processing + geo_loc_name_site__: + rank: 18 + slot_group: Sample collection and processing + geo_loc_latitude: + rank: 19 + slot_group: Sample collection and processing + geo_loc_longitude: + rank: 20 + slot_group: Sample collection and processing + organism: + rank: 21 + slot_group: Sample collection and processing + influenza_subtype: + rank: 22 + slot_group: Sample collection and processing + influenza_subtyping_scheme_name: + rank: 23 + slot_group: Sample collection and processing + taxonomic_identification_process: + rank: 24 + slot_group: Sample collection and processing + virus_identifier: + rank: 25 + slot_group: Sample collection and processing + who_oie_fao_h5_clade: + rank: 26 + slot_group: Sample collection and processing + sample_collection_date: + rank: 27 + slot_group: Sample collection and processing + sample_received_date: + rank: 28 + slot_group: Sample collection and processing + sample_processing_date: + rank: 29 + slot_group: Sample collection and processing + food_product_origin_geo_loc_name_country: + rank: 30 + slot_group: Sample collection and processing + food_product: + rank: 31 + slot_group: Sample collection and processing + food_product_properties: + rank: 32 + slot_group: Sample collection and processing + food_packaging: + rank: 33 + slot_group: Sample collection and processing + food_quality_date: + rank: 34 + slot_group: Sample collection and processing + food_packaging_date: + rank: 35 + slot_group: Sample collection and processing + environmental_site: + rank: 36 + slot_group: Sample collection and processing + environmental_material: + rank: 37 + slot_group: Sample collection and processing + collection_device: + rank: 38 + slot_group: Sample collection and processing + collection_method: + rank: 39 + slot_group: Sample collection and processing + sample_volume_measurement_value: + rank: 40 + slot_group: Sample collection and processing + sample_volume_measurement_unit: + rank: 41 + slot_group: Sample collection and processing + residual_sample_status: + rank: 42 + slot_group: Sample collection and processing + purpose_of_sampling: + rank: 43 + slot_group: Sample collection and processing + presampling_activity: + rank: 44 + slot_group: Sample collection and processing + presampling_activity_details: + rank: 45 + slot_group: Sample collection and processing + sample_storage_method: + rank: 46 + slot_group: Sample collection and processing + sample_storage_medium: + rank: 47 + slot_group: Sample collection and processing + sample_storage_duration_value: + rank: 48 + slot_group: Sample collection and processing + sample_storage_duration_unit: + rank: 49 + slot_group: Sample collection and processing + specimen_processing: + rank: 50 + slot_group: Sample collection and processing + specimen_processing_details: + rank: 51 + slot_group: Sample collection and processing + experimental_protocol: + rank: 52 + slot_group: Sample collection and processing + experimental_specimen_role_type: + rank: 53 + slot_group: Sample collection and processing + experimental_specimen_details: + rank: 54 + slot_group: Sample collection and processing + available_data_types: + rank: 55 + slot_group: Sample collection and processing + available_data_type_details: + rank: 56 + slot_group: Sample collection and processing + library_id: + rank: 57 + slot_group: Sequence information + sequencing_assay_type: + rank: 58 + slot_group: Sequence information + sequencing_date: + rank: 59 + slot_group: Sequence information + purpose_of_sequencing__: + rank: 60 + slot_group: Sequence information + purpose_of_sequencing_details: + rank: 61 + slot_group: Sequence information + sequenced_by: + rank: 62 + slot_group: Sequence information + sequenced_by_laboratory_name: + rank: 63 + slot_group: Sequence information + sequenced_by_contact_name: + rank: 64 + slot_group: Sequence information + sequenced_by_contact_email: + rank: 65 + slot_group: Sequence information + sequence_submitted_by: + rank: 66 + slot_group: Sequence information + sequence_submitter_contact_email: + rank: 67 + slot_group: Sequence information + nucleic_acid_extraction_method: + rank: 68 + slot_group: Sample collection and processing + nucleic_acid_extraction_kit: + rank: 69 + slot_group: Sample collection and processing + endogenous_control_details: + rank: 70 + slot_group: Sample collection and processing + sequencing_project_name: + rank: 71 + slot_group: Sequence information + sequencing_platform: + rank: 72 + slot_group: Sequence information + sequencing_instrument: + rank: 73 + slot_group: Sequence information + library_preparation_kit: + rank: 74 + slot_group: Sequence information + dna_fragment_length: + rank: 75 + slot_group: Sequence information + genomic_target_enrichment_method: + rank: 76 + slot_group: Sequence information + genomic_target_enrichment_method_details: + rank: 77 + slot_group: Sequence information + amplicon_pcr_primer_scheme: + rank: 78 + slot_group: Sequence information + amplicon_size: + rank: 79 + slot_group: Sequence information + sequencing_flow_cell_version: + rank: 80 + slot_group: Sequence information + sequencing_protocol: + rank: 81 + slot_group: Sequence information + r1_fastq_filename: + rank: 82 + slot_group: Sequence information + r2_fastq_filename: + rank: 83 + slot_group: Sequence information + fast5_filename: + rank: 84 + slot_group: Sequence information + genome_sequence_file_name: + rank: 85 + slot_group: Sequence information + assembly_filename: + rank: 86 + slot_group: Sequence information + quality_control_method_name: + rank: 87 + slot_group: Bioinformatics and QC metrics + quality_control_method_version: + rank: 88 + slot_group: Bioinformatics and QC metrics + quality_control_determination: + rank: 89 + slot_group: Bioinformatics and QC metrics + quality_control_issues: + rank: 90 + slot_group: Bioinformatics and QC metrics + quality_control_details: + rank: 91 + slot_group: Bioinformatics and QC metrics + raw_sequence_data_processing_method: + rank: 92 + slot_group: Bioinformatics and QC metrics + dehosting_method: + rank: 93 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_name: + rank: 94 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_version: + rank: 95 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_name: + rank: 96 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_version: + rank: 97 + slot_group: Bioinformatics and QC metrics + breadth_of_coverage_value: + rank: 98 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_value: + rank: 99 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_threshold: + rank: 100 + slot_group: Bioinformatics and QC metrics + genome_completeness: + rank: 101 + slot_group: Bioinformatics and QC metrics + number_of_base_pairs_sequenced: + rank: 102 + slot_group: Bioinformatics and QC metrics + number_of_total_reads: + rank: 103 + slot_group: Bioinformatics and QC metrics + number_of_unique_reads: + rank: 104 + slot_group: Bioinformatics and QC metrics + minimum_posttrimming_read_length: + rank: 105 + slot_group: Bioinformatics and QC metrics + number_of_contigs: + rank: 106 + slot_group: Bioinformatics and QC metrics + percent_ns_across_total_genome_length: + rank: 107 + slot_group: Bioinformatics and QC metrics + ns_per_100_kbp: + rank: 108 + slot_group: Bioinformatics and QC metrics + n50: + rank: 109 + slot_group: Bioinformatics and QC metrics + percent_read_contamination_: + rank: 110 + slot_group: Bioinformatics and QC metrics + sequence_assembly_length: + rank: 111 + slot_group: Bioinformatics and QC metrics + consensus_genome_length: + rank: 112 + slot_group: Bioinformatics and QC metrics + reference_genome_accession: + rank: 113 + slot_group: Bioinformatics and QC metrics + deduplication_method: + rank: 114 + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: + rank: 115 + slot_group: Bioinformatics and QC metrics + read_mapping_software_name: + rank: 116 + slot_group: Taxonomic identification information + read_mapping_software_version: + rank: 117 + slot_group: Taxonomic identification information + taxonomic_reference_database_name: + rank: 118 + slot_group: Taxonomic identification information + taxonomic_reference_database_version: + rank: 119 + slot_group: Taxonomic identification information + taxonomic_analysis_report_filename: + rank: 120 + slot_group: Taxonomic identification information + taxonomic_analysis_date: + rank: 121 + slot_group: Taxonomic identification information + read_mapping_criteria: + rank: 122 + slot_group: Taxonomic identification information + genetic_target_name: + rank: 123 + slot_group: Pathogen diagnostic testing + genetic_target_region: + rank: 124 + slot_group: Pathogen diagnostic testing + genetic_target_region_reference_genome: + rank: 125 + slot_group: Pathogen diagnostic testing + diagnostic_target_presence: + rank: 126 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value: + rank: 127 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit: + rank: 128 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method: + rank: 129 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_value: + rank: 130 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_units: + rank: 131 + slot_group: Pathogen diagnostic testing + diagnostic_testing_details: + rank: 132 + slot_group: Pathogen diagnostic testing + prevalence_metrics: + rank: 133 + slot_group: Risk assessment information + prevalence_metrics_details: + rank: 134 + slot_group: Risk assessment information + stage_of_production: + rank: 135 + slot_group: Risk assessment information + experimental_intervention: + rank: 136 + slot_group: Risk assessment information + experiment_intervention_details: + rank: 137 + slot_group: Risk assessment information + HPAIWW: + name: HPAIWW + title: HPAI Wastewater + description: null + is_a: dh_interface + see_also: null + annotations: + version: 1.0.0 + slots: + - specimen_collector_sample_id + - specimen_collector_subsample_id + - pooled_sample_id + - sampling_site_id + - sampling_event_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - insdc_assembly_accession + - sample_collection_data_steward_name + - sample_collection_data_steward_contact_email + - sample_collected_by + - sample_collector_contact_email + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_name_site__ + - geo_loc_latitude + - geo_loc_longitude + - organism + - influenza_subtype + - influenza_subtyping_scheme_name + - taxonomic_identification_process + - virus_identifier + - who_oie_fao_h5_clade + - sample_collection_date + - sample_collection_end_date + - sample_collection_start_time + - sample_collection_end_time + - sample_collection_time_of_day + - sample_collection_time_duration_value + - sample_collection_time_duration_unit + - sample_received_date + - sample_processing_date + - environmental_site + - environmental_material + - collection_device + - collection_method + - sample_volume_measurement_value + - sample_volume_measurement_unit + - residual_sample_status + - purpose_of_sampling + - presampling_activity + - presampling_activity_details + - sample_storage_method + - sample_storage_medium + - sample_storage_duration_value + - sample_storage_duration_unit + - specimen_processing + - specimen_processing_details + - experimental_protocol + - experimental_specimen_role_type + - experimental_specimen_details + - available_data_types + - available_data_type_details + - water_catchment_area_human_population_measurement_value + - water_catchment_area_human_population_range + - water_catchment_area_human_population_measurement_method + - water_catchment_area_human_population_density_value + - water_catchment_area_human_population_density_unit + - populated_area_type + - sampling_weather_conditions + - presampling_weather_conditions + - precipitation_measurement_value + - water_depth + - water_depth_units + - sediment_depth + - sediment_depth_units + - air_temperature + - air_temperature_units + - water_temperature + - water_temperature_units + - weather_type + - precipitation_measurement_unit + - precipitation_measurement_method + - ambient_temperature_measurement_value + - ambient_temperature_measurement_unit + - ph_measurement_value + - ph_measurement_method + - total_daily_flow_rate_measurement_value + - total_daily_flow_rate_measurement_unit + - total_daily_flow_rate_measurement_method + - instantaneous_flow_rate_measurement_value + - instantaneous_flow_rate_measurement_unit + - instantaneous_flow_rate_measurement_method + - turbidity_measurement_value + - turbidity_measurement_unit + - turbidity_measurement_method + - dissolved_oxygen_measurement_value + - dissolved_oxygen_measurement_unit + - dissolved_oxygen_measurement_method + - oxygen_reduction_potential_orp_measurement_value + - oxygen_reduction_potential_orp_measurement_unit + - oxygen_reduction_potential_orp_measurement_method + - chemical_oxygen_demand_cod_measurement_value + - chemical_oxygen_demand_cod_measurement_unit + - chemical_oxygen_demand_cod_measurement_method + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_value + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_method + - total_suspended_solids_tss_measurement_value + - total_suspended_solids_tss_measurement_unit + - total_suspended_solids_tss_measurement_method + - total_dissolved_solids_tds_measurement_value + - total_dissolved_solids_tds_measurement_unit + - total_dissolved_solids_tds_measurement_method + - total_solids_ts_measurement_value + - total_solids_ts_measurement_unit + - total_solids_ts_measurement_method + - alkalinity_measurement_value + - alkalinity_measurement_unit + - alkalinity_measurement_method + - conductivity_measurement_value + - conductivity_measurement_unit + - conductivity_measurement_method + - salinity_measurement_value + - salinity_measurement_unit + - salinity_measurement_method + - total_nitrogen_tn_measurement_value + - total_nitrogen_tn_measurement_unit + - total_nitrogen_tn_measurement_method + - total_phosphorus_tp_measurement_value + - total_phosphorus_tp_measurement_unit + - total_phosphorus_tp_measurement_method + - fecal_contamination_indicator_ + - fecal_contamination_value + - fecal_contamination_unit + - fecal_contamination_method + - fecal_coliform_count_value + - fecal_coliform_count_unit + - fecal_coliform_count_method + - urinary_contamination_indicator + - urinary_contamination_value + - urinary_contamination_unit + - urinary_contamination_method + - sample_temperature_value_at_collection + - sample_temperature_unit_at_collection + - sample_temperature_value_when_received + - sample_temperature_unit_when_received + - library_id + - sequencing_assay_type + - sequencing_date + - purpose_of_sequencing__ + - purpose_of_sequencing_details + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequence_submitted_by + - sequence_submitter_contact_email + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - endogenous_control_details + - sequencing_project_name + - sequencing_platform + - sequencing_instrument + - library_preparation_kit + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - sequencing_flow_cell_version + - sequencing_protocol + - r1_fastq_filename + - r2_fastq_filename + - fast5_filename + - genome_sequence_file_name + - assembly_filename + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - sequence_assembly_software_name + - sequence_assembly_software_version + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - genome_completeness + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - number_of_contigs + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - n50 + - percent_read_contamination_ + - sequence_assembly_length + - consensus_genome_length + - reference_genome_accession + - deduplication_method + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria + - genetic_target_name + - genetic_target_region + - genetic_target_region_reference_genome + - diagnostic_target_presence + - diagnostic_measurement_value + - diagnostic_measurement_unit + - diagnostic_measurement_method + - diagnostic_testing_threshold_value + - diagnostic_testing_threshold_units + - diagnostic_testing_details + - prevalence_metrics + - prevalence_metrics_details + - stage_of_production + - experimental_intervention + - experiment_intervention_details + slot_usage: + specimen_collector_sample_id: + rank: 1 + slot_group: Database identifiers + specimen_collector_subsample_id: + rank: 2 + slot_group: Database identifiers + pooled_sample_id: + rank: 3 + slot_group: Database identifiers + sampling_site_id: + rank: 4 + slot_group: Database identifiers + sampling_event_id: + rank: 5 + slot_group: Database identifiers + bioproject_accession: + rank: 6 + slot_group: Database identifiers + biosample_accession: + rank: 7 + slot_group: Database identifiers + insdc_sequence_read_accession: + rank: 8 + slot_group: Database identifiers + insdc_assembly_accession: + rank: 9 + slot_group: Database identifiers + sample_collection_data_steward_name: + rank: 10 + slot_group: Sample collection and processing + sample_collection_data_steward_contact_email: + rank: 11 + slot_group: Sample collection and processing + sample_collected_by: + rank: 12 + slot_group: Sample collection and processing + sample_collector_contact_email: + rank: 13 + slot_group: Sample collection and processing + geo_loc_name_country: + rank: 14 + slot_group: Sample collection and processing + geo_loc_name_state_province_territory: + rank: 15 + slot_group: Sample collection and processing + geo_loc_name_county_region: + rank: 16 + slot_group: Sample collection and processing + geo_loc_name_city: + rank: 17 + slot_group: Sample collection and processing + geo_loc_name_site__: + rank: 18 + slot_group: Sample collection and processing + geo_loc_latitude: + rank: 19 + slot_group: Sample collection and processing + geo_loc_longitude: + rank: 20 + slot_group: Sample collection and processing + organism: + rank: 21 + slot_group: Sample collection and processing + influenza_subtype: + rank: 22 + slot_group: Sample collection and processing + influenza_subtyping_scheme_name: + rank: 23 + slot_group: Sample collection and processing + taxonomic_identification_process: + rank: 24 + slot_group: Sample collection and processing + virus_identifier: + rank: 25 + slot_group: Sample collection and processing + who_oie_fao_h5_clade: + rank: 26 + slot_group: Sample collection and processing + sample_collection_date: + rank: 27 + slot_group: Sample collection and processing + sample_collection_end_date: + rank: 28 + slot_group: Sample collection and processing + sample_collection_start_time: + rank: 29 + slot_group: Sample collection and processing + sample_collection_end_time: + rank: 30 + slot_group: Sample collection and processing + sample_collection_time_of_day: + rank: 31 + slot_group: Sample collection and processing + sample_collection_time_duration_value: + rank: 32 + slot_group: Sample collection and processing + sample_collection_time_duration_unit: + rank: 33 + slot_group: Sample collection and processing + sample_received_date: + rank: 34 + slot_group: Sample collection and processing + sample_processing_date: + rank: 35 + slot_group: Sample collection and processing + environmental_site: + rank: 36 + slot_group: Sample collection and processing + environmental_material: + rank: 37 + slot_group: Sample collection and processing + collection_device: + rank: 38 + slot_group: Sample collection and processing + collection_method: + rank: 39 + slot_group: Sample collection and processing + sample_volume_measurement_value: + rank: 40 + slot_group: Sample collection and processing + sample_volume_measurement_unit: + rank: 41 + slot_group: Sample collection and processing + residual_sample_status: + rank: 42 + slot_group: Sample collection and processing + purpose_of_sampling: + rank: 43 + slot_group: Sample collection and processing + presampling_activity: + rank: 44 + slot_group: Sample collection and processing + presampling_activity_details: + rank: 45 + slot_group: Sample collection and processing + sample_storage_method: + rank: 46 + slot_group: Sample collection and processing + sample_storage_medium: + rank: 47 + slot_group: Sample collection and processing + sample_storage_duration_value: + rank: 48 + slot_group: Sample collection and processing + sample_storage_duration_unit: + rank: 49 + slot_group: Sample collection and processing + specimen_processing: + rank: 50 + slot_group: Sample collection and processing + specimen_processing_details: + rank: 51 + slot_group: Sample collection and processing + experimental_protocol: + rank: 52 + slot_group: Sample collection and processing + experimental_specimen_role_type: + rank: 53 + slot_group: Sample collection and processing + experimental_specimen_details: + rank: 54 + slot_group: Sample collection and processing + available_data_types: + rank: 55 + slot_group: Sample collection and processing + available_data_type_details: + rank: 56 + slot_group: Sample collection and processing + water_catchment_area_human_population_measurement_value: + rank: 57 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_range: + rank: 58 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_measurement_method: + rank: 59 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_density_value: + rank: 60 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_density_unit: + rank: 61 + slot_group: Environmental conditions and measurements + populated_area_type: + rank: 62 + slot_group: Environmental conditions and measurements + sampling_weather_conditions: + rank: 63 + slot_group: Environmental conditions and measurements + presampling_weather_conditions: + rank: 64 + slot_group: Environmental conditions and measurements + precipitation_measurement_value: + rank: 65 + slot_group: Environmental conditions and measurements + water_depth: + rank: 66 + slot_group: Environmental conditions and measurements + water_depth_units: + rank: 67 + slot_group: Environmental conditions and measurements + sediment_depth: + rank: 68 + slot_group: Environmental conditions and measurements + sediment_depth_units: + rank: 69 + slot_group: Environmental conditions and measurements + air_temperature: + rank: 70 + slot_group: Environmental conditions and measurements + air_temperature_units: + rank: 71 + slot_group: Environmental conditions and measurements + water_temperature: + rank: 72 + slot_group: Environmental conditions and measurements + water_temperature_units: + rank: 73 + slot_group: Environmental conditions and measurements + weather_type: + rank: 74 + slot_group: Environmental conditions and measurements + precipitation_measurement_unit: + rank: 75 + slot_group: Environmental conditions and measurements + precipitation_measurement_method: + rank: 76 + slot_group: Environmental conditions and measurements + ambient_temperature_measurement_value: + rank: 77 + slot_group: Environmental conditions and measurements + ambient_temperature_measurement_unit: + rank: 78 + slot_group: Environmental conditions and measurements + ph_measurement_value: + rank: 79 + slot_group: Environmental conditions and measurements + ph_measurement_method: + rank: 80 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_value: + rank: 81 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_unit: + rank: 82 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_method: + rank: 83 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_value: + rank: 84 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_unit: + rank: 85 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_method: + rank: 86 + slot_group: Environmental conditions and measurements + turbidity_measurement_value: + rank: 87 + slot_group: Environmental conditions and measurements + turbidity_measurement_unit: + rank: 88 + slot_group: Environmental conditions and measurements + turbidity_measurement_method: + rank: 89 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_value: + rank: 90 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_unit: + rank: 91 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_method: + rank: 92 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_value: + rank: 93 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_unit: + rank: 94 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_method: + rank: 95 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_value: + rank: 96 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_unit: + rank: 97 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_method: + rank: 98 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: + rank: 99 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: + rank: 100 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: + rank: 101 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_value: + rank: 102 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_unit: + rank: 103 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_method: + rank: 104 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_value: + rank: 105 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_unit: + rank: 106 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_method: + rank: 107 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_value: + rank: 108 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_unit: + rank: 109 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_method: + rank: 110 + slot_group: Environmental conditions and measurements + alkalinity_measurement_value: + rank: 111 + slot_group: Environmental conditions and measurements + alkalinity_measurement_unit: + rank: 112 + slot_group: Environmental conditions and measurements + alkalinity_measurement_method: + rank: 113 + slot_group: Environmental conditions and measurements + conductivity_measurement_value: + rank: 114 + slot_group: Environmental conditions and measurements + conductivity_measurement_unit: + rank: 115 + slot_group: Environmental conditions and measurements + conductivity_measurement_method: + rank: 116 + slot_group: Environmental conditions and measurements + salinity_measurement_value: + rank: 117 + slot_group: Environmental conditions and measurements + salinity_measurement_unit: + rank: 118 + slot_group: Environmental conditions and measurements + salinity_measurement_method: + rank: 119 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_value: + rank: 120 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_unit: + rank: 121 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_method: + rank: 122 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_value: + rank: 123 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_unit: + rank: 124 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_method: + rank: 125 + slot_group: Environmental conditions and measurements + fecal_contamination_indicator_: + rank: 126 + slot_group: Environmental conditions and measurements + fecal_contamination_value: + rank: 127 + slot_group: Environmental conditions and measurements + fecal_contamination_unit: + rank: 128 + slot_group: Environmental conditions and measurements + fecal_contamination_method: + rank: 129 + slot_group: Environmental conditions and measurements + fecal_coliform_count_value: + rank: 130 + slot_group: Environmental conditions and measurements + fecal_coliform_count_unit: + rank: 131 + slot_group: Environmental conditions and measurements + fecal_coliform_count_method: + rank: 132 + slot_group: Environmental conditions and measurements + urinary_contamination_indicator: + rank: 133 + slot_group: Environmental conditions and measurements + urinary_contamination_value: + rank: 134 + slot_group: Environmental conditions and measurements + urinary_contamination_unit: + rank: 135 + slot_group: Environmental conditions and measurements + urinary_contamination_method: + rank: 136 + slot_group: Environmental conditions and measurements + sample_temperature_value_at_collection: + rank: 137 + slot_group: Environmental conditions and measurements + sample_temperature_unit_at_collection: + rank: 138 + slot_group: Environmental conditions and measurements + sample_temperature_value_when_received: + rank: 139 + slot_group: Environmental conditions and measurements + sample_temperature_unit_when_received: + rank: 140 + slot_group: Environmental conditions and measurements + library_id: + rank: 141 + slot_group: Sequence information + sequencing_assay_type: + rank: 142 + slot_group: Sequence information + sequencing_date: + rank: 143 + slot_group: Sequence information + purpose_of_sequencing__: + rank: 144 + slot_group: Sequence information + purpose_of_sequencing_details: + rank: 145 + slot_group: Sequence information + sequenced_by: + rank: 146 + slot_group: Sequence information + sequenced_by_laboratory_name: + rank: 147 + slot_group: Sequence information + sequenced_by_contact_name: + rank: 148 + slot_group: Sequence information + sequenced_by_contact_email: + rank: 149 + slot_group: Sequence information + sequence_submitted_by: + rank: 150 + slot_group: Sequence information + sequence_submitter_contact_email: + rank: 151 + slot_group: Sequence information + nucleic_acid_extraction_method: + rank: 152 + slot_group: Sample collection and processing + nucleic_acid_extraction_kit: + rank: 153 + slot_group: Sample collection and processing + endogenous_control_details: + rank: 154 + slot_group: Sample collection and processing + sequencing_project_name: + rank: 155 + slot_group: Sequence information + sequencing_platform: + rank: 156 + slot_group: Sequence information + sequencing_instrument: + rank: 157 + slot_group: Sequence information + library_preparation_kit: + rank: 158 + slot_group: Sequence information + dna_fragment_length: + rank: 159 + slot_group: Sequence information + genomic_target_enrichment_method: + rank: 160 + slot_group: Sequence information + genomic_target_enrichment_method_details: + rank: 161 + slot_group: Sequence information + amplicon_pcr_primer_scheme: + rank: 162 + slot_group: Sequence information + amplicon_size: + rank: 163 + slot_group: Sequence information + sequencing_flow_cell_version: + rank: 164 + slot_group: Sequence information + sequencing_protocol: + rank: 165 + slot_group: Sequence information + r1_fastq_filename: + rank: 166 + slot_group: Sequence information + r2_fastq_filename: + rank: 167 + slot_group: Sequence information + fast5_filename: + rank: 168 + slot_group: Sequence information + genome_sequence_file_name: + rank: 169 + slot_group: Sequence information + assembly_filename: + rank: 170 + slot_group: Sequence information + quality_control_method_name: + rank: 171 + slot_group: Bioinformatics and QC metrics + quality_control_method_version: + rank: 172 + slot_group: Bioinformatics and QC metrics + quality_control_determination: + rank: 173 + slot_group: Bioinformatics and QC metrics + quality_control_issues: + rank: 174 + slot_group: Bioinformatics and QC metrics + quality_control_details: + rank: 175 + slot_group: Bioinformatics and QC metrics + raw_sequence_data_processing_method: + rank: 176 + slot_group: Bioinformatics and QC metrics + dehosting_method: + rank: 177 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_name: + rank: 178 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_version: + rank: 179 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_name: + rank: 180 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_version: + rank: 181 + slot_group: Bioinformatics and QC metrics + breadth_of_coverage_value: + rank: 182 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_value: + rank: 183 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_threshold: + rank: 184 + slot_group: Bioinformatics and QC metrics + genome_completeness: + rank: 185 + slot_group: Bioinformatics and QC metrics + number_of_base_pairs_sequenced: + rank: 186 + slot_group: Bioinformatics and QC metrics + number_of_total_reads: + rank: 187 + slot_group: Bioinformatics and QC metrics + number_of_unique_reads: + rank: 188 + slot_group: Bioinformatics and QC metrics + minimum_posttrimming_read_length: + rank: 189 + slot_group: Bioinformatics and QC metrics + number_of_contigs: + rank: 190 + slot_group: Bioinformatics and QC metrics + percent_ns_across_total_genome_length: + rank: 191 + slot_group: Bioinformatics and QC metrics + ns_per_100_kbp: + rank: 192 + slot_group: Bioinformatics and QC metrics + n50: + rank: 193 + slot_group: Bioinformatics and QC metrics + percent_read_contamination_: + rank: 194 + slot_group: Bioinformatics and QC metrics + sequence_assembly_length: + rank: 195 + slot_group: Bioinformatics and QC metrics + consensus_genome_length: + rank: 196 + slot_group: Bioinformatics and QC metrics + reference_genome_accession: + rank: 197 + slot_group: Bioinformatics and QC metrics + deduplication_method: + rank: 198 + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: + rank: 199 + slot_group: Bioinformatics and QC metrics + read_mapping_software_name: + rank: 200 + slot_group: Taxonomic identification information + read_mapping_software_version: + rank: 201 + slot_group: Taxonomic identification information + taxonomic_reference_database_name: + rank: 202 + slot_group: Taxonomic identification information + taxonomic_reference_database_version: + rank: 203 + slot_group: Taxonomic identification information + taxonomic_analysis_report_filename: + rank: 204 + slot_group: Taxonomic identification information + taxonomic_analysis_date: + rank: 205 + slot_group: Taxonomic identification information + read_mapping_criteria: + rank: 206 + slot_group: Taxonomic identification information + genetic_target_name: + rank: 207 + slot_group: Pathogen diagnostic testing + genetic_target_region: + rank: 208 + slot_group: Pathogen diagnostic testing + genetic_target_region_reference_genome: + rank: 209 + slot_group: Pathogen diagnostic testing + diagnostic_target_presence: + rank: 210 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value: + rank: 211 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit: + rank: 212 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method: + rank: 213 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_value: + rank: 214 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_units: + rank: 215 + slot_group: Pathogen diagnostic testing + diagnostic_testing_details: + rank: 216 + slot_group: Pathogen diagnostic testing + prevalence_metrics: + rank: 217 + slot_group: Risk assessment information + prevalence_metrics_details: + rank: 218 + slot_group: Risk assessment information + stage_of_production: + rank: 219 + slot_group: Risk assessment information + experimental_intervention: + rank: 220 + slot_group: Risk assessment information + experiment_intervention_details: + rank: 221 + slot_group: Risk assessment information + HPAIEnviro: + name: HPAIEnviro + title: HPAI Environmental + description: null + is_a: dh_interface + see_also: null + annotations: + version: 1.0.0 + slots: + - specimen_collector_sample_id + - specimen_collector_subsample_id + - pooled_sample_id + - sampling_site_id + - sampling_event_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - insdc_assembly_accession + - sample_collection_data_steward_name + - sample_collection_data_steward_contact_email + - sample_collected_by + - sample_collector_contact_email + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_name_site__ + - geo_loc_latitude + - geo_loc_longitude + - organism + - influenza_subtype + - influenza_subtyping_scheme_name + - taxonomic_identification_process + - virus_identifier + - who_oie_fao_h5_clade + - sample_collection_date + - sample_collection_end_date + - sample_collection_start_time + - sample_collection_end_time + - sample_collection_time_of_day + - sample_collection_time_duration_value + - sample_collection_time_duration_unit + - sample_received_date + - sample_processing_date + - environmental_site + - environmental_material + - collection_device + - collection_method + - sample_volume_measurement_value + - sample_volume_measurement_unit + - residual_sample_status + - purpose_of_sampling + - presampling_activity + - presampling_activity_details + - sample_storage_method + - sample_storage_medium + - sample_storage_duration_value + - sample_storage_duration_unit + - specimen_processing + - specimen_processing_details + - experimental_protocol + - experimental_specimen_role_type + - experimental_specimen_details + - available_data_types + - available_data_type_details + - water_catchment_area_human_population_measurement_value + - water_catchment_area_human_population_range + - water_catchment_area_human_population_measurement_method + - water_catchment_area_human_population_density_value + - water_catchment_area_human_population_density_unit + - populated_area_type + - sampling_weather_conditions + - presampling_weather_conditions + - precipitation_measurement_value + - water_depth + - water_depth_units + - sediment_depth + - sediment_depth_units + - air_temperature + - air_temperature_units + - water_temperature + - water_temperature_units + - weather_type + - precipitation_measurement_unit + - precipitation_measurement_method + - ambient_temperature_measurement_value + - ambient_temperature_measurement_unit + - ph_measurement_value + - ph_measurement_method + - total_daily_flow_rate_measurement_value + - total_daily_flow_rate_measurement_unit + - total_daily_flow_rate_measurement_method + - instantaneous_flow_rate_measurement_value + - instantaneous_flow_rate_measurement_unit + - instantaneous_flow_rate_measurement_method + - turbidity_measurement_value + - turbidity_measurement_unit + - turbidity_measurement_method + - dissolved_oxygen_measurement_value + - dissolved_oxygen_measurement_unit + - dissolved_oxygen_measurement_method + - oxygen_reduction_potential_orp_measurement_value + - oxygen_reduction_potential_orp_measurement_unit + - oxygen_reduction_potential_orp_measurement_method + - chemical_oxygen_demand_cod_measurement_value + - chemical_oxygen_demand_cod_measurement_unit + - chemical_oxygen_demand_cod_measurement_method + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_value + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_method + - total_suspended_solids_tss_measurement_value + - total_suspended_solids_tss_measurement_unit + - total_suspended_solids_tss_measurement_method + - total_dissolved_solids_tds_measurement_value + - total_dissolved_solids_tds_measurement_unit + - total_dissolved_solids_tds_measurement_method + - total_solids_ts_measurement_value + - total_solids_ts_measurement_unit + - total_solids_ts_measurement_method + - alkalinity_measurement_value + - alkalinity_measurement_unit + - alkalinity_measurement_method + - conductivity_measurement_value + - conductivity_measurement_unit + - conductivity_measurement_method + - salinity_measurement_value + - salinity_measurement_unit + - salinity_measurement_method + - total_nitrogen_tn_measurement_value + - total_nitrogen_tn_measurement_unit + - total_nitrogen_tn_measurement_method + - total_phosphorus_tp_measurement_value + - total_phosphorus_tp_measurement_unit + - total_phosphorus_tp_measurement_method + - fecal_contamination_indicator_ + - fecal_contamination_value + - fecal_contamination_unit + - fecal_contamination_method + - fecal_coliform_count_value + - fecal_coliform_count_unit + - fecal_coliform_count_method + - urinary_contamination_indicator + - urinary_contamination_value + - urinary_contamination_unit + - urinary_contamination_method + - sample_temperature_value_at_collection + - sample_temperature_unit_at_collection + - sample_temperature_value_when_received + - sample_temperature_unit_when_received + - library_id + - sequencing_assay_type + - sequencing_date + - purpose_of_sequencing__ + - purpose_of_sequencing_details + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequence_submitted_by + - sequence_submitter_contact_email + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - endogenous_control_details + - sequencing_project_name + - sequencing_platform + - sequencing_instrument + - library_preparation_kit + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - sequencing_flow_cell_version + - sequencing_protocol + - r1_fastq_filename + - r2_fastq_filename + - fast5_filename + - genome_sequence_file_name + - assembly_filename + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - sequence_assembly_software_name + - sequence_assembly_software_version + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - genome_completeness + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - number_of_contigs + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - n50 + - percent_read_contamination_ + - sequence_assembly_length + - consensus_genome_length + - reference_genome_accession + - deduplication_method + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria + - genetic_target_name + - genetic_target_region + - genetic_target_region_reference_genome + - diagnostic_target_presence + - diagnostic_measurement_value + - diagnostic_measurement_unit + - diagnostic_measurement_method + - diagnostic_testing_threshold_value + - diagnostic_testing_threshold_units + - diagnostic_testing_details + - prevalence_metrics + - prevalence_metrics_details + - stage_of_production + - experimental_intervention + - experiment_intervention_details + slot_usage: + specimen_collector_sample_id: + rank: 1 + slot_group: Database identifiers + specimen_collector_subsample_id: + rank: 2 + slot_group: Database identifiers + pooled_sample_id: + rank: 3 + slot_group: Database identifiers + sampling_site_id: + rank: 4 + slot_group: Database identifiers + sampling_event_id: + rank: 5 + slot_group: Database identifiers + bioproject_accession: + rank: 6 + slot_group: Database identifiers + biosample_accession: + rank: 7 + slot_group: Database identifiers + insdc_sequence_read_accession: + rank: 8 + slot_group: Database identifiers + insdc_assembly_accession: + rank: 9 + slot_group: Database identifiers + sample_collection_data_steward_name: + rank: 10 + slot_group: Sample collection and processing + sample_collection_data_steward_contact_email: + rank: 11 + slot_group: Sample collection and processing + sample_collected_by: + rank: 12 + slot_group: Sample collection and processing + sample_collector_contact_email: + rank: 13 + slot_group: Sample collection and processing + geo_loc_name_country: + rank: 14 + slot_group: Sample collection and processing + geo_loc_name_state_province_territory: + rank: 15 + slot_group: Sample collection and processing + geo_loc_name_county_region: + rank: 16 + slot_group: Sample collection and processing + geo_loc_name_city: + rank: 17 + slot_group: Sample collection and processing + geo_loc_name_site__: + rank: 18 + slot_group: Sample collection and processing + geo_loc_latitude: + rank: 19 + slot_group: Sample collection and processing + geo_loc_longitude: + rank: 20 + slot_group: Sample collection and processing + organism: + rank: 21 + slot_group: Sample collection and processing + influenza_subtype: + rank: 22 + slot_group: Sample collection and processing + influenza_subtyping_scheme_name: + rank: 23 + slot_group: Sample collection and processing + taxonomic_identification_process: + rank: 24 + slot_group: Sample collection and processing + virus_identifier: + rank: 25 + slot_group: Sample collection and processing + who_oie_fao_h5_clade: + rank: 26 + slot_group: Sample collection and processing + sample_collection_date: + rank: 27 + slot_group: Sample collection and processing + sample_collection_end_date: + rank: 28 + slot_group: Sample collection and processing + sample_collection_start_time: + rank: 29 + slot_group: Sample collection and processing + sample_collection_end_time: + rank: 30 + slot_group: Sample collection and processing + sample_collection_time_of_day: + rank: 31 + slot_group: Sample collection and processing + sample_collection_time_duration_value: + rank: 32 + slot_group: Sample collection and processing + sample_collection_time_duration_unit: + rank: 33 + slot_group: Sample collection and processing + sample_received_date: + rank: 34 + slot_group: Sample collection and processing + sample_processing_date: + rank: 35 + slot_group: Sample collection and processing + environmental_site: + rank: 36 + slot_group: Sample collection and processing + environmental_material: + rank: 37 + slot_group: Sample collection and processing + collection_device: + rank: 38 + slot_group: Sample collection and processing + collection_method: + rank: 39 + slot_group: Sample collection and processing + sample_volume_measurement_value: + rank: 40 + slot_group: Sample collection and processing + sample_volume_measurement_unit: + rank: 41 + slot_group: Sample collection and processing + residual_sample_status: + rank: 42 + slot_group: Sample collection and processing + purpose_of_sampling: + rank: 43 + slot_group: Sample collection and processing + presampling_activity: + rank: 44 + slot_group: Sample collection and processing + presampling_activity_details: + rank: 45 + slot_group: Sample collection and processing + sample_storage_method: + rank: 46 + slot_group: Sample collection and processing + sample_storage_medium: + rank: 47 + slot_group: Sample collection and processing + sample_storage_duration_value: + rank: 48 + slot_group: Sample collection and processing + sample_storage_duration_unit: + rank: 49 + slot_group: Sample collection and processing + specimen_processing: + rank: 50 + slot_group: Sample collection and processing + specimen_processing_details: + rank: 51 + slot_group: Sample collection and processing + experimental_protocol: + rank: 52 + slot_group: Sample collection and processing + experimental_specimen_role_type: + rank: 53 + slot_group: Sample collection and processing + experimental_specimen_details: + rank: 54 + slot_group: Sample collection and processing + available_data_types: + rank: 55 + slot_group: Sample collection and processing + available_data_type_details: + rank: 56 + slot_group: Sample collection and processing + water_catchment_area_human_population_measurement_value: + rank: 57 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_range: + rank: 58 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_measurement_method: + rank: 59 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_density_value: + rank: 60 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_density_unit: + rank: 61 + slot_group: Environmental conditions and measurements + populated_area_type: + rank: 62 + slot_group: Environmental conditions and measurements + sampling_weather_conditions: + rank: 63 + slot_group: Environmental conditions and measurements + presampling_weather_conditions: + rank: 64 + slot_group: Environmental conditions and measurements + precipitation_measurement_value: + rank: 65 + slot_group: Environmental conditions and measurements + water_depth: + rank: 66 + slot_group: Environmental conditions and measurements + water_depth_units: + rank: 67 + slot_group: Environmental conditions and measurements + sediment_depth: + rank: 68 + slot_group: Environmental conditions and measurements + sediment_depth_units: + rank: 69 + slot_group: Environmental conditions and measurements + air_temperature: + rank: 70 + slot_group: Environmental conditions and measurements + air_temperature_units: + rank: 71 + slot_group: Environmental conditions and measurements + water_temperature: + rank: 72 + slot_group: Environmental conditions and measurements + water_temperature_units: + rank: 73 + slot_group: Environmental conditions and measurements + weather_type: + rank: 74 + slot_group: Environmental conditions and measurements + precipitation_measurement_unit: + rank: 75 + slot_group: Environmental conditions and measurements + precipitation_measurement_method: + rank: 76 + slot_group: Environmental conditions and measurements + ambient_temperature_measurement_value: + rank: 77 + slot_group: Environmental conditions and measurements + ambient_temperature_measurement_unit: + rank: 78 + slot_group: Environmental conditions and measurements + ph_measurement_value: + rank: 79 + slot_group: Environmental conditions and measurements + ph_measurement_method: + rank: 80 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_value: + rank: 81 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_unit: + rank: 82 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_method: + rank: 83 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_value: + rank: 84 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_unit: + rank: 85 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_method: + rank: 86 + slot_group: Environmental conditions and measurements + turbidity_measurement_value: + rank: 87 + slot_group: Environmental conditions and measurements + turbidity_measurement_unit: + rank: 88 + slot_group: Environmental conditions and measurements + turbidity_measurement_method: + rank: 89 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_value: + rank: 90 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_unit: + rank: 91 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_method: + rank: 92 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_value: + rank: 93 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_unit: + rank: 94 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_method: + rank: 95 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_value: + rank: 96 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_unit: + rank: 97 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_method: + rank: 98 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: + rank: 99 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: + rank: 100 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: + rank: 101 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_value: + rank: 102 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_unit: + rank: 103 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_method: + rank: 104 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_value: + rank: 105 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_unit: + rank: 106 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_method: + rank: 107 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_value: + rank: 108 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_unit: + rank: 109 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_method: + rank: 110 + slot_group: Environmental conditions and measurements + alkalinity_measurement_value: + rank: 111 + slot_group: Environmental conditions and measurements + alkalinity_measurement_unit: + rank: 112 + slot_group: Environmental conditions and measurements + alkalinity_measurement_method: + rank: 113 + slot_group: Environmental conditions and measurements + conductivity_measurement_value: + rank: 114 + slot_group: Environmental conditions and measurements + conductivity_measurement_unit: + rank: 115 + slot_group: Environmental conditions and measurements + conductivity_measurement_method: + rank: 116 + slot_group: Environmental conditions and measurements + salinity_measurement_value: + rank: 117 + slot_group: Environmental conditions and measurements + salinity_measurement_unit: + rank: 118 + slot_group: Environmental conditions and measurements + salinity_measurement_method: + rank: 119 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_value: + rank: 120 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_unit: + rank: 121 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_method: + rank: 122 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_value: + rank: 123 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_unit: + rank: 124 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_method: + rank: 125 + slot_group: Environmental conditions and measurements + fecal_contamination_indicator_: + rank: 126 + slot_group: Environmental conditions and measurements + fecal_contamination_value: + rank: 127 + slot_group: Environmental conditions and measurements + fecal_contamination_unit: + rank: 128 + slot_group: Environmental conditions and measurements + fecal_contamination_method: + rank: 129 + slot_group: Environmental conditions and measurements + fecal_coliform_count_value: + rank: 130 + slot_group: Environmental conditions and measurements + fecal_coliform_count_unit: + rank: 131 + slot_group: Environmental conditions and measurements + fecal_coliform_count_method: + rank: 132 + slot_group: Environmental conditions and measurements + urinary_contamination_indicator: + rank: 133 + slot_group: Environmental conditions and measurements + urinary_contamination_value: + rank: 134 + slot_group: Environmental conditions and measurements + urinary_contamination_unit: + rank: 135 + slot_group: Environmental conditions and measurements + urinary_contamination_method: + rank: 136 + slot_group: Environmental conditions and measurements + sample_temperature_value_at_collection: + rank: 137 + slot_group: Environmental conditions and measurements + sample_temperature_unit_at_collection: + rank: 138 + slot_group: Environmental conditions and measurements + sample_temperature_value_when_received: + rank: 139 + slot_group: Environmental conditions and measurements + sample_temperature_unit_when_received: + rank: 140 + slot_group: Environmental conditions and measurements + library_id: + rank: 141 + slot_group: Sequence information + sequencing_assay_type: + rank: 142 + slot_group: Sequence information + sequencing_date: + rank: 143 + slot_group: Sequence information + purpose_of_sequencing__: + rank: 144 + slot_group: Sequence information + purpose_of_sequencing_details: + rank: 145 + slot_group: Sequence information + sequenced_by: + rank: 146 + slot_group: Sequence information + sequenced_by_laboratory_name: + rank: 147 + slot_group: Sequence information + sequenced_by_contact_name: + rank: 148 + slot_group: Sequence information + sequenced_by_contact_email: + rank: 149 + slot_group: Sequence information + sequence_submitted_by: + rank: 150 + slot_group: Sequence information + sequence_submitter_contact_email: + rank: 151 + slot_group: Sequence information + nucleic_acid_extraction_method: + rank: 152 + slot_group: Sample collection and processing + nucleic_acid_extraction_kit: + rank: 153 + slot_group: Sample collection and processing + endogenous_control_details: + rank: 154 + slot_group: Sample collection and processing + sequencing_project_name: + rank: 155 + slot_group: Sequence information + sequencing_platform: + rank: 156 + slot_group: Sequence information + sequencing_instrument: + rank: 157 + slot_group: Sequence information + library_preparation_kit: + rank: 158 + slot_group: Sequence information + dna_fragment_length: + rank: 159 + slot_group: Sequence information + genomic_target_enrichment_method: + rank: 160 + slot_group: Sequence information + genomic_target_enrichment_method_details: + rank: 161 + slot_group: Sequence information + amplicon_pcr_primer_scheme: + rank: 162 + slot_group: Sequence information + amplicon_size: + rank: 163 + slot_group: Sequence information + sequencing_flow_cell_version: + rank: 164 + slot_group: Sequence information + sequencing_protocol: + rank: 165 + slot_group: Sequence information + r1_fastq_filename: + rank: 166 + slot_group: Sequence information + r2_fastq_filename: + rank: 167 + slot_group: Sequence information + fast5_filename: + rank: 168 + slot_group: Sequence information + genome_sequence_file_name: + rank: 169 + slot_group: Sequence information + assembly_filename: + rank: 170 + slot_group: Sequence information + quality_control_method_name: + rank: 171 + slot_group: Bioinformatics and QC metrics + quality_control_method_version: + rank: 172 + slot_group: Bioinformatics and QC metrics + quality_control_determination: + rank: 173 + slot_group: Bioinformatics and QC metrics + quality_control_issues: + rank: 174 + slot_group: Bioinformatics and QC metrics + quality_control_details: + rank: 175 + slot_group: Bioinformatics and QC metrics + raw_sequence_data_processing_method: + rank: 176 + slot_group: Bioinformatics and QC metrics + dehosting_method: + rank: 177 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_name: + rank: 178 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_version: + rank: 179 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_name: + rank: 180 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_version: + rank: 181 + slot_group: Bioinformatics and QC metrics + breadth_of_coverage_value: + rank: 182 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_value: + rank: 183 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_threshold: + rank: 184 + slot_group: Bioinformatics and QC metrics + genome_completeness: + rank: 185 + slot_group: Bioinformatics and QC metrics + number_of_base_pairs_sequenced: + rank: 186 + slot_group: Bioinformatics and QC metrics + number_of_total_reads: + rank: 187 + slot_group: Bioinformatics and QC metrics + number_of_unique_reads: + rank: 188 + slot_group: Bioinformatics and QC metrics + minimum_posttrimming_read_length: + rank: 189 + slot_group: Bioinformatics and QC metrics + number_of_contigs: + rank: 190 + slot_group: Bioinformatics and QC metrics + percent_ns_across_total_genome_length: + rank: 191 + slot_group: Bioinformatics and QC metrics + ns_per_100_kbp: + rank: 192 + slot_group: Bioinformatics and QC metrics + n50: + rank: 193 + slot_group: Bioinformatics and QC metrics + percent_read_contamination_: + rank: 194 + slot_group: Bioinformatics and QC metrics + sequence_assembly_length: + rank: 195 + slot_group: Bioinformatics and QC metrics + consensus_genome_length: + rank: 196 + slot_group: Bioinformatics and QC metrics + reference_genome_accession: + rank: 197 + slot_group: Bioinformatics and QC metrics + deduplication_method: + rank: 198 + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: + rank: 199 + slot_group: Bioinformatics and QC metrics + read_mapping_software_name: + rank: 200 + slot_group: Taxonomic identification information + read_mapping_software_version: + rank: 201 + slot_group: Taxonomic identification information + taxonomic_reference_database_name: + rank: 202 + slot_group: Taxonomic identification information + taxonomic_reference_database_version: + rank: 203 + slot_group: Taxonomic identification information + taxonomic_analysis_report_filename: + rank: 204 + slot_group: Taxonomic identification information + taxonomic_analysis_date: + rank: 205 + slot_group: Taxonomic identification information + read_mapping_criteria: + rank: 206 + slot_group: Taxonomic identification information + genetic_target_name: + rank: 207 + slot_group: Pathogen diagnostic testing + genetic_target_region: + rank: 208 + slot_group: Pathogen diagnostic testing + genetic_target_region_reference_genome: + rank: 209 + slot_group: Pathogen diagnostic testing + diagnostic_target_presence: + rank: 210 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value: + rank: 211 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit: + rank: 212 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method: + rank: 213 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_value: + rank: 214 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_units: + rank: 215 + slot_group: Pathogen diagnostic testing + diagnostic_testing_details: + rank: 216 + slot_group: Pathogen diagnostic testing + prevalence_metrics: + rank: 217 + slot_group: Risk assessment information + prevalence_metrics_details: + rank: 218 + slot_group: Risk assessment information + stage_of_production: + rank: 219 + slot_group: Risk assessment information + experimental_intervention: + rank: 220 + slot_group: Risk assessment information + experiment_intervention_details: + rank: 221 + slot_group: Risk assessment information + HPAIHost: + name: HPAIHost + title: HPAI Host + description: null + is_a: dh_interface + see_also: null + annotations: + version: 1.0.0 + slots: + - specimen_collector_sample_id + - specimen_collector_subsample_id + - pooled_sample_id + - sampling_site_id + - sampling_event_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - insdc_assembly_accession + - sample_collection_data_steward_name + - sample_collection_data_steward_contact_email + - sample_collected_by + - sample_collector_contact_email + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_name_site__ + - geo_loc_latitude + - geo_loc_longitude + - organism + - influenza_subtype + - influenza_subtyping_scheme_name + - taxonomic_identification_process + - virus_identifier + - who_oie_fao_h5_clade + - sample_collection_date + - sample_received_date + - sample_processing_date + - host_origin_geo_loc_name_country + - anatomical_material + - body_product + - anatomical_part + - collection_device + - collection_method + - sample_volume_measurement_value + - sample_volume_measurement_unit + - residual_sample_status + - purpose_of_sampling + - presampling_activity + - presampling_activity_details + - sample_storage_method + - sample_storage_medium + - sample_storage_duration_value + - sample_storage_duration_unit + - specimen_processing + - specimen_processing_details + - experimental_protocol + - experimental_specimen_role_type + - experimental_specimen_details + - available_data_types + - available_data_type_details + - host_common_name + - host_scientific_name + - host_ecotype + - host_breed + - host_food_production_name + - host_age + - host_age_unit + - host_age_bin + - host_disease + - host_health_state + - host_health_status_details + - host_health_outcome + - host_subject_id + - case_id + - symptom_onset_date + - signs_and_symptoms + - preexisting_conditions_and_risk_factors + - complications + - exposure_event + - exposure_contact_level + - host_role + - exposure_setting + - exposure_details + - host_vaccination_status + - number_of_vaccine_doses_received + - vaccination_dose_1_vaccine_name + - vaccination_dose_1_vaccination_date + - vaccination_dose_2_vaccine_name + - vaccination_dose_2_vaccination_date + - vaccination_history + - influenza_antiviral_treatment_administration + - influenza_antiviral_agent__ + - influenza_antiviral_treatment_date + - library_id + - sequencing_assay_type + - sequencing_date + - purpose_of_sequencing__ + - purpose_of_sequencing_details + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequence_submitted_by + - sequence_submitter_contact_email + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - endogenous_control_details + - sequencing_project_name + - sequencing_platform + - sequencing_instrument + - library_preparation_kit + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - sequencing_flow_cell_version + - sequencing_protocol + - r1_fastq_filename + - r2_fastq_filename + - fast5_filename + - genome_sequence_file_name + - assembly_filename + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - sequence_assembly_software_name + - sequence_assembly_software_version + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - genome_completeness + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - number_of_contigs + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - n50 + - percent_read_contamination_ + - sequence_assembly_length + - consensus_genome_length + - reference_genome_accession + - deduplication_method + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria + - genetic_target_name + - genetic_target_region + - genetic_target_region_reference_genome + - diagnostic_target_presence + - diagnostic_measurement_value + - diagnostic_measurement_unit + - diagnostic_measurement_method + - diagnostic_testing_threshold_value + - diagnostic_testing_threshold_units + - diagnostic_testing_details + - prevalence_metrics + - prevalence_metrics_details + - stage_of_production + - experimental_intervention + - experiment_intervention_details + slot_usage: + specimen_collector_sample_id: + rank: 1 + slot_group: Database identifiers + specimen_collector_subsample_id: + rank: 2 + slot_group: Database identifiers + pooled_sample_id: + rank: 3 + slot_group: Database identifiers + sampling_site_id: + rank: 4 + slot_group: Database identifiers + sampling_event_id: + rank: 5 + slot_group: Database identifiers + bioproject_accession: + rank: 6 + slot_group: Database identifiers + biosample_accession: + rank: 7 + slot_group: Database identifiers + insdc_sequence_read_accession: + rank: 8 + slot_group: Database identifiers + insdc_assembly_accession: + rank: 9 + slot_group: Database identifiers + sample_collection_data_steward_name: + rank: 10 + slot_group: Sample collection and processing + sample_collection_data_steward_contact_email: + rank: 11 + slot_group: Sample collection and processing + sample_collected_by: + rank: 12 + slot_group: Sample collection and processing + sample_collector_contact_email: + rank: 13 + slot_group: Sample collection and processing + geo_loc_name_country: + rank: 14 + slot_group: Sample collection and processing + geo_loc_name_state_province_territory: + rank: 15 + slot_group: Sample collection and processing + geo_loc_name_county_region: + rank: 16 + slot_group: Sample collection and processing + geo_loc_name_city: + rank: 17 + slot_group: Sample collection and processing + geo_loc_name_site__: + rank: 18 + slot_group: Sample collection and processing + geo_loc_latitude: + rank: 19 + slot_group: Sample collection and processing + geo_loc_longitude: + rank: 20 + slot_group: Sample collection and processing + organism: + rank: 21 + slot_group: Sample collection and processing + influenza_subtype: + rank: 22 + slot_group: Sample collection and processing + influenza_subtyping_scheme_name: + rank: 23 + slot_group: Sample collection and processing + taxonomic_identification_process: + rank: 24 + slot_group: Sample collection and processing + virus_identifier: + rank: 25 + slot_group: Sample collection and processing + who_oie_fao_h5_clade: + rank: 26 + slot_group: Sample collection and processing + sample_collection_date: + rank: 27 + slot_group: Sample collection and processing + sample_received_date: + rank: 28 + slot_group: Sample collection and processing + sample_processing_date: + rank: 29 + slot_group: Sample collection and processing + host_origin_geo_loc_name_country: + rank: 30 + slot_group: Sample collection and processing + anatomical_material: + rank: 31 + slot_group: Sample collection and processing + body_product: + rank: 32 + slot_group: Sample collection and processing + anatomical_part: + rank: 33 + slot_group: Sample collection and processing + collection_device: + rank: 34 + slot_group: Sample collection and processing + collection_method: + rank: 35 + slot_group: Sample collection and processing + sample_volume_measurement_value: + rank: 36 + slot_group: Sample collection and processing + sample_volume_measurement_unit: + rank: 37 + slot_group: Sample collection and processing + residual_sample_status: + rank: 38 + slot_group: Sample collection and processing + purpose_of_sampling: + rank: 39 + slot_group: Sample collection and processing + presampling_activity: + rank: 40 + slot_group: Sample collection and processing + presampling_activity_details: + rank: 41 + slot_group: Sample collection and processing + sample_storage_method: + rank: 42 + slot_group: Sample collection and processing + sample_storage_medium: + rank: 43 + slot_group: Sample collection and processing + sample_storage_duration_value: + rank: 44 + slot_group: Sample collection and processing + sample_storage_duration_unit: + rank: 45 + slot_group: Sample collection and processing + specimen_processing: + rank: 46 + slot_group: Sample collection and processing + specimen_processing_details: + rank: 47 + slot_group: Sample collection and processing + experimental_protocol: + rank: 48 + slot_group: Sample collection and processing + experimental_specimen_role_type: + rank: 49 + slot_group: Sample collection and processing + experimental_specimen_details: + rank: 50 + slot_group: Sample collection and processing + available_data_types: + rank: 51 + slot_group: Sample collection and processing + available_data_type_details: + rank: 52 + slot_group: Sample collection and processing + host_common_name: + rank: 53 + slot_group: Host information + host_scientific_name: + rank: 54 + slot_group: Host information + host_ecotype: + rank: 55 + slot_group: Host information + host_breed: + rank: 56 + slot_group: Host information + host_food_production_name: + rank: 57 + slot_group: Host information + host_age: + rank: 58 + slot_group: Host Information + host_age_unit: + rank: 59 + slot_group: Host Information + host_age_bin: + rank: 60 + slot_group: Host information + host_disease: + rank: 61 + slot_group: Host information + host_health_state: + rank: 62 + slot_group: Host Information + host_health_status_details: + rank: 63 + slot_group: Host Information + host_health_outcome: + rank: 64 + slot_group: Host Information + host_subject_id: + rank: 65 + slot_group: Host Information + case_id: + rank: 66 + slot_group: Host Information + symptom_onset_date: + rank: 67 + slot_group: Host Information + signs_and_symptoms: + rank: 68 + slot_group: Host Information + preexisting_conditions_and_risk_factors: + rank: 69 + slot_group: Host Information + complications: + rank: 70 + slot_group: Host Information + exposure_event: + rank: 71 + slot_group: Host exposure information + exposure_contact_level: + rank: 72 + slot_group: Host exposure information + host_role: + rank: 73 + slot_group: Host exposure information + exposure_setting: + rank: 74 + slot_group: Host exposure information + exposure_details: + rank: 75 + slot_group: Host exposure information + host_vaccination_status: + rank: 76 + slot_group: Host vaccination information + number_of_vaccine_doses_received: + rank: 77 + slot_group: Host vaccination information + vaccination_dose_1_vaccine_name: + rank: 78 + slot_group: Host vaccination information + vaccination_dose_1_vaccination_date: + rank: 79 + slot_group: Host vaccination information + vaccination_dose_2_vaccine_name: + rank: 80 + slot_group: Host vaccination information + vaccination_dose_2_vaccination_date: + rank: 81 + slot_group: Host vaccination information + vaccination_history: + rank: 82 + slot_group: Host vaccination information + influenza_antiviral_treatment_administration: + rank: 83 + slot_group: Host treatment information + influenza_antiviral_agent__: + rank: 84 + slot_group: Host treatment information + influenza_antiviral_treatment_date: + rank: 85 + slot_group: Host treatment information + library_id: + rank: 86 + slot_group: Sequence information + sequencing_assay_type: + rank: 87 + slot_group: Sequence information + sequencing_date: + rank: 88 + slot_group: Sequence information + purpose_of_sequencing__: + rank: 89 + slot_group: Sequence information + purpose_of_sequencing_details: + rank: 90 + slot_group: Sequence information + sequenced_by: + rank: 91 + slot_group: Sequence information + sequenced_by_laboratory_name: + rank: 92 + slot_group: Sequence information + sequenced_by_contact_name: + rank: 93 + slot_group: Sequence information + sequenced_by_contact_email: + rank: 94 + slot_group: Sequence information + sequence_submitted_by: + rank: 95 + slot_group: Sequence information + sequence_submitter_contact_email: + rank: 96 + slot_group: Sequence information + nucleic_acid_extraction_method: + rank: 97 + slot_group: Sample collection and processing + nucleic_acid_extraction_kit: + rank: 98 + slot_group: Sample collection and processing + endogenous_control_details: + rank: 99 + slot_group: Sample collection and processing + sequencing_project_name: + rank: 100 + slot_group: Sequence information + sequencing_platform: + rank: 101 + slot_group: Sequence information + sequencing_instrument: + rank: 102 + slot_group: Sequence information + library_preparation_kit: + rank: 103 + slot_group: Sequence information + dna_fragment_length: + rank: 104 + slot_group: Sequence information + genomic_target_enrichment_method: + rank: 105 + slot_group: Sequence information + genomic_target_enrichment_method_details: + rank: 106 + slot_group: Sequence information + amplicon_pcr_primer_scheme: + rank: 107 + slot_group: Sequence information + amplicon_size: + rank: 108 + slot_group: Sequence information + sequencing_flow_cell_version: + rank: 109 + slot_group: Sequence information + sequencing_protocol: + rank: 110 + slot_group: Sequence information + r1_fastq_filename: + rank: 111 + slot_group: Sequence information + r2_fastq_filename: + rank: 112 + slot_group: Sequence information + fast5_filename: + rank: 113 + slot_group: Sequence information + genome_sequence_file_name: + rank: 114 + slot_group: Sequence information + assembly_filename: + rank: 115 + slot_group: Sequence information + quality_control_method_name: + rank: 116 + slot_group: Bioinformatics and QC metrics + quality_control_method_version: + rank: 117 + slot_group: Bioinformatics and QC metrics + quality_control_determination: + rank: 118 + slot_group: Bioinformatics and QC metrics + quality_control_issues: + rank: 119 + slot_group: Bioinformatics and QC metrics + quality_control_details: + rank: 120 + slot_group: Bioinformatics and QC metrics + raw_sequence_data_processing_method: + rank: 121 + slot_group: Bioinformatics and QC metrics + dehosting_method: + rank: 122 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_name: + rank: 123 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_version: + rank: 124 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_name: + rank: 125 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_version: + rank: 126 + slot_group: Bioinformatics and QC metrics + breadth_of_coverage_value: + rank: 127 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_value: + rank: 128 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_threshold: + rank: 129 + slot_group: Bioinformatics and QC metrics + genome_completeness: + rank: 130 + slot_group: Bioinformatics and QC metrics + number_of_base_pairs_sequenced: + rank: 131 + slot_group: Bioinformatics and QC metrics + number_of_total_reads: + rank: 132 + slot_group: Bioinformatics and QC metrics + number_of_unique_reads: + rank: 133 + slot_group: Bioinformatics and QC metrics + minimum_posttrimming_read_length: + rank: 134 + slot_group: Bioinformatics and QC metrics + number_of_contigs: + rank: 135 + slot_group: Bioinformatics and QC metrics + percent_ns_across_total_genome_length: + rank: 136 + slot_group: Bioinformatics and QC metrics + ns_per_100_kbp: + rank: 137 + slot_group: Bioinformatics and QC metrics + n50: + rank: 138 + slot_group: Bioinformatics and QC metrics + percent_read_contamination_: + rank: 139 + slot_group: Bioinformatics and QC metrics + sequence_assembly_length: + rank: 140 + slot_group: Bioinformatics and QC metrics + consensus_genome_length: + rank: 141 + slot_group: Bioinformatics and QC metrics + reference_genome_accession: + rank: 142 + slot_group: Bioinformatics and QC metrics + deduplication_method: + rank: 143 + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: + rank: 144 + slot_group: Bioinformatics and QC metrics + read_mapping_software_name: + rank: 145 + slot_group: Taxonomic identification information + read_mapping_software_version: + rank: 146 + slot_group: Taxonomic identification information + taxonomic_reference_database_name: + rank: 147 + slot_group: Taxonomic identification information + taxonomic_reference_database_version: + rank: 148 + slot_group: Taxonomic identification information + taxonomic_analysis_report_filename: + rank: 149 + slot_group: Taxonomic identification information + taxonomic_analysis_date: + rank: 150 + slot_group: Taxonomic identification information + read_mapping_criteria: + rank: 151 + slot_group: Taxonomic identification information + genetic_target_name: + rank: 152 + slot_group: Pathogen diagnostic testing + genetic_target_region: + rank: 153 + slot_group: Pathogen diagnostic testing + genetic_target_region_reference_genome: + rank: 154 + slot_group: Pathogen diagnostic testing + diagnostic_target_presence: + rank: 155 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value: + rank: 156 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit: + rank: 157 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method: + rank: 158 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_value: + rank: 159 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_units: + rank: 160 + slot_group: Pathogen diagnostic testing + diagnostic_testing_details: + rank: 161 + slot_group: Pathogen diagnostic testing + prevalence_metrics: + rank: 162 + slot_group: Risk assessment information + prevalence_metrics_details: + rank: 163 + slot_group: Risk assessment information + stage_of_production: + rank: 164 + slot_group: Risk assessment information + experimental_intervention: + rank: 165 + slot_group: Risk assessment information + experiment_intervention_details: + rank: 166 + slot_group: Risk assessment information +slots: + specimen_collector_sample_id: + name: specimen_collector_sample_id + title: specimen_collector_sample_ID + description: The user-defined name for the sample. + comments: Store the collector sample ID. If this number is considered identifiable + information, provide an alternative ID. Be sure to store the key that maps between + the original and alternative IDs for traceability and follow up if necessary. + Every collector sample ID from a single submitter must be unique. It can have + any format, but we suggest that you make it concise, unique and consistent within + your lab. + slot_uri: GENEPIO:0001123 + identifier: true + range: WhitespaceMinimizedString + required: true + examples: + - value: ASDFG123 + exact_mappings: + - BIOSAMPLE_Enterics:sample_name + specimen_collector_subsample_id: + name: specimen_collector_subsample_id + title: specimen_collector_subsample_ID + description: The user-defined identifier assigned to a portion of the original + sample. + comments: Store the ID for the subsample/aliquot. + slot_uri: GENEPIO:0100752 + range: WhitespaceMinimizedString + examples: + - value: ASDFG123_12 + pooled_sample_id: + name: pooled_sample_id + title: pooled_sample_ID + description: The user-defined identifier assigned to a combined (pooled) set of + samples. + comments: If the sample being analyzed is the result of pooling individual samples, + rename the pooled sample with a new identifier. Store the pooled sample ID. + slot_uri: GENEPIO:0100996 + range: WhitespaceMinimizedString + examples: + - value: 12345AYZ + sampling_site_id: + name: sampling_site_id + title: sampling_site_ID + description: The user-defined identifier assigned to a specific location from + which samples are taken. + comments: Store the ID for the site from which a sample was taken. The "site" + is user defined (e.g. it may be a building and its environs, a specific entity + within an environment). Please use the same site ID for all samples from a given + site, regardless of when these samples were taken. Any important changes in + site location, should be represented with a new site ID. + slot_uri: GENEPIO:0100760 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: Site 12A + sampling_event_id: + name: sampling_event_id + title: sampling_event_ID + description: The user-defined identifier assigned to a specific event during which + one or more samples are taken, from one or more sites. + comments: Store the ID for the event during which a sample or samples were taken. + For example, an event could be one person taking samples from multiple sites, + or multiple people taking samples from one site. + slot_uri: GENEPIO:0100761 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: Event 120522.1 + bioproject_accession: + name: bioproject_accession + title: BioProject_accession + description: The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) + to which the BioSample belongs. + comments: Store the BioProject accession number. BioProjects are an organizing + tool that links together raw sequence data, assemblies, and their associated + metadata. Each province will be assigned a different bioproject accession number + by the National Microbiology Lab. A valid NCBI BioProject accession has prefix + PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing + project. + slot_uri: GENEPIO:0001136 + range: WhitespaceMinimizedString + pattern: '{UPPER_CASE}' + structured_pattern: + syntax: '{UPPER_CASE}' + partial_match: false + interpolated: true + examples: + - value: PRJNA608651 + exact_mappings: + - BIOSAMPLE_Enterics:bioproject_accession + biosample_accession: + name: biosample_accession + title: BioSample_accession + description: The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, + or DDBJ) archives. + comments: Store the accession returned from the BioSample submission. NCBI BioSamples + will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD + slot_uri: GENEPIO:0001139 + range: WhitespaceMinimizedString + recommended: true + pattern: '{UPPER_CASE}' + structured_pattern: + syntax: '{UPPER_CASE}' + partial_match: false + interpolated: true + examples: + - value: SAMN14180202, SAMD00000001 + insdc_sequence_read_accession: + name: insdc_sequence_read_accession + title: INSDC sequence read accession + description: The identifier assigned to a sequence in one of the International + Nucleotide Sequence Database Collaboration (INSDC) repositories. + comments: Store the accession assigned to the submitted sequence. European Nucleotide + Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start + with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome + Sequence Archive (GSA) accessions start with CRR. + slot_uri: GENEPIO:0101203 + range: WhitespaceMinimizedString + pattern: '{UPPER_CASE}' + structured_pattern: + syntax: '{UPPER_CASE}' + partial_match: false + interpolated: true + examples: + - value: ERR123456, DRR123456, CRR123456 + insdc_assembly_accession: + name: insdc_assembly_accession + title: INSDC assembly accession + description: The versioned identifier assigned to an assembly or consensus sequence + in one of the International Nucleotide Sequence Database Collaboration (INSDC) + repositories. + comments: Store the versioned accession assigned to the submitted sequence e.g. + the GenBank accession version. + slot_uri: GENEPIO:0101204 + range: WhitespaceMinimizedString + pattern: '{UPPER_CASE}' + structured_pattern: + syntax: '{UPPER_CASE}' + partial_match: false + interpolated: true + examples: + - value: LZ986655.1 + sample_collection_data_steward_name: + name: sample_collection_data_steward_name + title: sample_collection_data_steward_name + description: The name of the individual responsible for the data governance, (meta)data + usage and distribution of the sample. + comments: Provide the name of the sample collection data steward. + slot_uri: GENEPIO:0100762 + range: WhitespaceMinimizedString + examples: + - value: Joe Bloggs + sample_collection_data_steward_contact_email: + name: sample_collection_data_steward_contact_email + title: sample_collection_data_steward_contact_email + description: The email address of the individual responsible for the data governance, + (meta)data usage and distribution of the sample. + comments: Provide the email address of the sample collection data steward. This + may or may not be the same individual/organization that collected the sample. + If the contact is the same, provide the same address as the "sample collector + contact email". + slot_uri: GENEPIO:0101107 + range: WhitespaceMinimizedString + examples: + - value: bloggsj@aglab.ca + sample_collected_by: + name: sample_collected_by + title: sample_collected_by + description: The name of the organization with which the sample collector is affiliated. + comments: The name of the agency should be written out in full, (with minor exceptions) + and be consistent across multiple submissions. + slot_uri: GENEPIO:0001153 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + required: true + examples: + - value: Public Health Agency of Canada + exact_mappings: + - BIOSAMPLE_Enterics:collected_by + sample_collector_contact_email: + name: sample_collector_contact_email + title: sample_collector_contact_email + description: The email address of the contact responsible for follow-up regarding + the sample. + comments: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, + or RespLab@lab.ca + slot_uri: GENEPIO:0001156 + range: WhitespaceMinimizedString + pattern: ^\S+@\S+\.\S+$ + examples: + - value: WaterTester@facility.ca + geo_loc_name_country: + name: geo_loc_name_country + title: geo_loc_name_(country) + description: The country of origin of the sample. + comments: If known, select a value from the pick list. + slot_uri: GENEPIO:0001181 + any_of: + - range: geo_loc_name_(country) menu + - range: null value menu + required: true + examples: + - value: Canada + exact_mappings: + - BIOSAMPLE_Enterics:geo_loc_name + geo_loc_name_state_province_territory: + name: geo_loc_name_state_province_territory + title: geo_loc_name_(state/province/territory) + description: The state/province/territory of origin of the sample. + comments: 'Provide the state/province/territory name from the GAZ geography ontology. + Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga' + slot_uri: GENEPIO:0001185 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + required: true + examples: + - value: Western Cape + exact_mappings: + - BIOSAMPLE_Enterics:geo_loc_name + geo_loc_name_county_region: + name: geo_loc_name_county_region + title: geo_loc_name_(county/region) + description: The county/region of origin of the sample. + comments: 'Provide the county/region name from the GAZ geography ontology. Search + for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz' + slot_uri: GENEPIO:0100280 + range: WhitespaceMinimizedString + examples: + - value: Derbyshire + geo_loc_name_city: + name: geo_loc_name_city + title: geo_loc_name_(city) + description: The city of origin of the sample. + comments: 'Provide the city name from the GAZ geography ontology. Search for geography + terms here: https://www.ebi.ac.uk/ols/ontologies/gaz' + slot_uri: GENEPIO:0001189 + range: WhitespaceMinimizedString + examples: + - value: Vancouver + geo_loc_name_site__: + name: geo_loc_name_site__ + title: geo_loc_name_(site) + description: The name of a specific geographical location e.g. Credit River (rather + than river). + comments: Provide the name of the specific geographical site using a specific + noun (a word that names a certain place, thing). + slot_uri: GENEPIO:0100436 + range: WhitespaceMinimizedString + examples: + - value: Credit River + geo_loc_latitude: + name: geo_loc_latitude + title: geo_loc_latitude + description: The latitude coordinates of the geographical location of sample collection. + comments: Provide latitude coordinates if available. Do not use the centre of + the city/region/province/state/country or the location of your agency as a proxy, + as this implicates a real location and is misleading. Specify as degrees latitude + in format "d[d.dddd] N|S". + slot_uri: GENEPIO:0100309 + range: WhitespaceMinimizedString + examples: + - value: 38.98 N + exact_mappings: + - BIOSAMPLE_Enterics:lat_lon + geo_loc_longitude: + name: geo_loc_longitude + title: geo_loc_longitude + description: The longitude coordinates of the geographical location of sample + collection. + comments: Provide longitude coordinates if available. Do not use the centre of + the city/region/province/state/country or the location of your agency as a proxy, + as this implicates a real location and is misleading. Specify as degrees longitude + in format "d[dd.dddd] W|E". + slot_uri: GENEPIO:0100310 + range: WhitespaceMinimizedString + examples: + - value: 77.11 W + exact_mappings: + - BIOSAMPLE_Enterics:lat_lon + organism: + name: organism + title: organism + description: Taxonomic name of the organism. + comments: 'Provide the official nomenclature for the organism(s) present in the + sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. + Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy.' + slot_uri: GENEPIO:0001191 + any_of: + - range: organism menu + - range: null value menu + multivalued: true + required: true + examples: + - value: Vibrio cholerae + exact_mappings: + - BIOSAMPLE_Enterics:organism + influenza_subtype: + name: influenza_subtype + title: influenza_subtype + slot_uri: GENEPIO:0101108 + range: influenza_subsubtype menu + multivalued: true + required: true + influenza_subtyping_scheme_name: + name: influenza_subtyping_scheme_name + title: influenza_subtyping_scheme_name + slot_uri: GENEPIO:0101109 + range: influenza_subtyping_scheme_name menu + taxonomic_identification_process: + name: taxonomic_identification_process + title: taxonomic_identification_process + slot_uri: GENEPIO:0100583 + range: taxonomic_identification_process menu + virus_identifier: + name: virus_identifier + title: virus_identifier + slot_uri: GENEPIO:0101110 + range: WhitespaceMinimizedString + who_oie_fao_h5_clade: + name: who_oie_fao_h5_clade + title: WHO/OIE/FAO_H5_clade + slot_uri: GENEPIO:0101111 + range: WhitespaceMinimizedString + sample_collection_date: + name: sample_collection_date + title: sample_collection_date + description: The date on which the sample was collected, or sampling began for + a continuous sample. + comments: If your sample is a continuous sample please use this field to capture + your start date. Sample collection date is critical for surveillance and many + types of analyses. Required granularity includes year, month and day. The date + should be provided in ISO 8601 standard format "YYYY-MM-DD". + slot_uri: GENEPIO:0001174 + any_of: + - range: date + - range: null value menu + required: true + examples: + - value: '2020-03-16' + exact_mappings: + - BIOSAMPLE_Enterics:collection_date + sample_collection_end_date: + name: sample_collection_end_date + title: sample_collection_end_date + description: The date on which sample collection ended for a continuous sample. + comments: Provide the date that sample collection ended in ISO 8601 format i.e. + YYYY-MM-DD + slot_uri: GENEPIO:0101071 + any_of: + - range: date + - range: null value menu + recommended: true + examples: + - value: '2020-03-18' + sample_collection_start_time: + name: sample_collection_start_time + title: sample_collection_start_time + description: The time at which sample collection began. + comments: Provide this time in ISO 8601 24hr format, in your local time. + slot_uri: GENEPIO:0101072 + any_of: + - range: time + - range: null value menu + recommended: true + examples: + - value: 17:15 PST + sample_collection_end_time: + name: sample_collection_end_time + title: sample_collection_end_time + description: The time at which sample collection ended. + comments: Provide this time in ISO 8601 24hr format, in your local time. + slot_uri: GENEPIO:0101073 + any_of: + - range: time + - range: null value menu + recommended: true + examples: + - value: 19:15 PST + sample_collection_time_of_day: + name: sample_collection_time_of_day + title: sample_collection_time_of_day + description: The descriptive time of day during which the sample was collected. + comments: If known, select a value from the pick list. The time of sample processing + matters especially for grab samples, as fecal concentration in wastewater fluctuates + over the course of the day. + slot_uri: GENEPIO:0100765 + any_of: + - range: sample_collection_time_of_day menu + - range: null value menu + examples: + - value: Morning + sample_collection_time_duration_value: + name: sample_collection_time_duration_value + title: sample_collection_time_duration_value + description: The amount of time over which the sample was collected. + comments: Provide the numerical value of time. + slot_uri: GENEPIO:0100766 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + recommended: true + examples: + - value: '4' + sample_collection_time_duration_unit: + name: sample_collection_time_duration_unit + title: sample_collection_time_duration_unit + description: The units of the time duration measurement of sample collection. + comments: Provide the units from the pick list. + slot_uri: GENEPIO:0100767 + any_of: + - range: sample_collection_duration_unit menu + - range: null value menu + recommended: true + examples: + - value: Hour + sample_received_date: + name: sample_received_date + title: sample received date + description: The date on which the sample was received. + comments: Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". + slot_uri: GENEPIO:0001179 + any_of: + - range: date + - range: null value menu + examples: + - value: '2020-03-28' + sample_processing_date: + name: sample_processing_date + title: sample processing date + description: The date on which the sample was processed. + comments: Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". + The sample may be collected and processed (e.g. filtered, extraction) on the + same day, or on different dates. + slot_uri: GENEPIO:0100763 + any_of: + - range: date + - range: null value menu + examples: + - value: '2020-03-16' + host_origin_geo_loc_name_country: + name: host_origin_geo_loc_name_country + title: host_origin_geo_loc_name (country) + description: The country of origin of the host. + comments: If a sample is from a human or animal host that originated from outside + of Canada, provide the the name of the country where the host originated by + selecting a value from the template pick list. If the information is unknown + or cannot be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100438 + any_of: + - range: geo_loc_name (country) menu + - range: null value menu + examples: + - value: South Africa [GAZ:00001094] + food_product_origin_geo_loc_name_country: + name: food_product_origin_geo_loc_name_country + title: food_product_origin_geo_loc_name (country) + description: The country of origin of a food product. + comments: If a food product was sampled and the food product was manufactured + outside of Canada, provide the name of the country where the food product originated + by selecting a value from the template pick list. If the information is unknown + or cannot be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100437 + any_of: + - range: geo_loc_name (country) menu + - range: null value menu + examples: + - value: United States of America [GAZ:00002459] + exact_mappings: + - BIOSAMPLE_Enterics:food_origin + food_product: + name: food_product + title: food_product + description: A material consumed and digested for nutritional value or enjoyment. + comments: This field includes animal feed. If applicable, select the standardized + term and ontology ID for the anatomical material from the picklist provided. + Multiple values can be provided, separated by a semi-colon. + slot_uri: GENEPIO:0100444 + any_of: + - range: food_product menu + - range: null value menu + multivalued: true + required: true + examples: + - value: Feather meal [FOODON:00003927] + - value: Bone meal [ENVO:02000054] + - value: Chicken breast [FOODON:00002703] + exact_mappings: + - GISAID:isolation_source + - GISAID:food_product + - BIOSAMPLE_Enterics:isolation_source + - BIOSAMPLE_Enterics:food_product_type + food_product_properties: + name: food_product_properties + title: food_product_properties + description: Any characteristic of the food product pertaining to its state, processing, + a label claim, or implications for consumers. + comments: Provide any characteristics of the food product including whether it + has been cooked, processed, preserved, any known information about its state + (e.g. raw, ready-to-eat), any known information about its containment (e.g. + canned), and any information about a label claim (e.g. organic, fat-free). + slot_uri: GENEPIO:0100445 + any_of: + - range: food_product_properties menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Food (chopped) [FOODON:00002777] + - value: Ready-to-eat (RTE) [FOODON:03316636] + exact_mappings: + - GISAID:isolation_source + - GISAID:food_product_properties + - BIOSAMPLE_Enterics:isolation_source + food_packaging: + name: food_packaging + title: food_packaging + description: The type of packaging used to contain a food product. + comments: If known, provide information regarding how the food product was packaged. + slot_uri: GENEPIO:0100447 + any_of: + - range: food_packaging menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Plastic tray or pan [FOODON:03490126] + exact_mappings: + - GISAID:isolation_source + - GISAID:food_packaging + - BIOSAMPLE_Enterics:food_contain_wrap + food_quality_date: + name: food_quality_date + title: food_quality_date + description: A date recommended for the use of a product while at peak quality, + this date is not a reflection of safety unless used on infant formula. + comments: This date is typically labeled on a food product as "best if used by", + best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave + blank or provide a null value. + slot_uri: GENEPIO:0100615 + range: date + examples: + - value: '2020-05-25' + exact_mappings: + - BIOSAMPLE_Enterics:food_quality_date + food_packaging_date: + name: food_packaging_date + title: food_packaging_date + description: A food product's packaging date as marked by a food manufacturer + or retailer. + comments: The packaging date should not be confused with, nor replaced by a Best + Before date or other food quality date. If the date is known, leave blank or + provide a null value. + slot_uri: GENEPIO:0100616 + range: date + examples: + - value: '2020-05-25' + environmental_site: + name: environmental_site + title: environmental_site + description: An environmental location may describe a site in the natural or built + environment e.g. hospital, wet market, bat cave. + comments: If applicable, select the standardized term and ontology ID for the + environmental site from the picklist provided. Multiple values can be provided, + separated by a semi-colon. + slot_uri: GENEPIO:0001232 + any_of: + - range: environmental_site menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Poultry hatchery [ENVO:01001874] + exact_mappings: + - GISAID:isolation_source + - GISAID:environmental_site + - BIOSAMPLE_Enterics:isolation_source + - BIOSAMPLE_Enterics:animal_env + environmental_material: + name: environmental_material + title: environmental_material + description: A substance obtained from the natural or man-made environment e.g. + soil, water, sewage, door handle, bed handrail, face mask. + comments: If applicable, select the standardized term and ontology ID for the + environmental material from the picklist provided. Multiple values can be provided, + separated by a semi-colon. + slot_uri: GENEPIO:0001223 + any_of: + - range: environmental_material menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Soil [ENVO:00001998] + - value: Water [CHEBI:15377] + - value: Wastewater [ENVO:00002001] + - value: Broom [ENVO:03501377] + exact_mappings: + - GISAID:isolation_source + - GISAID:environmental_material + - BIOSAMPLE_Enterics:isolation_source + anatomical_material: + name: anatomical_material + title: anatomical_material + description: A substance obtained from an anatomical part of an organism e.g. + tissue, blood. + comments: An anatomical material is a substance taken from the body. If applicable, + select the standardized term and ontology ID for the anatomical material from + the picklist provided. Multiple values can be provided, separated by a semi-colon. + slot_uri: GENEPIO:0001211 + any_of: + - range: anatomical_material menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Tissue [UBERON:0000479] + - value: Blood [UBERON:0000178] + exact_mappings: + - GISAID:isolation_source + - GISAID:anatomical_material + - BIOSAMPLE_Enterics:host_tissue_sampled + - BIOSAMPLE_Enterics:isolation_source + body_product: + name: body_product + title: body_product + description: A substance excreted/secreted from an organism e.g. feces, urine, + sweat. + comments: A body product is a substance produced by the body but meant to be excreted/secreted + (i.e. not part of the body). If applicable, select the standardized term and + ontology ID for the body product from the picklist provided. Multiple values + can be provided, separated by a semi-colon. + slot_uri: GENEPIO:0001216 + any_of: + - range: body_product menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Feces [UBERON:0001988] + - value: Urine [UBERON:0001088] + exact_mappings: + - GISAID:isolation_source + - GISAID:body_product + - BIOSAMPLE_Enterics:host_body_product + - BIOSAMPLE_Enterics:isolation_source + anatomical_part: + name: anatomical_part + title: anatomical_part + description: An anatomical part of an organism e.g. oropharynx. + comments: An anatomical part is a structure or location in the body. If applicable, + select the standardized term and ontology ID for the anatomical material from + the picklist provided. Multiple values can be provided, separated by a semi-colon. + slot_uri: GENEPIO:0001214 + any_of: + - range: anatomical_part menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Snout [UBERON:0006333] + exact_mappings: + - GISAID:isolation_source + - GISAID:anatomical_part + - BIOSAMPLE_Enterics:isolation_source + collection_device: + name: collection_device + title: collection_device + description: The instrument or container used to collect the sample e.g. swab. + comments: This field includes animal feed. If applicable, select the standardized + term and ontology ID for the anatomical material from the picklist provided. + Multiple values can be provided, separated by a semi-colon. + slot_uri: GENEPIO:0001234 + any_of: + - range: collection_device menu + - range: null value menu + recommended: true + examples: + - value: Drag swab [OBI:0002822] + exact_mappings: + - GISAID:isolation_source + - GISAID:collection_device + - BIOSAMPLE_Enterics:samp_collect_device + - BIOSAMPLE_Enterics:isolation_source + collection_method: + name: collection_method + title: collection_method + description: The process used to collect the sample e.g. phlebotomy, necropsy. + comments: If applicable, provide the standardized term and ontology ID for the + anatomical material from the picklist provided. Multiple values can be provided, + separated by a semi-colon. + slot_uri: GENEPIO:0001241 + any_of: + - range: collection_method menu + - range: null value menu + recommended: true + examples: + - value: Rinsing for specimen collection [GENEPIO_0002116] + exact_mappings: + - GISAID:isolation_source + - GISAID:collection_method + - BIOSAMPLE_Enterics:isolation_source + sample_volume_measurement_value: + name: sample_volume_measurement_value + title: sample_volume_measurement_value + description: The numerical value of the volume measurement of the sample collected. + comments: Provide the numerical value of volume. + slot_uri: GENEPIO:0100768 + range: WhitespaceMinimizedString + examples: + - value: '5' + sample_volume_measurement_unit: + name: sample_volume_measurement_unit + title: sample_volume_measurement_unit + description: The units of the volume measurement of the sample collected. + comments: Provide the units from the pick list. + slot_uri: GENEPIO:0100769 + range: sample_volume_measurement_unit menu + examples: + - value: milliliter (mL) [UO:0000098] + residual_sample_status: + name: residual_sample_status + title: residual_sample_status + description: The status of the residual sample (whether any sample remains after + its original use). + comments: Residual samples are samples that remain after the sample material was + used for its original purpose. Select a residual sample status from the picklist. + If sample still exists, select "Residual sample remaining (some sample left)". + slot_uri: GENEPIO:0101090 + range: residual_sample_status menu + examples: + - value: No residual sample (sample all used) [GENEPIO:0101088] + purpose_of_sampling: + name: purpose_of_sampling + title: purpose_of_sampling + description: The reason that the sample was collected. + comments: The reason a sample was collected may provide information about potential + biases in sampling strategy. Provide the purpose of sampling from the picklist + in the template. Most likely, the sample was collected for Public health surveillance. + The reason why a sample was originally collected may differ from the reason + why it was selected for sequencing, which should be indicated in the "purpose + of sequencing" field. + slot_uri: GENEPIO:0001198 + any_of: + - range: purpose_of_sampling menu + - range: null value menu + multivalued: true + required: true + examples: + - value: Public health surveillance + exact_mappings: + - BIOSAMPLE_Enterics:purpose_of_sampling + presampling_activity: + name: presampling_activity + title: presampling_activity + description: The activities or variables upstream of sample collection that may + affect the sample. + comments: If there was an activity that would affect the sample prior to collection + (this is different than sample processing), provide the activities by selecting + one or more values from the template pick list. If the information is unknown + or cannot be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100433 + any_of: + - range: presampling_activity menu + - range: null value menu + multivalued: true + examples: + - value: Agricultural activity + presampling_activity_details: + name: presampling_activity_details + title: presampling_activity_details + description: The details of the activities or variables that affected the sample + collected. + comments: Briefly describe the presampling activities using free text. + slot_uri: GENEPIO:0100434 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + examples: + - value: Agricultural waste from large farm contributes waste to the site sampled. + sample_storage_method: + name: sample_storage_method + title: sample_storage_method + description: The process used to store the sample. + comments: Provide details of how the sample was stored from time of collection + until time of processing. If there were issues with the cold chain storage, + note those here. + slot_uri: GENEPIO:0100448 + range: WhitespaceMinimizedString + examples: + - value: The sample was placed in a tube in a cooler bag during transportation + (~3 hours) to the lab site. At this point the sample was placed in storage + medium and put in a -10C freezer until it was processed and extracted 5 days + later. + sample_storage_medium: + name: sample_storage_medium + title: sample_storage_medium + description: The medium in which a sample is stored. + comments: Provide the name of the transport medium or storage medium used for + this sample. If none was used, leave blank or write "None". + slot_uri: GENEPIO:0100449 + range: WhitespaceMinimizedString + examples: + - value: Cary-Blair transport medium + sample_storage_duration_value: + name: sample_storage_duration_value + title: sample_storage_duration_value + description: The numerical value of the time measurement during which a sample + is in storage. + comments: Provide the numerical value of time. + slot_uri: GENEPIO:0101014 + range: WhitespaceMinimizedString + examples: + - value: '5' + sample_storage_duration_unit: + name: sample_storage_duration_unit + title: sample_storage_duration_unit + description: The units of a measured sample storage duration. + comments: Provide the units from the pick list. + slot_uri: GENEPIO:0101015 + any_of: + - range: sample_storage_duration_unit menu + - range: null value menu + examples: + - value: Day + specimen_processing: + name: specimen_processing + title: specimen_processing + description: Any processing applied to the sample during or after receiving the + sample. + comments: Select processes from the picklist that were applied to this sample. + slot_uri: GENEPIO:0001253 + any_of: + - range: specimen_processing menu + - range: null value menu + multivalued: true + examples: + - value: Centrifugation + specimen_processing_details: + name: specimen_processing_details + title: specimen_processing_details + description: The details of the processing applied to the sample during or after + receiving the sample. + comments: Briefly describe the processes applied to the sample. + slot_uri: GENEPIO:0100311 + range: WhitespaceMinimizedString + examples: + - value: 25 samples were pooled and further prepared as a single sample during + library prep. + experimental_protocol: + name: experimental_protocol + title: experimental_protocol + description: The name of the overarching experimental methodology that was used + to process the biomaterial. + comments: Provide the name of the methodology used in your study. If available, + provide a link to the protocol. + slot_uri: GENEPIO:0101029 + range: WhitespaceMinimizedString + experimental_specimen_role_type: + name: experimental_specimen_role_type + title: experimental_specimen_role_type + description: The type of role that the sample represents in the experiment. + comments: Samples can play different types of roles in experiments. A sample under + study in one experiment may act as a control or be a replicate of another sample + in another experiment. This field is used to distinguish samples under study + from controls, replicates, etc. If the sample acted as an experimental control + or a replicate, select a role type from the picklist. If the sample was not + a control, leave blank or select "Not Applicable". + slot_uri: GENEPIO:0100921 + any_of: + - range: experimental_specimen_role_type menu + - range: null value menu + multivalued: true + examples: + - value: Positive experimental control + experimental_specimen_details: + name: experimental_specimen_details + title: experimental_specimen_details + slot_uri: GENEPIO:0101112 + range: WhitespaceMinimizedString + available_data_types: + name: available_data_types + title: available_data_types + description: The type of data that is available, that may or may not require permission + to access. + comments: This field provides information about additional data types that are + available that may provide context for interpretation of the sequence data. + Provide a term from the picklist for additional data types that are available. + Additional data types may require special permission to access. Contact the + data provider for more information. + slot_uri: GENEPIO:0100690 + any_of: + - range: available_data_types menu + - range: null value menu + multivalued: true + examples: + - value: Total coliform count [GENEPIO:0100729] + available_data_type_details: + name: available_data_type_details + title: available_data_type_details + description: Detailed information regarding other available data types. + comments: Use this field to provide free text details describing other available + data types that may provide context for interpreting genomic sequence data. + slot_uri: GENEPIO:0101023 + range: WhitespaceMinimizedString + examples: + - value: Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) + bacteria + host_common_name: + name: host_common_name + title: host_(common_name) + description: The commonly used name of the host. + comments: If the sample is directly from a host, either a common or scientific + name must be provided (although both can be included, if known). If known, + provide the common name. + slot_uri: GENEPIO:0001386 + any_of: + - range: host (common name) menu + - range: null value menu + recommended: true + examples: + - value: Cow [NCBITaxon:9913] + - value: Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] + exact_mappings: + - BIOSAMPLE_Enterics:host + host_scientific_name: + name: host_scientific_name + title: host_(scientific_name) + description: The taxonomic, or scientific name of the host. + comments: If the sample is directly from a host, either a common or scientific + name must be provided (although both can be included, if known). If known, + select the scientific name from the picklist provided. + slot_uri: GENEPIO:0001387 + any_of: + - range: host (scientific name) menu + - range: null value menu + recommended: true + examples: + - value: Bos taurus [NCBITaxon:9913] + - value: Homo sapiens [NCBITaxon:9103] + exact_mappings: + - GISAID:host + - BIOSAMPLE_Enterics:isolation_source + - BIOSAMPLE_Enterics:host + host_ecotype: + name: host_ecotype + title: host_(ecotype) + description: The biotype resulting from selection in a particular habitat, e.g. + the A. thaliana Ecotype Ler. + comments: Provide the name of the ecotype of the host organism. + slot_uri: GENEPIO:0100450 + range: WhitespaceMinimizedString + examples: + - value: Sea ecotype + exact_mappings: + - BIOSAMPLE_Enterics:host_variety + host_breed: + name: host_breed + title: host_(breed) + description: A breed is a specific group of domestic animals or plants having + homogeneous appearance, homogeneous behavior, and other characteristics that + distinguish it from other animals or plants of the same species and that were + arrived at through selective breeding. + comments: Provide the name of the breed of the host organism. + slot_uri: GENEPIO:0100451 + range: WhitespaceMinimizedString + examples: + - value: Holstein + exact_mappings: + - GISAID:host_disease + - BIOSAMPLE_Enterics:host_animal_breed + host_food_production_name: + name: host_food_production_name + title: host_(food production name) + description: The name of the host at a certain stage of food production, which + may depend on its age or stage of sexual maturity. + comments: Select the host's food production name from the pick list. + slot_uri: GENEPIO:0100452 + any_of: + - range: host (food production name) menu + - range: null value menu + examples: + - value: Calf [FOODON:03411349] + exact_mappings: + - BIOSAMPLE_Enterics:host + host_age: + name: host_age + title: host_age + description: Age of host at the time of sampling. + comments: If known, provide age. Age-binning is also acceptable. + slot_uri: GENEPIO:0001392 + any_of: + - range: decimal + - range: null value menu + maximum_value: 130 + required: true + examples: + - value: '79' + exact_mappings: + - GISAID:Patient%20age + - CNPHI:host_age + host_age_unit: + name: host_age_unit + title: host_age_unit + description: The units used to measure the host's age. + comments: If known, provide the age units used to measure the host's age from + the pick list. + slot_uri: GENEPIO:0001393 + any_of: + - range: host_age_unit menu + - range: null value menu + required: true + examples: + - value: year [UO:0000036] + host_age_bin: + name: host_age_bin + title: host_age_bin + description: Age of host at the time of sampling, expressed as an age group. + comments: Select the corresponding host age bin from the pick list provided in + the template. If not available, provide a null value or leave blank. + slot_uri: GENEPIO:0001394 + any_of: + - range: host_age_bin menu + - range: null value menu + exact_mappings: + - BIOSAMPLE_Enterics:host_age + host_disease: + name: host_disease + title: host_disease + description: The name of the disease experienced by the host. + comments: "This field is only required if the Pathogen.cl package was selected.\ + \ If the host was sick, provide the name of the disease.The standardized term\ + \ can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid\ + \ If the disease is not known, put \u201Cmissing\u201D." + slot_uri: GENEPIO:0001391 + any_of: + - range: host_disease menu + - range: null value menu + examples: + - value: mastitis, gastroenteritis + exact_mappings: + - BIOSAMPLE_Enterics:host_disease + host_health_state: + name: host_health_state + title: host_health_state + description: Health status of the host at the time of sample collection. + comments: If known, select a value from the pick list. + slot_uri: GENEPIO:0001388 + any_of: + - range: host_health_state menu + - range: null value menu + examples: + - value: Asymptomatic [NCIT:C3833] + exact_mappings: + - GISAID:Patient%20status + - CNPHI:host_health_state + host_health_status_details: + name: host_health_status_details + title: host_health_status_details + description: Further details pertaining to the health or disease status of the + host at time of collection. + comments: If known, select a value from the pick list. + slot_uri: GENEPIO:0001389 + any_of: + - range: host_health_status_details menu + - range: null value menu + examples: + - value: Hospitalized (ICU) [GENEPIO:0100046] + host_health_outcome: + name: host_health_outcome + title: host_health_outcome + description: Disease outcome in the host. + comments: If known, select a value from the pick list. + slot_uri: GENEPIO:0001390 + any_of: + - range: host_health_outcome menu + - range: null value menu + examples: + - value: Recovered [NCIT:C49498] + exact_mappings: + - CNPHI:host_disease_outcome + host_subject_id: + name: host_subject_id + title: host_subject_ID + description: 'A unique identifier by which each host can be referred to e.g. #131' + comments: Should be a unique, user-defined identifier. This ID can help link laboratory + data with epidemiological data, however, is likely sensitive information. Consult + the data steward. + slot_uri: GENEPIO:0001398 + range: WhitespaceMinimizedString + examples: + - value: BCxy123 + exact_mappings: + - CNPHI:host_subject_id + case_id: + name: case_id + title: case_ID + description: The identifier used to specify an epidemiologically detected case + of disease. + comments: Provide the case identifer. The case ID greatly facilitates linkage + between laboratory and epidemiological data. The case ID may be considered identifiable + information. Consult the data steward before sharing. + slot_uri: GENEPIO:0100281 + range: WhitespaceMinimizedString + examples: + - value: ABCD1234 + symptom_onset_date: + name: symptom_onset_date + title: symptom_onset_date + description: The date on which the symptoms began or were first noted. + comments: If known, provide the symptom onset date in ISO 8601 standard format + "YYYY-MM-DD". + slot_uri: GENEPIO:0001399 + any_of: + - range: date + - range: null value menu + examples: + - value: '2020-03-16' + signs_and_symptoms: + name: signs_and_symptoms + title: signs_and_symptoms + description: A perceived change in function or sensation, (loss, disturbance or + appearance) indicative of a disease, reported by a patient. + comments: Select all of the symptoms experienced by the host from the pick list. + slot_uri: GENEPIO:0001400 + any_of: + - range: signs_and_symptoms menu + - range: null value menu + recommended: true + examples: + - value: Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] + preexisting_conditions_and_risk_factors: + name: preexisting_conditions_and_risk_factors + title: pre-existing_conditions_and_risk_factors + description: 'Patient pre-existing conditions and risk factors. + + Pre-existing condition: A medical condition that existed prior to the current + infection. + + Risk Factor: A variable associated with an increased risk of disease or infection.' + comments: Select all of the pre-existing conditions and risk factors experienced + by the host from the pick list. If the desired term is missing, contact the + curation team. + slot_uri: GENEPIO:0001401 + any_of: + - range: pre-existing_conditions_and_risk_factors menu + - range: null value menu + recommended: true + examples: + - value: Asthma [HP:0002099] + complications: + name: complications + title: complications + description: Patient medical complications that are believed to have occurred + as a result of host disease. + comments: Select all of the complications experienced by the host from the pick + list. + slot_uri: GENEPIO:0001402 + any_of: + - range: complications menu + - range: null value menu + recommended: true + examples: + - value: Acute respiratory failure [MONDO:0001208] + exposure_event: + name: exposure_event + title: exposure event + description: Event leading to exposure. + comments: Select an exposure event from the pick list provided in the template. + If the desired term is missing, contact the curation team. + slot_uri: GENEPIO:0001417 + any_of: + - range: exposure event menu + - range: null value menu + examples: + - value: Social Gathering + exact_mappings: + - GISAID:Additional%20location%20information + - CNPHI:Exposure%20Event + - NML_LIMS:PH_EXPOSURE + exposure_contact_level: + name: exposure_contact_level + title: exposure contact level + description: The exposure transmission contact type. + comments: Select direct or indirect exposure from the pick-list. + slot_uri: GENEPIO:0001418 + any_of: + - range: exposure contact level menu + - range: null value menu + examples: + - value: Direct + exact_mappings: + - NML_LIMS:exposure%20contact%20level + host_role: + name: host_role + title: host role + description: The role of the host in relation to the exposure setting. + comments: Select the host's personal role(s) from the pick list provided in the + template. If the desired term is missing, contact the curation team. + slot_uri: GENEPIO:0001419 + range: host role menu + multivalued: true + examples: + - value: Inpatient + exact_mappings: + - NML_LIMS:PH_HOST_ROLE + exposure_setting: + name: exposure_setting + title: exposure setting + description: The setting leading to exposure. + comments: Select the host exposure setting(s) from the pick list provided in the + template. If a desired term is missing, contact the curation team. + slot_uri: GENEPIO:0001428 + range: exposure setting menu + multivalued: true + examples: + - value: Healthcare Setting + exact_mappings: + - NML_LIMS:PH_EXPOSURE + exposure_details: + name: exposure_details + title: exposure details + description: Additional host exposure information. + comments: Free text description of the exposure. + slot_uri: GENEPIO:0001431 + range: WhitespaceMinimizedString + examples: + - value: Case infected family at home + exact_mappings: + - NML_LIMS:PH_EXPOSURE_DETAILS + host_vaccination_status: + name: host_vaccination_status + title: host_vaccination_status + description: The vaccination status of the host (fully vaccinated, partially vaccinated, + or not vaccinated). + comments: Select the vaccination status of the host from the pick list. + slot_uri: GENEPIO:0001404 + any_of: + - range: host_vaccination_status menu + - range: null value menu + examples: + - value: Fully Vaccinated [GENEPIO:0100100] + exact_mappings: + - CNPHI:prior_sars_cov_2_vaccination + number_of_vaccine_doses_received: + name: number_of_vaccine_doses_received + title: number_of_vaccine_doses_received + description: The number of doses of the vaccine recived by the host. + comments: Record how many doses of the vaccine the host has received. + slot_uri: GENEPIO:0001406 + range: integer + minimum_value: 0 + examples: + - value: '2' + vaccination_dose_1_vaccine_name: + name: vaccination_dose_1_vaccine_name + title: vaccination_dose_1_vaccine_name + description: The name of the vaccine administered as the first dose of a vaccine + regimen. + comments: Provide the name and the corresponding manufacturer of the COVID-19 + vaccine administered as the first dose by selecting a value from the pick list + slot_uri: GENEPIO:0100313 + range: WhitespaceMinimizedString + examples: + - value: Pfizer-BioNTech (Comirnaty) + vaccination_dose_1_vaccination_date: + name: vaccination_dose_1_vaccination_date + title: vaccination_dose_1_vaccination_date + description: The date the first dose of a vaccine was administered. + comments: Provide the date the first dose of COVID-19 vaccine was administered. + The date should be provided in ISO 8601 standard format "YYYY-MM-DD". + slot_uri: GENEPIO:0100314 + range: date + examples: + - value: '2021-03-01' + vaccination_dose_2_vaccine_name: + name: vaccination_dose_2_vaccine_name + title: vaccination_dose_2_vaccine_name + description: The name of the vaccine administered as the second dose of a vaccine + regimen. + comments: Provide the name and the corresponding manufacturer of the COVID-19 + vaccine administered as the second dose by selecting a value from the pick list + slot_uri: GENEPIO:0100315 + range: WhitespaceMinimizedString + examples: + - value: Pfizer-BioNTech (Comirnaty) + vaccination_dose_2_vaccination_date: + name: vaccination_dose_2_vaccination_date + title: vaccination_dose_2_vaccination_date + description: The date the second dose of a vaccine was administered. + comments: Provide the date the second dose of COVID-19 vaccine was administered. + The date should be provided in ISO 8601 standard format "YYYY-MM-DD". + slot_uri: GENEPIO:0100316 + range: date + examples: + - value: '2021-09-01' + vaccination_history: + name: vaccination_history + title: vaccination history + description: A description of the vaccines received and the administration dates + of a series of vaccinations against a specific disease or a set of diseases. + comments: Free text description of the dates and vaccines administered against + a particular disease/set of diseases. It is also acceptable to concatenate the + individual dose information (vaccine name, vaccination date) separated by semicolons. + slot_uri: GENEPIO:0100321 + range: WhitespaceMinimizedString + examples: + - value: Pfizer-BioNTech (Comirnaty) + - value: '2021-03-01' + - value: Pfizer-BioNTech (Comirnaty) + - value: '2022-01-15' + exact_mappings: + - GISAID:Last%20vaccinated + influenza_antiviral_treatment_administration: + name: influenza_antiviral_treatment_administration + title: influenza_antiviral_treatment_administration + description: An action of giving or applying an influenza antiviral agent to a + patient as part of a treatment regimen. + slot_uri: GENEPIO:0101113 + any_of: + - range: influenza_antiviral_treatment_administration menu + - range: null value menu + examples: + - value: Influenza antiviral treatment administered [GENEPIO:0101194] + influenza_antiviral_agent__: + name: influenza_antiviral_agent__ + title: influenza_antiviral_agent + description: A substance that destroys or inhibits replication of viruses. + slot_uri: GENEPIO:0101114 + range: WhitespaceMinimizedString + influenza_antiviral_treatment_date: + name: influenza_antiviral_treatment_date + title: influenza_antiviral_treatment_date + description: The date on which the influenza antiviral agent was administered + to a patient as part of treatment + comments: This field records the exact date when the antiviral treatment was administered. + The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect + the first administration date if multiple doses were given. + slot_uri: GENEPIO:0101115 + range: date + water_catchment_area_human_population_measurement_value: + name: water_catchment_area_human_population_measurement_value + title: water_catchment_area_human_population_measurement_value + description: The numerical value of the human population measurement that contributes + to the composition of water in a catchment area. + comments: Where known, provide the numerical value of population size, i.e. the + number of people. + slot_uri: GENEPIO:0100773 + any_of: + - range: integer + - range: null value menu + recommended: true + examples: + - value: 10,500 + water_catchment_area_human_population_range: + name: water_catchment_area_human_population_range + title: water_catchment_area_human_population_range + description: The human population range of the water catchment that contributes + effluent to a wastewater site. + comments: Where catchment population is not well known, provide an estimation + of population size by selecting a value from the picklist. + slot_uri: GENEPIO:0100774 + any_of: + - range: water catchment area human population range menu + - range: null value menu + examples: + - value: 1,000 - 10,000 people + water_catchment_area_human_population_measurement_method: + name: water_catchment_area_human_population_measurement_method + title: water_catchment_area_human_population_measurement_method + description: The method by which a water catchment 's human population size was + measured or estimated + comments: Provide a brief description of how catchment population size was measured + or estimated. + slot_uri: GENEPIO:0100775 + range: WhitespaceMinimizedString + examples: + - value: population of jurisdiction encompassing the wastewater service area + water_catchment_area_human_population_density_value: + name: water_catchment_area_human_population_density_value + title: water catchment area human population density value + description: The numerical value describing the number of humans per geographical + area in a water catchment. + comments: Provide the numerical value of the population density in the catchement + area. + slot_uri: GENEPIO:0100776 + range: WhitespaceMinimizedString + examples: + - value: '4' + water_catchment_area_human_population_density_unit: + name: water_catchment_area_human_population_density_unit + title: water catchment area human population density unit + description: The unit describing the number of humans per geographical area in + a water catchment. + comments: Provide the unit of the population density in the catchement area. + slot_uri: GENEPIO:0100777 + any_of: + - range: water catchment area human population density unit menu + - range: null value menu + examples: + - value: persons per Km^2 + populated_area_type: + name: populated_area_type + title: populated area type + description: A type of area that is populated by humans to different degrees. + comments: Provide the populated area type from the pick list. + slot_uri: GENEPIO:0100778 + any_of: + - range: populated area type menu + - range: null value menu + examples: + - value: Urban area + sampling_weather_conditions: + name: sampling_weather_conditions + title: sampling weather conditions + description: The state of the atmosphere at a place and time as regards heat, + dryness, sunshine, wind, rain, etc. + comments: Provide the weather conditions at the time of sample collection. + slot_uri: GENEPIO:0100779 + any_of: + - range: sampling weather conditions menu + - range: null value menu + multivalued: true + examples: + - value: Rain + presampling_weather_conditions: + name: presampling_weather_conditions + title: presampling weather conditions + description: Weather conditions prior to collection that may affect the sample. + comments: Provide the weather conditions prior to sample collection. + slot_uri: GENEPIO:0100780 + any_of: + - range: presampling weather conditions menu + - range: null value menu + multivalued: true + examples: + - value: Drizzle + precipitation_measurement_value: + name: precipitation_measurement_value + title: precipitation measurement value + description: The amount of water which has fallen during a precipitation process. + comments: Provide the quantity of precipitation in the area leading up to the + time of sample collection. + slot_uri: GENEPIO:0100911 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + recommended: true + examples: + - value: '12' + water_depth: + name: water_depth + title: water_depth + description: The depth of some water. + comments: Provide the numerical depth only of water only (without units). + slot_uri: GENEPIO:0100440 + range: WhitespaceMinimizedString + examples: + - value: '5' + water_depth_units: + name: water_depth_units + title: water_depth_units + description: The units of measurement for water depth. + comments: Provide the units of measurement for which the depth was recorded. + slot_uri: GENEPIO:0101025 + any_of: + - range: water_depth_units menu + - range: null value menu + examples: + - value: meter (m) [UO:0000008] + sediment_depth: + name: sediment_depth + title: sediment_depth + description: The depth of some sediment. + comments: Provide the numerical depth only of the sediment (without units). + slot_uri: GENEPIO:0100697 + range: WhitespaceMinimizedString + examples: + - value: '2' + sediment_depth_units: + name: sediment_depth_units + title: sediment_depth_units + description: The units of measurement for sediment depth. + comments: Provide the units of measurement for which the depth was recorded. + slot_uri: GENEPIO:0101026 + any_of: + - range: sediment_depth_units menu + - range: null value menu + examples: + - value: meter (m) [UO:0000008] + air_temperature: + name: air_temperature + title: air_temperature + description: The temperature of some air. + comments: Provide the numerical value for the temperature of the air (without + units). + slot_uri: GENEPIO:0100441 + range: WhitespaceMinimizedString + examples: + - value: '25' + air_temperature_units: + name: air_temperature_units + title: air_temperature_units + description: The units of measurement for air temperature. + comments: Provide the units of measurement for which the temperature was recorded. + slot_uri: GENEPIO:0101027 + any_of: + - range: air_temperature_units menu + - range: null value menu + examples: + - value: degree Celsius (C) [UO:0000027] + water_temperature: + name: water_temperature + title: water_temperature + description: The temperature of some water. + comments: Provide the numerical value for the temperature of the water (without + units). + slot_uri: GENEPIO:0100698 + range: WhitespaceMinimizedString + examples: + - value: '4' + water_temperature_units: + name: water_temperature_units + title: water_temperature_units + description: The units of measurement for water temperature. + comments: Provide the units of measurement for which the temperature was recorded. + slot_uri: GENEPIO:0101028 + any_of: + - range: water_temperature_units menu + - range: null value menu + examples: + - value: degree Celsius (C) [UO:0000027] + weather_type: + name: weather_type + title: weather_type + description: The state of the atmosphere at a place and time as regards heat, + dryness, sunshine, wind, rain, etc. + comments: Provide the weather conditions at the time of sample collection. + slot_uri: GENEPIO:0100442 + any_of: + - range: weather_type menu + - range: null value menu + multivalued: true + examples: + - value: Rain [ENVO:01001564] + precipitation_measurement_unit: + name: precipitation_measurement_unit + title: precipitation measurement unit + description: The units of measurement for the amount of water which has fallen + during a precipitation process. + comments: Provide the units of precipitation by selecting a value from the pick + list. + slot_uri: GENEPIO:0100912 + any_of: + - range: precipitation measurement unit menu + - range: null value menu + recommended: true + examples: + - value: inch + precipitation_measurement_method: + name: precipitation_measurement_method + title: precipitation measurement method + description: The process used to measure the amount of water which has fallen + during a precipitation process. + comments: Provide the name of the procedure or method used to measure precipitation. + slot_uri: GENEPIO:0100913 + range: WhitespaceMinimizedString + examples: + - value: Rain gauge over a 12 hour period prior to sample collection + ambient_temperature_measurement_value: + name: ambient_temperature_measurement_value + title: ambient temperature measurement value + description: The numerical value of a measurement of the ambient temperature. + comments: Provide the numerical value of the measured temperature. + slot_uri: GENEPIO:0100935 + range: WhitespaceMinimizedString + examples: + - value: '70' + ambient_temperature_measurement_unit: + name: ambient_temperature_measurement_unit + title: ambient temperature measurement unit + description: The units of a measurement of the ambient temperature. + comments: Provide the units of the measured temperature. + slot_uri: GENEPIO:0100936 + any_of: + - range: ambient temperature measurement unit menu + - range: null value menu + examples: + - value: degree Celsius (C) + ph_measurement_value: + name: ph_measurement_value + title: pH measurement value + description: The measured pH value indicating the acidity or basicity(alkalinity) + of an aqueous solution. + comments: Provide the numerical value of the measured pH. + slot_uri: GENEPIO:0001736 + range: WhitespaceMinimizedString + examples: + - value: '7.4' + ph_measurement_method: + name: ph_measurement_method + title: pH measurement method + description: The process used to measure pH value. + comments: Provide the name of the procedure or technology used to measure pH. + slot_uri: GENEPIO:0100781 + range: WhitespaceMinimizedString + examples: + - value: pH test strip (litmus test) + total_daily_flow_rate_measurement_value: + name: total_daily_flow_rate_measurement_value + title: total daily flow rate measurement value + description: The numerical value of a measured fluid flow rate over the course + of a day. + comments: Provide the numerical value of the measured flow rate. + slot_uri: GENEPIO:0100905 + range: WhitespaceMinimizedString + examples: + - value: '10' + total_daily_flow_rate_measurement_unit: + name: total_daily_flow_rate_measurement_unit + title: total daily flow rate measurement unit + description: The units of a measured fluid flow rate over the course of a day. + comments: Provide the units of the measured flow rate by selecting a value from + the pick list. + slot_uri: GENEPIO:0100906 + any_of: + - range: total daily flow rate measurement unit menu + - range: null value menu + examples: + - value: million gallons per day (MGD) + total_daily_flow_rate_measurement_method: + name: total_daily_flow_rate_measurement_method + title: total daily flow rate measurement method + description: The process used to measure total daily fluid flow rate. + comments: Provide the name of the procedure or technology used to measure flow + rate. + slot_uri: GENEPIO:0100907 + range: WhitespaceMinimizedString + examples: + - value: Flow meter + instantaneous_flow_rate_measurement_value: + name: instantaneous_flow_rate_measurement_value + title: instantaneous flow rate measurement value + description: The numerical value of a measured instantaneous fluid flow rate. + comments: Provide the numerical value of the measured flow rate. + slot_uri: GENEPIO:0100908 + range: WhitespaceMinimizedString + examples: + - value: '25' + instantaneous_flow_rate_measurement_unit: + name: instantaneous_flow_rate_measurement_unit + title: instantaneous flow rate measurement unit + description: The units of a measured instantaneous fluid flow rate. + comments: Provide the units of the measured flow rate by selecting a value from + the pick list. + slot_uri: GENEPIO:0100909 + any_of: + - range: instantaneous flow rate measurement unit menu + - range: null value menu + examples: + - value: cubic meter per hour (m^3/h) + instantaneous_flow_rate_measurement_method: + name: instantaneous_flow_rate_measurement_method + title: instantaneous flow rate measurement method + description: The process used to measure instantaneous fluid flow rate. + comments: Provide the name of the procedure or technology used to measure flow + rate. + slot_uri: GENEPIO:0100910 + range: WhitespaceMinimizedString + examples: + - value: Flow meter + turbidity_measurement_value: + name: turbidity_measurement_value + title: turbidity measurement value + description: The numerical value of a measurement of turbidity. + comments: Provide the numerical value of the measured turbidity. + slot_uri: GENEPIO:0100783 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: '0.02' + turbidity_measurement_unit: + name: turbidity_measurement_unit + title: turbidity measurement unit + description: The units of a measurement of turbidity. + comments: Provide the units of the measured turbidity by selecting a value from + the pick list. + slot_uri: GENEPIO:0100914 + any_of: + - range: turbidity measurement unit menu + - range: null value menu + recommended: true + examples: + - value: nephelometric turbidity unit (NTU) + turbidity_measurement_method: + name: turbidity_measurement_method + title: turbidity measurement method + description: The process used to measure turbidity. + comments: Provide the name of the procedure or technology used to measure turbidity. + slot_uri: GENEPIO:0101013 + range: WhitespaceMinimizedString + examples: + - value: Nephelometric method + dissolved_oxygen_measurement_value: + name: dissolved_oxygen_measurement_value + title: dissolved oxygen measurement value + description: The numerical value of a measurement of dissolved oxygen. + comments: Provide the numerical value of the measured dissolved oxygen. + slot_uri: GENEPIO:0100915 + range: WhitespaceMinimizedString + examples: + - value: '5' + dissolved_oxygen_measurement_unit: + name: dissolved_oxygen_measurement_unit + title: dissolved oxygen measurement unit + description: The units of a measurement of dissolved oxygen. + comments: Provide the units of the measured dissolved oxygen by selecting a value + from the pick list. + slot_uri: GENEPIO:0100784 + any_of: + - range: dissolved oxygen measurement unit menu + - range: null value menu + examples: + - value: part per million (ppm) + dissolved_oxygen_measurement_method: + name: dissolved_oxygen_measurement_method + title: dissolved oxygen measurement method + description: The method used to measure dissolved oxygen. + comments: Provide the name of the procedure or technology used to measure dissolved + oxygen. + slot_uri: GENEPIO:0100785 + range: WhitespaceMinimizedString + examples: + - value: Dissolved oxygen meter in vertical direction + oxygen_reduction_potential_orp_measurement_value: + name: oxygen_reduction_potential_orp_measurement_value + title: oxygen reduction potential (ORP) measurement value + description: The numerical value of a measurement of oxygen reduction potential + (ORP). + comments: Provide the numerical value of the measured oxygen reduction potential. + slot_uri: GENEPIO:0100917 + range: WhitespaceMinimizedString + examples: + - value: '-50' + oxygen_reduction_potential_orp_measurement_unit: + name: oxygen_reduction_potential_orp_measurement_unit + title: oxygen reduction potential (ORP) measurement unit + description: The units of a measurement of oxygen reduction potential (ORP). + comments: Provide the units of the measured oxygen reduction potential by selecting + a value from the pick list. + slot_uri: GENEPIO:0100786 + any_of: + - range: oxygen reduction potential (ORP) measurement unit menu + - range: null value menu + examples: + - value: milliVolt (mV) + oxygen_reduction_potential_orp_measurement_method: + name: oxygen_reduction_potential_orp_measurement_method + title: oxygen reduction potential (ORP) measurement method + description: The method used to measure oxygen reduction potential (ORP). + comments: Provide the name of the procedure or technology used to measure oxygen + reduction potential. + slot_uri: GENEPIO:0100787 + range: WhitespaceMinimizedString + examples: + - value: ORP sensor + chemical_oxygen_demand_cod_measurement_value: + name: chemical_oxygen_demand_cod_measurement_value + title: chemical oxygen demand (COD) measurement value + description: The measured value from a chemical oxygen demand (COD) test. + comments: Provide the numerical value of the COD test result. + slot_uri: GENEPIO:0100788 + range: WhitespaceMinimizedString + examples: + - value: '26' + chemical_oxygen_demand_cod_measurement_unit: + name: chemical_oxygen_demand_cod_measurement_unit + title: chemical oxygen demand (COD) measurement unit + description: The units associated with a value from a chemical oxygen demand (COD) + test. + comments: Provide the units of the COD test result. + slot_uri: GENEPIO:0100789 + any_of: + - range: chemical oxygen demand (COD) measurement unit menu + - range: null value menu + examples: + - value: milligram per liter (mg/L) + chemical_oxygen_demand_cod_measurement_method: + name: chemical_oxygen_demand_cod_measurement_method + title: chemical oxygen demand (COD) measurement method + description: The method used to measure chemical oxygen demand (COD). + comments: Provide the name of the procedure or technology used to measure COD. + slot_uri: GENEPIO:0100790 + range: WhitespaceMinimizedString + examples: + - value: Hach LCK test kit + carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: + name: carbonaceous_biochemical_oxygen_demand_cbod_measurement_value + title: carbonaceous biochemical oxygen demand (CBOD) measurement value + description: The numerical value of a measurement of carbonaceous biochemical + oxygen demand (CBOD). + comments: Provide the numerical value of the measured CBOD. + slot_uri: GENEPIO:0100791 + range: WhitespaceMinimizedString + examples: + - value: '20' + carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: + name: carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit + title: carbonaceous biochemical oxygen demand (CBOD) measurement unit + description: The units of a measurement of carbonaceous biochemical oxygen demand + (CBOD). + comments: Provide the units of the measured CBOD by selecting a value from the + pick list. + slot_uri: GENEPIO:0100792 + any_of: + - range: carbonaceous biochemical oxygen demand (CBOD) measurement unit menu + - range: null value menu + examples: + - value: milligram per liter (mg/L) + carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: + name: carbonaceous_biochemical_oxygen_demand_cbod_measurement_method + title: carbonaceous biochemical oxygen demand (CBOD) measurement method + description: The method used to measure carbonaceous biochemical oxygen demand + (CBOD). + comments: Provide the name of the procedure or technology used to measure CBOD. + slot_uri: GENEPIO:0100793 + range: WhitespaceMinimizedString + examples: + - value: CBOD measurement by optical probe + total_suspended_solids_tss_measurement_value: + name: total_suspended_solids_tss_measurement_value + title: total suspended solids (TSS) measurement value + description: The numerical value from a total suspended solids (TSS) test. + comments: Provide the numerical value of the measured TSS. + slot_uri: GENEPIO:0100794 + range: WhitespaceMinimizedString + examples: + - value: '8' + total_suspended_solids_tss_measurement_unit: + name: total_suspended_solids_tss_measurement_unit + title: total suspended solids (TSS) measurement unit + description: The units associated with a value from a total suspended solids (TSS) + test. + comments: Provide the units of the measured TSS. + slot_uri: GENEPIO:0100795 + any_of: + - range: total suspended solids (TSS) measurement unit menu + - range: null value menu + examples: + - value: percent (%) + total_suspended_solids_tss_measurement_method: + name: total_suspended_solids_tss_measurement_method + title: total suspended solids (TSS) measurement method + description: The method used to measure total suspended solids (TSS). + comments: Provide the name of the procedure or technology used to measure TSS. + slot_uri: GENEPIO:0100796 + range: WhitespaceMinimizedString + examples: + - value: Vacuum filter through a 2-micron filter, then oven-dried and weighed + sample + total_dissolved_solids_tds_measurement_value: + name: total_dissolved_solids_tds_measurement_value + title: total dissolved solids (TDS) measurement value + description: The numerical value from a total dissolved solids (TDS) test. + comments: Provide the numerical value of the measured TDS. + slot_uri: GENEPIO:0100797 + range: WhitespaceMinimizedString + examples: + - value: '2' + total_dissolved_solids_tds_measurement_unit: + name: total_dissolved_solids_tds_measurement_unit + title: total dissolved solids (TDS) measurement unit + description: The units associated with a value from a total dissolved solids (TDS) + test. + comments: Provide the units of the measured TDS. + slot_uri: GENEPIO:0100798 + any_of: + - range: total dissolved solids (TDS) measurement unit menu + - range: null value menu + examples: + - value: percent (%) + total_dissolved_solids_tds_measurement_method: + name: total_dissolved_solids_tds_measurement_method + title: total dissolved solids (TDS) measurement method + description: The method used to measure total dissolved solids (TDS). + comments: Provide the name of the procedure or technology used to measure TDS. + slot_uri: GENEPIO:0100799 + range: WhitespaceMinimizedString + examples: + - value: Subtract calculated TSS from calculated TS + total_solids_ts_measurement_value: + name: total_solids_ts_measurement_value + title: total solids (TS) measurement value + description: The numerical value from a total solids (TS) test. + comments: Provide the numerical value of the measured TS. + slot_uri: GENEPIO:0100800 + range: WhitespaceMinimizedString + examples: + - value: '10' + total_solids_ts_measurement_unit: + name: total_solids_ts_measurement_unit + title: total solids (TS) measurement unit + description: The units associated with a value from a total solids (TS) test. + comments: Provide the units of the measured TS. + slot_uri: GENEPIO:0100801 + any_of: + - range: total solids (TS) measurement unit menu + - range: null value menu + examples: + - value: percent (%) + total_solids_ts_measurement_method: + name: total_solids_ts_measurement_method + title: total solids (TS) measurement method + description: The method used to measure total solids (TS). + comments: Provide the name of the procedure or technology used to measure TS. + slot_uri: GENEPIO:0100802 + range: WhitespaceMinimizedString + examples: + - value: Gravimetric method by oven drying, then weighing + alkalinity_measurement_value: + name: alkalinity_measurement_value + title: alkalinity measurement value + description: The numerical value of a measurement of alkalinity. + comments: Provide the numerical value of the measured alkalinity. + slot_uri: GENEPIO:0100878 + range: WhitespaceMinimizedString + examples: + - value: '3' + alkalinity_measurement_unit: + name: alkalinity_measurement_unit + title: alkalinity measurement unit + description: The units of a measurement of alkalinity. + comments: Provide the units of the measured alkalinity. + slot_uri: GENEPIO:0100879 + any_of: + - range: alkalinity measurement unit menu + - range: null value menu + examples: + - value: milligram per liter of calcium carbonate (mg/L CaCO3) + alkalinity_measurement_method: + name: alkalinity_measurement_method + title: alkalinity measurement method + description: The process used to measure alkalinity. + comments: Provide the name of the procedure or technology used to measure alkalinity. + slot_uri: GENEPIO:0100880 + range: WhitespaceMinimizedString + examples: + - value: Titration method + conductivity_measurement_value: + name: conductivity_measurement_value + title: conductivity measurement value + description: The numerical value of a measurement of conductivity. + comments: Provide the numerical value of the measured conductivity. + slot_uri: GENEPIO:0100916 + range: WhitespaceMinimizedString + examples: + - value: '1412' + conductivity_measurement_unit: + name: conductivity_measurement_unit + title: conductivity measurement unit + description: The units of a measurement of conductivity. + comments: Provide the units of the measured conductivity. + slot_uri: GENEPIO:0100803 + any_of: + - range: conductivity measurement unit menu + - range: null value menu + examples: + - value: "microSiemen per centimeter (\u03BCS/cm)" + conductivity_measurement_method: + name: conductivity_measurement_method + title: conductivity measurement method + description: The method used to measure conductivity. + comments: Provide the name of the procedure or technology used to measure conductivity. + slot_uri: GENEPIO:0100804 + range: WhitespaceMinimizedString + examples: + - value: Conductivity electrode and meter + salinity_measurement_value: + name: salinity_measurement_value + title: salinity measurement value + description: The numerical value of a measurement of salinity. + comments: Provide the numerical value of the measured salinity. + slot_uri: GENEPIO:0100805 + range: WhitespaceMinimizedString + examples: + - value: '35' + salinity_measurement_unit: + name: salinity_measurement_unit + title: salinity measurement unit + description: The units of a measurement of salinity. + comments: Provide the units of the measured salinity. + slot_uri: GENEPIO:0100806 + any_of: + - range: salinity measurement unit menu + - range: null value menu + examples: + - value: practical salinity unit (PSU) + salinity_measurement_method: + name: salinity_measurement_method + title: salinity measurement method + description: The method used to measure salinity. + comments: Provide the name of the procedure or technology used to measure salinity. + slot_uri: GENEPIO:0100807 + range: WhitespaceMinimizedString + examples: + - value: conductivity meter + total_nitrogen_tn_measurement_value: + name: total_nitrogen_tn_measurement_value + title: total nitrogen (TN) measurement value + description: The numerical value of a measurement of total nitrogen (TN). + comments: Provide the numerical value of the measured TN. + slot_uri: GENEPIO:0100808 + range: WhitespaceMinimizedString + examples: + - value: '120' + total_nitrogen_tn_measurement_unit: + name: total_nitrogen_tn_measurement_unit + title: total nitrogen (TN) measurement unit + description: The units of a measurement of total nitrogen (TN). + comments: Provide the units of the measured TN. + slot_uri: GENEPIO:0100809 + any_of: + - range: total nitrogen (TN) measurement unit menu + - range: null value menu + examples: + - value: milligram per liter (mg/L) + total_nitrogen_tn_measurement_method: + name: total_nitrogen_tn_measurement_method + title: total nitrogen (TN) measurement method + description: The method used to measure total nitrogen (TN). + comments: Provide the name of the procedure or technology used to measure TN. + slot_uri: GENEPIO:0100810 + range: WhitespaceMinimizedString + examples: + - value: Hach total nitrogen spectrophotometric test + total_phosphorus_tp_measurement_value: + name: total_phosphorus_tp_measurement_value + title: total phosphorus (TP) measurement value + description: The numerical value of a measurement of total phosphorus (TP). + comments: Provide the numerical value of the measured TP. + slot_uri: GENEPIO:0100811 + range: WhitespaceMinimizedString + examples: + - value: '2' + total_phosphorus_tp_measurement_unit: + name: total_phosphorus_tp_measurement_unit + title: total phosphorus (TP) measurement unit + description: The units of a measurement of total phosphorus (TP). + comments: Provide the units of the measured TP. + slot_uri: GENEPIO:0100812 + any_of: + - range: total phosphorus (TP) measurement unit menu + - range: null value menu + examples: + - value: milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) + total_phosphorus_tp_measurement_method: + name: total_phosphorus_tp_measurement_method + title: total phosphorus (TP) measurement method + description: The method used to measure total phosphorus (TP). + comments: Provide the name of the procedure or technology used to measure TP. + slot_uri: GENEPIO:0100813 + range: WhitespaceMinimizedString + examples: + - value: Merck phosphate spectrophotometric test kit + fecal_contamination_indicator_: + name: fecal_contamination_indicator_ + title: fecal contamination indicator + description: A gene, virus, bacteria, or substance used to measure the sanitary + quality of water in regards to fecal contamination. + comments: If a fecal contamination indicator was measured, select it from the + picklist. + slot_uri: GENEPIO:0100814 + any_of: + - range: fecal contamination indicator menu + - range: null value menu + recommended: true + examples: + - value: crAssphage + fecal_contamination_value: + name: fecal_contamination_value + title: fecal contamination value + description: The numerical value of a measurement of fecal contamination. + comments: Provide the numerical value of the measured fecal contamination. + slot_uri: GENEPIO:0100815 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: '10' + fecal_contamination_unit: + name: fecal_contamination_unit + title: fecal contamination unit + description: The units of a measurement of fecal contamination. + comments: Provide the units of the measured fecal contamination. + slot_uri: GENEPIO:0100816 + any_of: + - range: fecal contamination unit menu + - range: null value menu + recommended: true + examples: + - value: cycle threshold (Ct) / quantification cycle (Cq) + fecal_contamination_method: + name: fecal_contamination_method + title: fecal contamination method + description: The method used to measure fecal contamination. + comments: Provide the name of the procedure or technology used to measure fecal + contamination. + slot_uri: GENEPIO:0100817 + range: WhitespaceMinimizedString + examples: + - value: quantitative PCR assay + fecal_coliform_count_value: + name: fecal_coliform_count_value + title: fecal coliform count value + description: The numerical value of a measurement of fecal coliforms within a + sample. + comments: Provide the numerical value of the measured fecal coliforms. + slot_uri: GENEPIO:0100818 + range: WhitespaceMinimizedString + examples: + - value: '3' + fecal_coliform_count_unit: + name: fecal_coliform_count_unit + title: fecal coliform count unit + description: The units of a measurement of fecal coliforms. + comments: Provide the units of the measured fecal coliforms. + slot_uri: GENEPIO:0100819 + any_of: + - range: fecal coliform count unit menu + - range: null value menu + examples: + - value: most probable number per milliliter (MPN/mL) + fecal_coliform_count_method: + name: fecal_coliform_count_method + title: fecal coliform count method + description: The method used to measure fecal coliforms. + comments: Provide the name of the procedure or technology used to measure fecal + coliforms. + slot_uri: GENEPIO:0100820 + range: WhitespaceMinimizedString + examples: + - value: MPN method via serial dilutions until lack of growth + urinary_contamination_indicator: + name: urinary_contamination_indicator + title: urinary contamination indicator + description: A gene, virus, bacteria, or substance used to measure the sanitary + quality of water in regards to urinary contamination. + comments: If a urinary contamination indicator was measured, select it from the + picklist. + slot_uri: GENEPIO:0100837 + any_of: + - range: urinary contamination indicator menu + - range: null value menu + examples: + - value: urobilin + urinary_contamination_value: + name: urinary_contamination_value + title: urinary contamination value + description: The numerical value of a measurement of urinary contamination. + comments: Provide the numerical value of the measured urinary contamination. + slot_uri: GENEPIO:0100838 + range: WhitespaceMinimizedString + examples: + - value: '3' + urinary_contamination_unit: + name: urinary_contamination_unit + title: urinary contamination unit + description: The units of a measurement of urinary contamination. + comments: Provide the units of the measured urinary contamination. + slot_uri: GENEPIO:0100839 + any_of: + - range: urinary contamination unit menu + - range: null value menu + examples: + - value: nanograms per liter + urinary_contamination_method: + name: urinary_contamination_method + title: urinary contamination method + description: The method used to measure urinary contamination. + comments: Provide the name of the procedure or technology used to measure urinary + contamination. + slot_uri: GENEPIO:0100840 + range: WhitespaceMinimizedString + examples: + - value: Urobilin Concentration Test + sample_temperature_value_at_collection: + name: sample_temperature_value_at_collection + title: sample temperature value (at collection) + description: The numerical value of a measurement of temperature of a sample at + collection. + comments: Provide the numerical value of the measured temperature. + slot_uri: GENEPIO:0100821 + range: WhitespaceMinimizedString + examples: + - value: '20' + sample_temperature_unit_at_collection: + name: sample_temperature_unit_at_collection + title: sample temperature unit (at collection) + description: The units of a measurement of temperature of a sample at the time + of collection. + comments: Provide the units of the measured temperature. + slot_uri: GENEPIO:0100822 + any_of: + - range: sample temperature unit (at collection) menu + - range: null value menu + examples: + - value: degree Celsius (C) + sample_temperature_value_when_received: + name: sample_temperature_value_when_received + title: sample temperature value (when received) + description: The numerical value of a measurement of temperature of a sample upon + receipt. + comments: Provide the numerical value of the measured temperature. + slot_uri: GENEPIO:0100823 + range: WhitespaceMinimizedString + examples: + - value: '22' + sample_temperature_unit_when_received: + name: sample_temperature_unit_when_received + title: sample temperature unit (when received) + description: The units of a measurement of temperature of a sample at the time + upon receipt. + comments: Provide the units of the measured temperature. + slot_uri: GENEPIO:0100824 + any_of: + - range: sample temperature unit (when received) menu + - range: null value menu + examples: + - value: degree Celsius (C) + library_id: + name: library_id + title: library_ID + description: The user-specified identifier for the library prepared for sequencing. + comments: Every "library ID" from a single submitter must be unique. It can have + any format, but we suggest that you make it concise, unique and consistent within + your lab, and as informative as possible. + slot_uri: GENEPIO:0001448 + range: WhitespaceMinimizedString + examples: + - value: LS_2010_NP_123446 + sequencing_assay_type: + name: sequencing_assay_type + title: sequencing_assay_type + description: The overarching sequencing methodology that was used to determine + the sequence of a biomaterial. + comments: 'Example Guidance: Provide the name of the DNA or RNA sequencing technology + used in your study. If unsure refer to the protocol documentation, or provide + a null value.' + slot_uri: GENEPIO:0100997 + range: sequencing_assay_type menu + examples: + - value: whole genome sequencing assay [OBI:0002117] + sequencing_date: + name: sequencing_date + title: sequencing_date + description: The date the sample was sequenced. + comments: ISO 8601 standard "YYYY-MM-DD". + slot_uri: GENEPIO:0001447 + range: date + todos: + - '>={sample collection date}' + examples: + - value: '2020-06-22' + purpose_of_sequencing__: + name: purpose_of_sequencing__ + title: purpose_of_sequencing + description: The reason that the sample was sequenced. + comments: The reason why a sample was originally collected may differ from the + reason why it was selected for sequencing. The reason a sample was sequenced + may provide information about potential biases in sequencing strategy. Provide + the purpose of sequencing from the picklist in the template. The reason for + sample collection should be indicated in the "purpose of sampling" field. + slot_uri: GENEPIO:0001445 + any_of: + - range: purpose_of_sequencing menu + - range: null value menu + multivalued: true + required: true + examples: + - value: Travel-associated surveillance + purpose_of_sequencing_details: + name: purpose_of_sequencing_details + title: purpose_of_sequencing_details + description: The description of why the sample was sequenced providing specific + details. + comments: 'Provide an expanded description of why the sample was sequenced using + free text. The description may include the importance of the sequences for a + particular public health investigation/surveillance activity/research question. + Suggested standardized descriptions include: Assessing public health control + measures, Determining early introductions and spread, Investigating airline-related + exposures, Investigating remote regions, Investigating health care workers, + Investigating schools/universities.' + slot_uri: GENEPIO:0001446 + range: WhitespaceMinimizedString + examples: + - value: Investigating schools/universities + sequenced_by: + name: sequenced_by + title: sequenced_by + description: The name of the agency, organization or institution responsible for + sequencing the isolate's genome. + comments: Provide the name of the agency, organization or institution that performed + the sequencing in full (avoid abbreviations). If the information is unknown + or cannot be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100416 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + required: true + examples: + - value: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + exact_mappings: + - GISAID:sequenced_by + - BIOSAMPLE_Enterics:sequenced_by + sequenced_by_laboratory_name: + name: sequenced_by_laboratory_name + title: sequenced_by_laboratory_name + description: The specific laboratory affiliation of the responsible for sequencing + the isolate's genome. + comments: Provide the name of the specific laboratory that that performed the + sequencing in full (avoid abbreviations). If the information is unknown or cannot + be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100470 + range: WhitespaceMinimizedString + examples: + - value: Topp Lab + sequenced_by_contact_name: + name: sequenced_by_contact_name + title: sequenced_by_contact_name + description: The name or title of the contact responsible for follow-up regarding + the sequence. + comments: Provide the name of an individual or their job title. As personnel turnover + may render the contact's name obsolete, it is more prefereable to provide a + job title for ensuring accuracy of information and institutional memory. If + the information is unknown or cannot be provided, leave blank or provide a null + value. + slot_uri: GENEPIO:0100471 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + required: true + examples: + - value: Enterics Lab Manager + sequenced_by_contact_email: + name: sequenced_by_contact_email + title: sequenced_by_contact_email + description: The email address of the contact responsible for follow-up regarding + the sequence. + comments: Provide the email associated with the listed contact. As personnel turnover + may render an individual's email obsolete, it is more prefereable to provide + an address for a position or lab, to ensure accuracy of information and institutional + memory. If the information is unknown or cannot be provided, leave blank or + provide a null value. + slot_uri: GENEPIO:0100422 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + required: true + examples: + - value: enterics@lab.ca + sequence_submitted_by: + name: sequence_submitted_by + title: sequence_submitted_by + description: The name of the agency that submitted the sequence to a database. + comments: The name of the agency should be written out in full, (with minor exceptions) + and be consistent across multiple submissions. For Canadian institutions submitting + specimens rather than sequencing data, please put the "National Microbiology + Laboratory (NML)". + slot_uri: GENEPIO:0001159 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + recommended: true + examples: + - value: Public Health Ontario (PHO) + sequence_submitter_contact_email: + name: sequence_submitter_contact_email + title: sequence_submitter_contact_email + description: The email address of the contact responsible for follow-up regarding + the sequence. + comments: The email address can represent a specific individual or laboratory. + slot_uri: GENEPIO:0001165 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + recommended: true + pattern: ^\S+@\S+\.\S+$ + examples: + - value: RespLab@lab.ca + nucleic_acid_extraction_method: + name: nucleic_acid_extraction_method + title: nucleic_acid_extraction_method + description: The process used to extract genomic material from a sample. + comments: Briefly describe the extraction method used. + slot_uri: GENEPIO:0100939 + range: WhitespaceMinimizedString + examples: + - value: Direct wastewater RNA capture and purification via the "Sewage, Salt, + Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 + nucleic_acid_extraction_kit: + name: nucleic_acid_extraction_kit + title: nucleic_acid_extraction_kit + description: The kit used to extract genomic material from a sample + comments: Provide the name of the genomic extraction kit used. + slot_uri: GENEPIO:0100772 + range: WhitespaceMinimizedString + examples: + - value: QIAamp PowerFecal Pro DNA Kit + endogenous_control_details: + name: endogenous_control_details + title: endogenous control details + description: The description of the endogenous controls included when extracting + a sample. + comments: Provide the names of endogenous controls that were used as a reference + during extraction. If relevant, include titers of these controls, as well as + whether any controls were expected but not identified in the sample. + slot_uri: GENEPIO:0100923 + range: WhitespaceMinimizedString + recommended: true + sequencing_project_name: + name: sequencing_project_name + title: sequencing_project_name + description: The name of the project/initiative/program for which sequencing was + performed. + comments: Provide the name of the project and/or the project ID here. If the information + is unknown or cannot be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100472 + range: WhitespaceMinimizedString + examples: + - value: AMR-GRDI (PA-1356) + sequencing_platform: + name: sequencing_platform + title: sequencing_platform + description: The platform technology used to perform the sequencing. + comments: Provide the name of the company that created the sequencing instrument + by selecting a value from the template pick list. If the information is unknown + or cannot be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100473 + any_of: + - range: sequencing_platform menu + - range: null value menu + examples: + - value: Illumina [GENEPIO:0001923] + sequencing_instrument: + name: sequencing_instrument + title: sequencing_instrument + description: The model of the sequencing instrument used. + comments: Provide the model sequencing instrument by selecting a value from the + template pick list. If the information is unknown or cannot be provided, leave + blank or provide a null value. + slot_uri: GENEPIO:0001452 + any_of: + - range: sequencing_instrument menu + - range: null value menu + examples: + - value: Illumina HiSeq 2500 [GENEPIO:0100117] + library_preparation_kit: + name: library_preparation_kit + title: library_preparation_kit + description: The name of the DNA library preparation kit used to generate the + library being sequenced. + comments: Provide the name of the library preparation kit used. + slot_uri: GENEPIO:0001450 + range: WhitespaceMinimizedString + examples: + - value: Nextera XT + dna_fragment_length: + name: dna_fragment_length + title: DNA_fragment_length + description: The length of the DNA fragment generated by mechanical shearing or + enzymatic digestion for the purposes of library preparation. + comments: Provide the fragment length in base pairs (do not include the units). + slot_uri: GENEPIO:0100843 + range: Integer + examples: + - value: '400' + genomic_target_enrichment_method: + name: genomic_target_enrichment_method + title: genomic_target_enrichment_method + description: The molecular technique used to selectively capture and amplify specific + regions of interest from a genome. + comments: Provide the name of the enrichment method + slot_uri: GENEPIO:0100966 + range: genomic_target_enrichment_method menu + examples: + - value: Hybrid selection method (bait-capture) [GENEPIO:0001950] + genomic_target_enrichment_method_details: + name: genomic_target_enrichment_method_details + title: genomic_target_enrichment_method_details + description: Details that provide additional context to the molecular technique + used to selectively capture and amplify specific regions of interest from a + genome. + comments: 'Provide details that are applicable to the method you used. Note: If + bait-capture methods were used for enrichment, provide the panel name and version + number (or a URL providing that information).' + slot_uri: GENEPIO:0100967 + range: WhitespaceMinimizedString + examples: + - value: 'enrichment was done using Twist''s respiratory virus research panel: + https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel' + amplicon_pcr_primer_scheme: + name: amplicon_pcr_primer_scheme + title: amplicon_pcr_primer_scheme + description: The specifications of the primers (primer sequences, binding positions, + fragment size generated etc) used to generate the amplicons to be sequenced. + comments: Provide the name and version of the primer scheme used to generate the + amplicons for sequencing. + slot_uri: GENEPIO:0001456 + range: WhitespaceMinimizedString + examples: + - value: artic v3 + amplicon_size: + name: amplicon_size + title: amplicon_size + description: The length of the amplicon generated by PCR amplification. + comments: Provide the amplicon size expressed in base pairs. + slot_uri: GENEPIO:0001449 + range: Integer + examples: + - value: '300' + sequencing_flow_cell_version: + name: sequencing_flow_cell_version + title: sequencing_flow_cell_version + description: The version number of the flow cell used for generating sequence + data. + comments: Flow cells can vary in terms of design, chemistry, capacity, etc. The + version of the flow cell used to generate sequence data can affect sequence + quantity and quality. Record the version of the flow cell used to generate sequence + data. Do not include "version" or "v" in the version number. + slot_uri: GENEPIO:0101102 + range: WhitespaceMinimizedString + examples: + - value: R.9.4.1 + sequencing_protocol: + name: sequencing_protocol + title: sequencing_protocol + description: The protocol or method used for sequencing. + comments: Provide the name and version of the procedure or protocol used for sequencing. + You can also provide a link to a protocol online. + slot_uri: GENEPIO:0001454 + range: WhitespaceMinimizedString + examples: + - value: https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no + r1_fastq_filename: + name: r1_fastq_filename + title: r1_fastq_filename + description: The user-specified filename of the r1 FASTQ file. + comments: Provide the r1 FASTQ filename. + slot_uri: GENEPIO:0001476 + range: WhitespaceMinimizedString + examples: + - value: ABC123_S1_L001_R1_001.fastq.gz + r2_fastq_filename: + name: r2_fastq_filename + title: r2_fastq_filename + description: The user-specified filename of the r2 FASTQ file. + comments: Provide the r2 FASTQ filename. + slot_uri: GENEPIO:0001477 + range: WhitespaceMinimizedString + examples: + - value: ABC123_S1_L001_R2_001.fastq.gz + fast5_filename: + name: fast5_filename + title: fast5_filename + description: The user-specified filename of the FAST5 file. + comments: Provide the FAST5 filename. + slot_uri: GENEPIO:0001480 + range: WhitespaceMinimizedString + examples: + - value: batch1a_sequences.fast5 + genome_sequence_file_name: + name: genome_sequence_file_name + title: genome sequence file name + description: The name of the sequence file. + comments: Provide the name and version number, with the file extension, of the + processed genome sequence file e.g. a consensus sequence FASTA file or a genome + assembly file. + slot_uri: GENEPIO:0101715 + range: WhitespaceMinimizedString + examples: + - value: mpxvassembly.fasta + assembly_filename: + name: assembly_filename + title: assembly_filename + description: The user-defined filename of the FASTA file. + comments: Provide the FASTA filename. + slot_uri: GENEPIO:0001461 + range: WhitespaceMinimizedString + examples: + - value: pathogenassembly123.fasta + quality_control_method_name: + name: quality_control_method_name + title: quality control method name + description: The name of the method used to assess whether a sequence passed a + predetermined quality control threshold. + comments: Providing the name of the method used for quality control is very important + for interpreting the rest of the QC information. Method names can be provided + as the name of a pipeline or a link to a GitHub repository. Multiple methods + should be listed and separated by a semi-colon. Do not include QC tags in other + fields if no method name is provided. + slot_uri: GENEPIO:0100557 + range: WhitespaceMinimizedString + examples: + - value: ncov-tools + quality_control_method_version: + name: quality_control_method_version + title: quality control method version + description: The version number of the method used to assess whether a sequence + passed a predetermined quality control threshold. + comments: Methods updates can make big differences to their outputs. Provide the + version of the method used for quality control. The version can be expressed + using whatever convention the developer implements (e.g. date, semantic versioning). + If multiple methods were used, record the version numbers in the same order + as the method names. Separate the version numbers using a semi-colon. + slot_uri: GENEPIO:0100558 + range: WhitespaceMinimizedString + examples: + - value: 1.2.3 + quality_control_determination: + name: quality_control_determination + title: quality control determination + description: The determination of a quality control assessment. + comments: Select a value from the pick list provided. If a desired value is missing, + submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the + New Term Request form. + slot_uri: GENEPIO:0100559 + any_of: + - range: quality_control_determination menu + - range: null value menu + multivalued: true + examples: + - value: sequence failed quality control + quality_control_issues: + name: quality_control_issues + title: quality control issues + description: The reason contributing to, or causing, a low quality determination + in a quality control assessment. + comments: Select a value from the pick list provided. If a desired value is missing, + submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the + New Term Request form. + slot_uri: GENEPIO:0100560 + any_of: + - range: quality_control_issues menu + - range: null value menu + multivalued: true + examples: + - value: low average genome coverage + quality_control_details: + name: quality_control_details + title: quality control details + description: The details surrounding a low quality determination in a quality + control assessment. + comments: Provide notes or details regarding QC results using free text. + slot_uri: GENEPIO:0100561 + range: WhitespaceMinimizedString + examples: + - value: CT value of 39. Low viral load. Low DNA concentration after amplification. + raw_sequence_data_processing_method: + name: raw_sequence_data_processing_method + title: raw sequence data processing method + description: The method used for raw data processing such as removing barcodes, + adapter trimming, filtering etc. + comments: Raw data processing can have a significant impact on data quality and + how it can be used. Provide the names and version numbers of software used for + trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop + v. 0.2.3), or a link to a GitHub protocol. + slot_uri: GENEPIO:0001458 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + recommended: true + examples: + - value: Porechop 0.2.3 + dehosting_method: + name: dehosting_method + title: dehosting method + description: The method used to remove host reads from the pathogen sequence. + comments: Provide the name and version number of the software used to remove host + reads. + slot_uri: GENEPIO:0001459 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + recommended: true + examples: + - value: Nanostripper + sequence_assembly_software_name: + name: sequence_assembly_software_name + title: sequence assembly software name + description: The name of the software used to assemble a sequence. + comments: Provide the name of the software used to assemble the sequence. + slot_uri: GENEPIO:0100825 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + examples: + - value: SPAdes Genome Assembler, Canu, wtdbg2, velvet + sequence_assembly_software_version: + name: sequence_assembly_software_version + title: sequence assembly software version + description: The version of the software used to assemble a sequence. + comments: Provide the version of the software used to assemble the sequence. + slot_uri: GENEPIO:0100826 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + examples: + - value: 3.15.5 + consensus_sequence_software_name: + name: consensus_sequence_software_name + title: consensus sequence software name + description: The name of the software used to generate the consensus sequence. + comments: Provide the name of the software used to generate the consensus sequence. + slot_uri: GENEPIO:0001463 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + examples: + - value: iVar + consensus_sequence_software_version: + name: consensus_sequence_software_version + title: consensus sequence software version + description: The version of the software used to generate the consensus sequence. + comments: Provide the version of the software used to generate the consensus sequence. + slot_uri: GENEPIO:0001469 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + examples: + - value: '1.3' + breadth_of_coverage_value: + name: breadth_of_coverage_value + title: breadth of coverage value + description: The percentage of the reference genome covered by the sequenced data, + to a prescribed depth. + comments: Provide value as a percent. + slot_uri: GENEPIO:0001472 + range: WhitespaceMinimizedString + examples: + - value: '95' + depth_of_coverage_value: + name: depth_of_coverage_value + title: depth of coverage value + description: The average number of reads representing a given nucleotide in the + reconstructed sequence. + comments: Provide value as a fold of coverage. + slot_uri: GENEPIO:0001474 + range: WhitespaceMinimizedString + examples: + - value: '400' + depth_of_coverage_threshold: + name: depth_of_coverage_threshold + title: depth of coverage threshold + description: The threshold used as a cut-off for the depth of coverage. + comments: Provide the threshold fold coverage. + slot_uri: GENEPIO:0001475 + range: WhitespaceMinimizedString + examples: + - value: '100' + genome_completeness: + name: genome_completeness + title: genome completeness + description: The percentage of expected genes identified in the genome being sequenced. + Missing genes indicate missing genomic regions (incompleteness) in the data. + comments: Provide the genome completeness as a percent (no need to include units). + slot_uri: GENEPIO:0100844 + range: WhitespaceMinimizedString + examples: + - value: '85' + number_of_base_pairs_sequenced: + name: number_of_base_pairs_sequenced + title: number of base pairs sequenced + description: The number of total base pairs generated by the sequencing process. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0001482 + range: integer + examples: + - value: '387566' + number_of_total_reads: + name: number_of_total_reads + title: number of total reads + description: The total number of non-unique reads generated by the sequencing + process. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100827 + range: integer + examples: + - value: '423867' + number_of_unique_reads: + name: number_of_unique_reads + title: number of unique reads + description: The number of unique reads generated by the sequencing process. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100828 + range: integer + examples: + - value: '248236' + minimum_posttrimming_read_length: + name: minimum_posttrimming_read_length + title: minimum post-trimming read length + description: The threshold used as a cut-off for the minimum length of a read + after trimming. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100829 + range: integer + examples: + - value: '150' + number_of_contigs: + name: number_of_contigs + title: number of contigs + description: The number of contigs (contiguous sequences) in a sequence assembly. + comments: Provide a numerical value. + slot_uri: GENEPIO:0100937 + range: integer + examples: + - value: '10' + percent_ns_across_total_genome_length: + name: percent_ns_across_total_genome_length + title: percent Ns across total genome length + description: The percentage of the assembly that consists of ambiguous bases (Ns). + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100830 + range: integer + examples: + - value: '2' + ns_per_100_kbp: + name: ns_per_100_kbp + title: Ns per 100 kbp + description: The number of ambiguous bases (Ns) normalized per 100 kilobasepairs + (kbp). + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0001484 + range: integer + examples: + - value: '342' + n50: + name: n50 + title: N50 + description: The length of the shortest read that, together with other reads, + represents at least 50% of the nucleotides in a set of sequences. + comments: Provide the N50 value in Mb. + slot_uri: GENEPIO:0100938 + range: integer + examples: + - value: '150' + percent_read_contamination_: + name: percent_read_contamination_ + title: percent read contamination + description: The percent of the total number of reads identified as contamination + (not belonging to the target organism) in a sequence dataset. + comments: Provide the percent contamination value (no need to include units). + slot_uri: GENEPIO:0100845 + range: integer + examples: + - value: '2' + sequence_assembly_length: + name: sequence_assembly_length + title: sequence assembly length + description: The length of the genome generated by assembling reads using a scaffold + or by reference-based mapping. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100846 + range: integer + examples: + - value: '34272' + consensus_genome_length: + name: consensus_genome_length + title: consensus genome length + description: The length of the genome defined by the most common nucleotides at + each position. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0001483 + range: integer + examples: + - value: '38677' + reference_genome_accession: + name: reference_genome_accession + title: reference genome accession + description: A persistent, unique identifier of a genome database entry. + comments: Provide the accession number of the reference genome. + slot_uri: GENEPIO:0001485 + range: WhitespaceMinimizedString + examples: + - value: NC_045512.2 + deduplication_method: + name: deduplication_method + title: deduplication method + description: The method used to remove duplicated reads in a sequence read dataset. + comments: Provide the deduplication software name followed by the version, or + a link to a tool or method. + slot_uri: GENEPIO:0100831 + range: WhitespaceMinimizedString + examples: + - value: DeDup 0.12.8 + bioinformatics_protocol: + name: bioinformatics_protocol + title: bioinformatics protocol + description: A description of the overall bioinformatics strategy used. + comments: Further details regarding the methods used to process raw data, and/or + generate assemblies, and/or generate consensus sequences can. This information + can be provided in an SOP or protocol or pipeline/workflow. Provide the name + and version number of the protocol, or a GitHub link to a pipeline or workflow. + slot_uri: GENEPIO:0001489 + range: WhitespaceMinimizedString + examples: + - value: https://github.com/phac-nml/ncov2019-artic-nf + read_mapping_software_name: + name: read_mapping_software_name + title: read mapping software name + description: The name of the software used to map sequence reads to a reference + genome or set of reference genes. + comments: Provide the name of the read mapping software. + slot_uri: GENEPIO:0100832 + range: WhitespaceMinimizedString + examples: + - value: Bowtie2, BWA-MEM, TopHat + read_mapping_software_version: + name: read_mapping_software_version + title: read mapping software version + description: The version of the software used to map sequence reads to a reference + genome or set of reference genes. + comments: Provide the version number of the read mapping software. + slot_uri: GENEPIO:0100833 + range: WhitespaceMinimizedString + examples: + - value: 2.5.1 + taxonomic_reference_database_name: + name: taxonomic_reference_database_name + title: taxonomic reference database name + description: The name of the taxonomic reference database used to identify the + organism. + comments: Provide the name of the taxonomic reference database. + slot_uri: GENEPIO:0100834 + range: WhitespaceMinimizedString + examples: + - value: NCBITaxon + taxonomic_reference_database_version: + name: taxonomic_reference_database_version + title: taxonomic reference database version + description: The version of the taxonomic reference database used to identify + the organism. + comments: Provide the version number of the taxonomic reference database. + slot_uri: GENEPIO:0100835 + range: WhitespaceMinimizedString + examples: + - value: '1.3' + taxonomic_analysis_report_filename: + name: taxonomic_analysis_report_filename + title: taxonomic analysis report filename + description: The filename of the report containing the results of a taxonomic + analysis. + comments: Provide the filename of the report containing the results of the taxonomic + analysis. + slot_uri: GENEPIO:0101074 + range: WhitespaceMinimizedString + examples: + - value: WWtax_report_Feb1_2024.doc + taxonomic_analysis_date: + name: taxonomic_analysis_date + title: taxonomic analysis date + description: The date a taxonomic analysis was performed. + comments: Providing the date that an analyis was performed can help provide context + for tool and reference database versions. Provide the date that the taxonomic + analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". + slot_uri: GENEPIO:0101075 + range: date + examples: + - value: '2024-02-01' + read_mapping_criteria: + name: read_mapping_criteria + title: read mapping criteria + description: A description of the criteria used to map reads to a reference sequence. + comments: Provide a description of the read mapping criteria. + slot_uri: GENEPIO:0100836 + range: WhitespaceMinimizedString + examples: + - value: Phred score >20 + genetic_target_name: + name: genetic_target_name + title: genetic target name + description: The name of the genetic marker used for testing. + comments: 'Provide the full name of the gene used in the test. Standardized gene + names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI' + slot_uri: GENEPIO:0101116 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + examples: + - value: gyrase A + genetic_target_region: + name: genetic_target_region + title: genetic target region + description: The specific region or segment of a genetic sequence used for testing + or analysis. + slot_uri: GENEPIO:0101117 + range: WhitespaceMinimizedString + genetic_target_region_reference_genome: + name: genetic_target_region_reference_genome + title: genetic target region reference genome + description: The reference genome version used to determine the coordinates or + identity of the genetic target region in testing or analysis. + slot_uri: GENEPIO:0101118 + range: WhitespaceMinimizedString + diagnostic_target_presence: + name: diagnostic_target_presence + title: diagnostic target presence + description: The binary value of the result from a diagnostic test. + comments: Select a value from the pick list provided, to describe whether a target + was determined to be present or absent within a sample. + slot_uri: GENEPIO:0100962 + any_of: + - range: diagnostic target presence menu + - range: null value menu + examples: + - value: diagnostic target present + diagnostic_measurement_value: + name: diagnostic_measurement_value + title: diagnostic measurement value + description: The value of the result from a diagnostic test. + comments: Provide the numerical result of a diagnostic test (no need to include + units). + slot_uri: GENEPIO:0100963 + range: WhitespaceMinimizedString + examples: + - value: '1000' + diagnostic_measurement_unit: + name: diagnostic_measurement_unit + title: diagnostic measurement unit + description: The unit of the result from a diagnostic test. + comments: Select a value from the pick list provided, to describe the units of + the given diagnostic test. + slot_uri: GENEPIO:0100964 + any_of: + - range: diagnostic measurement unit menu + - range: null value menu + examples: + - value: cycle threshold (Ct) + diagnostic_measurement_method: + name: diagnostic_measurement_method + title: diagnostic measurement method + description: The method by which a diagnostic result was determined. + comments: Select a value from the pick list provided to describe the method used + for a given diagnostic test. + slot_uri: GENEPIO:0100965 + any_of: + - range: diagnostic measurement method menu + - range: null value menu + examples: + - value: qPCR + diagnostic_testing_threshold_value: + name: diagnostic_testing_threshold_value + title: diagnostic testing threshold value + description: The numerical value which represents the threshold above/below which + interpretation can be drawn on the diagnostic test + slot_uri: GENEPIO:0101104 + range: integer + diagnostic_testing_threshold_units: + name: diagnostic_testing_threshold_units + title: diagnostic testing threshold units + description: The unit which are attributed to the threshold above/below which + interpretation can be drawn on the diagnostic test + slot_uri: GENEPIO:0101105 + range: WhitespaceMinimizedString + diagnostic_testing_details: + name: diagnostic_testing_details + title: diagnostic testing details + description: Describe any details of the diagnsotic testing. + slot_uri: GENEPIO:0101106 + range: WhitespaceMinimizedString + prevalence_metrics: + name: prevalence_metrics + title: prevalence_metrics + description: Metrics regarding the prevalence of the pathogen of interest obtained + from a surveillance project. + comments: Risk assessment requires detailed information regarding the quantities + of a pathogen in a specified location, commodity, or environment. As such, it + is useful for risk assessors to know what types of information are available + through documented methods and results. Provide the metric types that are available + in the surveillance project sample plan by selecting them from the pick list. + The metrics of interest are " Number of total samples collected", "Number of + positive samples", "Average count of hazard organism", "Average count of indicator + organism". You do not need to provide the actual values, just indicate that + the information is available. + slot_uri: GENEPIO:0100480 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: Number of total samples collected, Number of positive samples + prevalence_metrics_details: + name: prevalence_metrics_details + title: prevalence_metrics_details + description: The details pertaining to the prevalence metrics from a surveillance + project. + comments: If there are details pertaining to samples or organism counts in the + sample plan that might be informative, provide details using free text. + slot_uri: GENEPIO:0100481 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. + stage_of_production: + name: stage_of_production + title: stage_of_production + description: The stage of food production. + comments: Provide the stage of food production as free text. + slot_uri: GENEPIO:0100482 + any_of: + - range: stage_of_production menu + - range: null value menu + recommended: true + examples: + - value: Abattoir [ENVO:01000925] + experimental_intervention: + name: experimental_intervention + title: experimental_intervention + description: The category of the experimental intervention applied in the food + production system. + comments: In some surveys, a particular intervention in the food supply chain + in studied. If there was an intervention specified in the sample plan, select + the intervention category from the pick list provided. + slot_uri: GENEPIO:0100483 + any_of: + - range: experimental_intervention menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Vaccination [NCIT:C15346] + experiment_intervention_details: + name: experiment_intervention_details + title: experiment_intervention_details + description: The details of the experimental intervention applied in the food + production system. + comments: If an experimental intervention was applied in the survey, provide details + in this field as free text. + slot_uri: GENEPIO:0100484 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: 2% cranberry solution mixed in feed +enums: + NullValue: + name: NullValue + title: null value + permissible_values: + Not Applicable [GENEPIO:0001619]: + text: Not Applicable [GENEPIO:0001619] + description: A categorical choice recorded when a datum does not apply to + a given context. + meaning: GENEPIO:0001619 + Missing [GENEPIO:0001618]: + text: Missing [GENEPIO:0001618] + description: A categorical choice recorded when a datum is not included for + an unknown reason. + meaning: GENEPIO:0001618 + Not Collected [GENEPIO:0001620]: + text: Not Collected [GENEPIO:0001620] + description: A categorical choice recorded when a datum was not measured or + collected. + meaning: GENEPIO:0001620 + Not Provided [GENEPIO:0001668]: + text: Not Provided [GENEPIO:0001668] + description: A categorical choice recorded when a datum was collected but + is not currently provided in the information being shared. This value indicates + the information may be shared at the later stage. + meaning: GENEPIO:0001668 + Restricted Access [GENEPIO:0001810]: + text: Restricted Access [GENEPIO:0001810] + description: A categorical choice recorded when a given datum is available + but not shared publicly because of information privacy concerns. + meaning: GENEPIO:0001810 + OrganismMenu: + name: OrganismMenu + title: organism menu + permissible_values: + Influenza A virus [NCBITaxon:11320]: + text: Influenza A virus [NCBITaxon:11320] + meaning: NCBITaxon:11320 + InfluenzaSubtypeMenu: + name: InfluenzaSubtypeMenu + title: influenza_subtype menu + permissible_values: + H5N1 subtype (Influenza A virus) [NCBITaxon:102793]: + text: H5N1 subtype (Influenza A virus) [NCBITaxon:102793] + meaning: NCBITaxon:102793 + InfluenzaSubtypingSchemeNameMenu: + name: InfluenzaSubtypingSchemeNameMenu + title: influenza_subtyping_scheme_name menu + permissible_values: + Tripartite Influenza A scheme [GENEPIO:0101121]: + text: Tripartite Influenza A scheme [GENEPIO:0101121] + meaning: GENEPIO:0101121 + USDA GenoFLU scheme [GENEPIO:0101122]: + text: USDA GenoFLU scheme [GENEPIO:0101122] + meaning: GENEPIO:0101122 + TaxonomicIdentificationProcessMenu: + name: TaxonomicIdentificationProcessMenu + title: taxonomic_identification_process menu + permissible_values: + Whole genome sequencing assay [OBI:0002117]: + text: Whole genome sequencing assay [OBI:0002117] + description: A DNA sequencing assay that intends to provide information about + the sequence of an entire genome of an organism. + meaning: OBI:0002117 + Whole metagenome sequencing assay [OBI:0002623]: + text: Whole metagenome sequencing assay [OBI:0002623] + description: A DNA sequencing assay that intends to provide information on + the DNA sequences of multiple genomes (a metagenome) from different organisms + present in the same input sample. + meaning: OBI:0002623 + 16S ribosomal gene sequencing assay [OBI:0002763]: + text: 16S ribosomal gene sequencing assay [OBI:0002763] + description: An amplicon sequencing assay in which the amplicon is derived + from universal primers used to amplify the 16S ribosomal RNA gene from isolate + bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting + sequences are compared to reference 16S sequence databases to identify or + classify bacteria present within a given sample. + meaning: OBI:0002763 + PCR assay [OBI:0002740]: + text: PCR assay [OBI:0002740] + description: An organism identification assay that is based on PCR. + meaning: OBI:0002740 + Comparative phenotypic assessment [OBI:0001546]: + text: Comparative phenotypic assessment [OBI:0001546] + description: Interpreting data from assays that evaluate the qualities or + dispositions inhering in an organism or organism part and comparing it to + data from other organisms to make a conclusion about a phenotypic difference + meaning: OBI:0001546 + SampleCollectionTimeOfDayMenu: + name: SampleCollectionTimeOfDayMenu + title: sample_collection_time_of_day menu + permissible_values: + Morning [NCIT:C64934]: + text: Morning [NCIT:C64934] + description: The time period between dawn and noon. + meaning: NCIT:C64934 + Afternoon [NCIT:C64935]: + text: Afternoon [NCIT:C64935] + description: The time period between noon and sunset. + meaning: NCIT:C64935 + Evening [NCIT:C64936]: + text: Evening [NCIT:C64936] + description: The time period between late afternoon and bedtime. + meaning: NCIT:C64936 + Night [NCIT:C65001]: + text: Night [NCIT:C65001] + description: The time in every 24 hour period when it is dark. + meaning: NCIT:C65001 + SampleCollectionDurationUnitMenu: + name: SampleCollectionDurationUnitMenu + title: sample_collection_duration_unit menu + permissible_values: + Second [UO:0000010]: + text: Second [UO:0000010] + description: A time unit which is equal to the duration of 9 192 631 770 periods + of the radiation corresponding to the transition between the two hyperfine + levels of the ground state of the caesium 133 atom. + meaning: UO:0000010 + Minute [UO:0000031]: + text: Minute [UO:0000031] + description: A time unit which is equal to 60 seconds. + meaning: UO:0000031 + Hour [UO:0000032]: + text: Hour [UO:0000032] + description: A time unit which is equal to 60 minutes. + meaning: UO:0000032 + Day [UO:0000033]: + text: Day [UO:0000033] + description: A time unit which is equal to 24 hours. + meaning: UO:0000033 + Week [UO:0000034]: + text: Week [UO:0000034] + description: A time unit which is equal to 7 days. + meaning: UO:0000034 + Month [UO:0000035]: + text: Month [UO:0000035] + description: A time unit which is equal to approximately 4-4.5 weeks or 28-31 + days. + meaning: UO:0000035 + Year [UO:0000036]: + text: Year [UO:0000036] + description: A time unit which is equal to 365 days, or 366 days during a + leap year. + meaning: UO:0000036 + FoodProductMenu: + name: FoodProductMenu + title: food_product menu + permissible_values: + Animal feed [ENVO:02000047]: + text: Animal feed [ENVO:02000047] + description: Food material which can be used to meet nutritional requirements + of animals, particularly livestock such as cattle, goats, sheep, horses, + chickens and pigs. + meaning: ENVO:02000047 + Blood meal [FOODON:00001564]: + text: Blood meal [FOODON:00001564] + description: Blood meal is a dry, inert powder made from blood used as a high-nitrogen + organic fertilizer and a high protein animal feed. + meaning: FOODON:00001564 + is_a: Animal feed [ENVO:02000047] + Bone meal [ENVO:02000054]: + text: Bone meal [ENVO:02000054] + description: A mixture of crushed and coarsely ground bones that is used as + an organic fertilizer for plants and formerly in animal feed. + meaning: ENVO:02000054 + is_a: Animal feed [ENVO:02000047] + Brassica carinata meal [FOODON:00004310]: + text: Brassica carinata meal [FOODON:00004310] + description: A meal that is a co-product produced after the extraction of + oil from the seed of the Ethiopian mustard plant (Brassica carinata). + meaning: FOODON:00004310 + is_a: Animal feed [ENVO:02000047] + Canola meal [FOODON:00002694]: + text: Canola meal [FOODON:00002694] + description: Canola meal is an oilseed meal made from canola grain. Canola + meal is a by-product of the oil crushing process. + meaning: FOODON:00002694 + is_a: Animal feed [ENVO:02000047] + Compound feed premix [FOODON:00004323]: + text: Compound feed premix [FOODON:00004323] + description: A formula mixture of micronutrients that is used as a component + in compound feed. + meaning: FOODON:00004323 + is_a: Animal feed [ENVO:02000047] + Compound feed premix (medicated) [FOODON:00004324]: + text: Compound feed premix (medicated) [FOODON:00004324] + description: A compound feed premix in which medicinal substance has been + added. + meaning: FOODON:00004324 + is_a: Compound feed premix [FOODON:00004323] + Feather meal [FOODON:00003927]: + text: Feather meal [FOODON:00003927] + description: A by product of processing poultry which is made from poultry + feathers by partially grinding them under elevated heat and pressure, and + then grinding and drying. + meaning: FOODON:00003927 + is_a: Animal feed [ENVO:02000047] + Fish meal [FOODON:03301620]: + text: Fish meal [FOODON:03301620] + description: Fish meal is primarily used as a protein supplement in compound + feed. As of 2010, about 56% of fish meal was used to feed farmed fish, about + 20% was used in pig feed, about 12% in poultry feed, and about 12% in other + uses, which included fertilizer. + meaning: FOODON:03301620 + is_a: Animal feed [ENVO:02000047] + Lay ration [FOODON:00004286]: + text: Lay ration [FOODON:00004286] + description: Food formulated for the laying hens to increase egg production + and egg shell quality. + meaning: FOODON:00004286 + is_a: Animal feed [ENVO:02000047] + Meat and bone meal [FOODON:00002738]: + text: Meat and bone meal [FOODON:00002738] + description: "Meat and bone meal (MBM) is a product of the rendering industry.\ + \ It is typically about 48\u201352% protein, 33\u201335% ash, 8\u201312%\ + \ fat, and 4\u20137% water. It is primarily used in the formulation of animal\ + \ feed to improve the amino acid profile of the feed." + meaning: FOODON:00002738 + is_a: Animal feed [ENVO:02000047] + Meat meal [FOODON:00004282]: + text: Meat meal [FOODON:00004282] + description: A meal that is obtained by cooking, defatting, sterilizing, grinding, + and sifting by-products of an animal. + meaning: FOODON:00004282 + is_a: Animal feed [ENVO:02000047] + Pet food [FOODON:00002682]: + text: Pet food [FOODON:00002682] + description: Pet food is plant or animal material intended for consumption + by pets. + meaning: FOODON:00002682 + is_a: Animal feed [ENVO:02000047] + Soybean meal [FOODON:03302757]: + text: Soybean meal [FOODON:03302757] + description: A type of ground protein-rich residue from the production of + soybean oil used chiefly in animal feeds, in adhesives and plastics, in + making synthetic protein fibers, and in fermentation media (as for the production + of antibiotics). + meaning: FOODON:03302757 + is_a: Animal feed [ENVO:02000047] + Animal feed ingredient [FOODON:00004322]: + text: Animal feed ingredient [FOODON:00004322] + description: An ingredient that is used in the preparation of animal feed. + meaning: FOODON:00004322 + Dairy food product [FOODON:00001256]: + text: Dairy food product [FOODON:00001256] + description: A dairy food product has mammilian milk or a milk component as + an ingredient. + meaning: FOODON:00001256 + Cheese block (whole or parts) [FOODON:03000287]: + text: Cheese block (whole or parts) [FOODON:03000287] + description: A whole cheese block or some substance made from a block of processed + cheese. + meaning: FOODON:03000287 + is_a: Dairy food product [FOODON:00001256] + Cow skim milk (powdered) [FOODON:03310016]: + text: Cow skim milk (powdered) [FOODON:03310016] + description: Milk powder that is obtained by removing all of the water from + pasteurized skim milk. + meaning: FOODON:03310016 + is_a: Dairy food product [FOODON:00001256] + Milk [UBERON:0001913]: + text: Milk [UBERON:0001913] + description: An emulsion of fat globules within a fluid that is secreted by + the mammary gland during lactation. + meaning: UBERON:0001913 + is_a: Dairy food product [FOODON:00001256] + Meat, poultry and fish (organizational term): + text: Meat, poultry and fish (organizational term) + Beef (ground or minced) [FOODON:00001282]: + text: Beef (ground or minced) [FOODON:00001282] + description: A ground beef product is made of beef that has been finely chopped + with a knife or a meat grinder (American English) or mincing machine (British + English). Ground beef is used in many recipes including hamburgers and spaghetti + Bolognese. + meaning: FOODON:00001282 + is_a: Meat, poultry and fish (organizational term) + Beef (ground or minced, boneless) [FOODON:03000412]: + text: Beef (ground or minced, boneless) [FOODON:03000412] + meaning: FOODON:03000412 + is_a: Beef (ground or minced) [FOODON:00001282] + Beef (ground or minced, extra lean) [FOODON:03000398]: + text: Beef (ground or minced, extra lean) [FOODON:03000398] + meaning: FOODON:03000398 + is_a: Beef (ground or minced) [FOODON:00001282] + Beef (ground or minced, lean) [FOODON:03000394]: + text: Beef (ground or minced, lean) [FOODON:03000394] + meaning: FOODON:03000394 + is_a: Beef (ground or minced) [FOODON:00001282] + Beef (ground or minced, medium) [FOODON:03000402]: + text: Beef (ground or minced, medium) [FOODON:03000402] + meaning: FOODON:03000402 + is_a: Beef (ground or minced) [FOODON:00001282] + Beef (ground or minced, regular) [FOODON:03000406]: + text: Beef (ground or minced, regular) [FOODON:03000406] + meaning: FOODON:03000406 + is_a: Beef (ground or minced) [FOODON:00001282] + Beef (ground or minced, sirloin) [FOODON:03000408]: + text: Beef (ground or minced, sirloin) [FOODON:03000408] + meaning: FOODON:03000408 + is_a: Beef (ground or minced) [FOODON:00001282] + Beef hamburger (dish) [FOODON:00002737]: + text: Beef hamburger (dish) [FOODON:00002737] + description: 'A hamburger (short: burger) is a sandwich consisting of one + or more cooked patties of ground meat, usually beef, placed inside a sliced + bread roll or bun. The patty may be pan fried, grilled, or flame broiled.' + meaning: FOODON:00002737 + is_a: Meat, poultry and fish (organizational term) + Beef shoulder [FOODON:03000377]: + text: Beef shoulder [FOODON:03000377] + meaning: FOODON:03000377 + is_a: Meat, poultry and fish (organizational term) + Beef shoulder chop [FOODON:03000387]: + text: Beef shoulder chop [FOODON:03000387] + description: Meat chop from the shoulder region of beef. + meaning: FOODON:03000387 + is_a: Beef shoulder [FOODON:03000377] + Beef sirloin chop [FOODON:03000389]: + text: Beef sirloin chop [FOODON:03000389] + description: Meat chop from the sirloin region of beef + meaning: FOODON:03000389 + is_a: Meat, poultry and fish (organizational term) + Beef stew chunk [FOODON:00004288]: + text: Beef stew chunk [FOODON:00004288] + description: A chunk of beef used as an ingredient in making stew. + meaning: FOODON:00004288 + is_a: Meat, poultry and fish (organizational term) + Beef tenderloin [FOODON:00003302]: + text: Beef tenderloin [FOODON:00003302] + description: A cut of beef corresponding to the psoas major muscle, which + is very tender. + meaning: FOODON:00003302 + is_a: Meat, poultry and fish (organizational term) + Beef (whole cut or parts) [FOODON:03000333]: + text: Beef (whole cut or parts) [FOODON:03000333] + meaning: FOODON:03000333 + is_a: Meat, poultry and fish (organizational term) + Brisket [FOODON:03530020]: + text: Brisket [FOODON:03530020] + description: A cut of meat from the breast or lower chest of beef or veal. + meaning: FOODON:03530020 + is_a: Meat, poultry and fish (organizational term) + Chicken breast [FOODON:00002703]: + text: Chicken breast [FOODON:00002703] + description: Chicken breast consists mainly of the breast meat portion of + a chicken, and may or may not include connected bone (boneless versus "with + bone") and skin. + meaning: FOODON:00002703 + is_a: Meat, poultry and fish (organizational term) + Chicken breast (back off) [FOODON:03000385]: + text: Chicken breast (back off) [FOODON:03000385] + description: A chicken breast with its backbone removed. + meaning: FOODON:03000385 + is_a: Chicken breast [FOODON:00002703] + Chicken breast (skinless) [FOODON:00003332]: + text: Chicken breast (skinless) [FOODON:00003332] + meaning: FOODON:00003332 + is_a: Chicken breast [FOODON:00002703] + Chicken breast (with skin) [FOODON:03000374]: + text: Chicken breast (with skin) [FOODON:03000374] + meaning: FOODON:03000374 + is_a: Chicken breast [FOODON:00002703] + Chicken breast (skinless, boneless) [FOODON:00003364]: + text: Chicken breast (skinless, boneless) [FOODON:00003364] + meaning: FOODON:00003364 + is_a: Chicken breast [FOODON:00002703] + Chicken breast cutlet [FOODON:00004308]: + text: Chicken breast cutlet [FOODON:00004308] + description: A cutlet made from chicken breast. + meaning: FOODON:00004308 + is_a: Chicken breast [FOODON:00002703] + Chicken drumstick [FOODON:00002716]: + text: Chicken drumstick [FOODON:00002716] + description: The segment of a chicken's leg between the thigh and tarsus (ankle). + meaning: FOODON:00002716 + is_a: Meat, poultry and fish (organizational term) + Chicken drumstick (skinless) [FOODON:03000366]: + text: Chicken drumstick (skinless) [FOODON:03000366] + meaning: FOODON:03000366 + is_a: Chicken drumstick [FOODON:00002716] + Chicken drumstick (with skin) [FOODON:03000368]: + text: Chicken drumstick (with skin) [FOODON:03000368] + meaning: FOODON:03000368 + is_a: Chicken drumstick [FOODON:00002716] + Chicken meat [FOODON:00001040]: + text: Chicken meat [FOODON:00001040] + meaning: FOODON:00001040 + is_a: Meat, poultry and fish (organizational term) + Chicken meat (ground or minced) [FOODON:03311826]: + text: Chicken meat (ground or minced) [FOODON:03311826] + description: A food product made of ground or minced chicken meat. + meaning: FOODON:03311826 + is_a: Chicken meat [FOODON:00001040] + Chicken meat (ground or minced, lean) [FOODON:03000392]: + text: Chicken meat (ground or minced, lean) [FOODON:03000392] + description: A food product made of lean, ground or minced chicken meat. + meaning: FOODON:03000392 + is_a: Chicken meat (ground or minced) [FOODON:03311826] + Chicken meat (ground or minced, extra lean) [FOODON:03000396]: + text: Chicken meat (ground or minced, extra lean) [FOODON:03000396] + description: A food product made of extra lean, ground or minced chicken meat. + meaning: FOODON:03000396 + is_a: Chicken meat (ground or minced) [FOODON:03311826] + Chicken meat (ground or minced, medium) [FOODON:03000400]: + text: Chicken meat (ground or minced, medium) [FOODON:03000400] + description: A food product made of medium, ground or minced chicken meat. + meaning: FOODON:03000400 + is_a: Chicken meat (ground or minced) [FOODON:03311826] + Chicken meat (ground or minced, regular) [FOODON:03000404]: + text: Chicken meat (ground or minced, regular) [FOODON:03000404] + description: A food product made of regular, ground or minced chicken meat. + meaning: FOODON:03000404 + is_a: Chicken meat (ground or minced) [FOODON:03311826] + Chicken meat (ground or minced, boneless) [FOODON:03000410]: + text: Chicken meat (ground or minced, boneless) [FOODON:03000410] + meaning: FOODON:03000410 + is_a: Chicken meat (ground or minced) [FOODON:03311826] + Chicken nugget [FOODON:00002672]: + text: Chicken nugget [FOODON:00002672] + description: A chicken nugget is a chicken product made from chicken meat + that is breaded or battered, then deep-fried or baked. + meaning: FOODON:00002672 + is_a: Meat, poultry and fish (organizational term) + Chicken thigh [FOODON:02020219]: + text: Chicken thigh [FOODON:02020219] + description: A whole thigh that derives from a chicken. + meaning: FOODON:02020219 + is_a: Meat, poultry and fish (organizational term) + Chicken thigh (skinless) [FOODON:00003331]: + text: Chicken thigh (skinless) [FOODON:00003331] + description: A chicken thigh after the skin has been removed. + meaning: FOODON:00003331 + is_a: Chicken thigh [FOODON:02020219] + Chicken thigh (skinless, with bone) [FOODON:02020227]: + text: Chicken thigh (skinless, with bone) [FOODON:02020227] + description: A chicken thigh that is skinless and contains bone element. + meaning: FOODON:02020227 + is_a: Chicken thigh [FOODON:02020219] + Chicken thigh (skinless, boneless) [FOODON:03000417]: + text: Chicken thigh (skinless, boneless) [FOODON:03000417] + meaning: FOODON:03000417 + is_a: Chicken thigh [FOODON:02020219] + Chicken upper thigh [FOODON:03000381]: + text: Chicken upper thigh [FOODON:03000381] + description: Meat from the upper thigh of a chicken. + meaning: FOODON:03000381 + is_a: Chicken thigh (skinless, boneless) [FOODON:03000417] + Chicken thigh (with skin) [FOODON:00003330]: + text: Chicken thigh (with skin) [FOODON:00003330] + meaning: FOODON:00003330 + is_a: Chicken thigh [FOODON:02020219] + Chicken thigh (with skin, with bone) [FOODON_00003363]: + text: Chicken thigh (with skin, with bone) [FOODON_00003363] + description: A chicken thigh that contains skin and bone material. + meaning: FOODON:00003363 + is_a: Chicken thigh [FOODON:02020219] + Chicken wing [FOODON:00002674]: + text: Chicken wing [FOODON:00002674] + description: A whole wing that derives from a chicken. + meaning: FOODON:00002674 + is_a: Meat, poultry and fish (organizational term) + Fish food product [FOODON:00001248]: + text: Fish food product [FOODON:00001248] + description: A fish food product includes products made from any fish species + (aquatic vertebrate with gills and fins). + meaning: FOODON:00001248 + is_a: Meat, poultry and fish (organizational term) + Fish steak [FOODON:00002986]: + text: Fish steak [FOODON:00002986] + description: A fish steak, alternatively known as a fish cutlet, is a cut + of fish which is cut perpendicular to the spine and can either include the + bones or be boneless. + meaning: FOODON:00002986 + is_a: Fish food product [FOODON:00001248] + Ham food product [FOODON:00002502]: + text: Ham food product [FOODON:00002502] + description: Ham is pork from a leg cut that has been preserved by wet or + dry curing, with or without smoking. As a processed meat, the term "ham" + includes both whole cuts of meat and ones that have been mechanically formed. + meaning: FOODON:00002502 + is_a: Meat, poultry and fish (organizational term) + Head cheese [FOODON:03315658]: + text: Head cheese [FOODON:03315658] + description: Head cheese is a cold cut that originated in Europe. Head cheese + is not a dairy cheese, but a terrine or meat jelly made with flesh from + the head of a calf or pig, or less commonly a sheep or cow, and often set + in aspic. A version pickled with vinegar is known as souse. + meaning: FOODON:03315658 + is_a: Meat, poultry and fish (organizational term) + Lamb [FOODON:03411669]: + text: Lamb [FOODON:03411669] + description: A whole lamb or some material processed from a lamb. + meaning: FOODON:03411669 + is_a: Meat, poultry and fish (organizational term) + Meat strip [FOODON:00004285]: + text: Meat strip [FOODON:00004285] + description: A cut of meat which is long, narrow and boneless. + meaning: FOODON:00004285 + is_a: Meat, poultry and fish (organizational term) + Mutton [FOODON:00002912]: + text: Mutton [FOODON:00002912] + description: The meat of an adult sheep is mutton, a term only used for the + meat, not the living animals. + meaning: FOODON:00002912 + is_a: Meat, poultry and fish (organizational term) + Pork chop [FOODON:00001049]: + text: Pork chop [FOODON:00001049] + description: A cut of meat (a meat chop) cut perpendicularly to the spine + of the pig and usually containing a rib or part of a vertebra, served as + an individual portion. + meaning: FOODON:00001049 + is_a: Meat, poultry and fish (organizational term) + Pork meat (ground or minced) [FOODON:03309969]: + text: Pork meat (ground or minced) [FOODON:03309969] + description: Meat from a pig that has been ground or minced. + meaning: FOODON:03309969 + is_a: Meat, poultry and fish (organizational term) + Pork meat (ground or minced, boneless) [FOODON:03000413]: + text: Pork meat (ground or minced, boneless) [FOODON:03000413] + meaning: FOODON:03000413 + is_a: Pork meat (ground or minced) [FOODON:03309969] + Pork meat (ground or minced, extra lean) [FOODON:03000399]: + text: Pork meat (ground or minced, extra lean) [FOODON:03000399] + description: A food product made of extra-lean, ground or minced pork meat. + meaning: FOODON:03000399 + is_a: Pork meat (ground or minced) [FOODON:03309969] + Pork meat (ground or minced, lean) [FOODON:03000395]: + text: Pork meat (ground or minced, lean) [FOODON:03000395] + description: A food product made of lean, ground or minced pork meat. + meaning: FOODON:03000395 + is_a: Pork meat (ground or minced) [FOODON:03309969] + Pork meat (ground or minced, medium) [FOODON:03000403]: + text: Pork meat (ground or minced, medium) [FOODON:03000403] + description: A food product made of medium, ground or minced pork meat. + meaning: FOODON:03000403 + is_a: Pork meat (ground or minced) [FOODON:03309969] + Pork meat (ground or minced, regular) [FOODON:03000407]: + text: Pork meat (ground or minced, regular) [FOODON:03000407] + description: A food product made of regular, ground or minced pork meat. + meaning: FOODON:03000407 + is_a: Pork meat (ground or minced) [FOODON:03309969] + Pork meat (ground or minced, Sirloin) [FOODON:03000409]: + text: Pork meat (ground or minced, Sirloin) [FOODON:03000409] + description: Ground or minced pork meat that comes from the sirloin region. + meaning: FOODON:03000409 + is_a: Pork meat (ground or minced) [FOODON:03309969] + Pork shoulder [FOODON:03000376]: + text: Pork shoulder [FOODON:03000376] + meaning: FOODON:03000376 + is_a: Meat, poultry and fish (organizational term) + Pork shoulder chop [FOODON:03000388]: + text: Pork shoulder chop [FOODON:03000388] + description: Meat chop from the blade roast of pork. + meaning: FOODON:03000388 + is_a: Pork shoulder [FOODON:03000376] + Pork sirloin chop [FOODON:03000390]: + text: Pork sirloin chop [FOODON:03000390] + meaning: FOODON:03000390 + is_a: Meat, poultry and fish (organizational term) + Pork steak [FOODON:00003148]: + text: Pork steak [FOODON:00003148] + meaning: FOODON:00003148 + is_a: Meat, poultry and fish (organizational term) + Pork tenderloin [FOODON:03000416]: + text: Pork tenderloin [FOODON:03000416] + meaning: FOODON:03000416 + is_a: Meat, poultry and fish (organizational term) + Poultry meat [FOODON:03315883]: + text: Poultry meat [FOODON:03315883] + description: Any meat from one or more poultry birds. + meaning: FOODON:03315883 + is_a: Meat, poultry and fish (organizational term) + Leg (poultry meat cut) [FOODON:03530159]: + text: Leg (poultry meat cut) [FOODON:03530159] + description: The leg cut of a poultry bird. + meaning: FOODON:03530159 + is_a: Poultry meat [FOODON:03315883] + Poultry drumstick [FOODON:00003469]: + text: Poultry drumstick [FOODON:00003469] + description: The calf part of a poultry hindleg (hindlimb zeugopod) + meaning: FOODON:00003469 + is_a: Leg (poultry meat cut) [FOODON:03530159] + Neck (poultry meat cut) [FOODON:03530294]: + text: Neck (poultry meat cut) [FOODON:03530294] + description: The neck cut of a poultry bird. + meaning: FOODON:03530294 + is_a: Poultry meat [FOODON:03315883] + Thigh (poultry meat cut) [FOODON:03530160]: + text: Thigh (poultry meat cut) [FOODON:03530160] + description: The thigh cut of a poultry bird. + meaning: FOODON:03530160 + is_a: Poultry meat [FOODON:03315883] + Wing (poultry meat cut) [FOODON:03530157]: + text: Wing (poultry meat cut) [FOODON:03530157] + description: The wing cut of a poultry bird. + meaning: FOODON:03530157 + is_a: Poultry meat [FOODON:03315883] + Sausage (whole) [FOODON:03315904]: + text: Sausage (whole) [FOODON:03315904] + description: A food product that is highly seasoned minced meat and is encased + in a skin in the shape of a cylinder. + meaning: FOODON:03315904 + is_a: Meat, poultry and fish (organizational term) + Pepperoni [FOODON:03311003]: + text: Pepperoni [FOODON:03311003] + description: A highly seasoned and spicy beef or pork sausage. + meaning: FOODON:03311003 + is_a: Sausage (whole) [FOODON:03315904] + Salami [FOODON:03312067]: + text: Salami [FOODON:03312067] + description: A cured sausage which consists of fermented and air-dried meat, + typically pork. + meaning: FOODON:03312067 + is_a: Sausage (whole) [FOODON:03315904] + Shellfish [FOODON:03411433]: + text: Shellfish [FOODON:03411433] + description: The term shellfish is used both broadly and specifically. For + regulatory purposes it is often narrowly defined as filter-feeding molluscs + such as clams, mussels, and oyster to the exclusion of crustaceans and all + else. Although their shells may differ, all shellfish are invertebrates. + meaning: FOODON:03411433 + is_a: Meat, poultry and fish (organizational term) + Shrimp [FOODON:03301673]: + text: Shrimp [FOODON:03301673] + description: A whole shrimp or some material processed from a shrimp. + meaning: FOODON:03301673 + is_a: Shellfish [FOODON:03411433] + Scallop [FOODON:03411489]: + text: Scallop [FOODON:03411489] + meaning: FOODON:03411489 + is_a: Shellfish [FOODON:03411433] + Turkey breast [FOODON:00002690]: + text: Turkey breast [FOODON:00002690] + description: Turkey breast consists mainly of the breast meat portion of a + turkey, and may or may not include connected bone ("deboned or boneless + versus bone-in") and skin. + meaning: FOODON:00002690 + is_a: Meat, poultry and fish (organizational term) + Turkey breast (back off) [FOODON:03000386]: + text: Turkey breast (back off) [FOODON:03000386] + description: A turkey breast with its backbone removed. + meaning: FOODON:03000386 + is_a: Turkey breast [FOODON:00002690] + Turkey breast (skinless) [FOODON:03000372]: + text: Turkey breast (skinless) [FOODON:03000372] + meaning: FOODON:03000372 + is_a: Turkey breast [FOODON:00002690] + Turkey breast (skinless, boneless) [FOODON:03000373]: + text: Turkey breast (skinless, boneless) [FOODON:03000373] + meaning: FOODON:03000373 + is_a: Turkey breast [FOODON:00002690] + Turkey breast (with skin) [FOODON:03000375]: + text: Turkey breast (with skin) [FOODON:03000375] + meaning: FOODON:03000375 + is_a: Turkey breast [FOODON:00002690] + Turkey drumstick [FOODON:03000365]: + text: Turkey drumstick [FOODON:03000365] + meaning: FOODON:03000365 + is_a: Meat, poultry and fish (organizational term) + Turkey drumstick (skinless) [FOODON:03000367]: + text: Turkey drumstick (skinless) [FOODON:03000367] + meaning: FOODON:03000367 + is_a: Turkey drumstick [FOODON:03000365] + Turkey drumstick (with skin) [FOODON:03000369]: + text: Turkey drumstick (with skin) [FOODON:03000369] + meaning: FOODON:03000369 + is_a: Turkey drumstick [FOODON:03000365] + Turkey meat [FOODON:00001286]: + text: Turkey meat [FOODON:00001286] + description: A turkey meat food product is any food product made predominantly + of turkey parts. + meaning: FOODON:00001286 + is_a: Meat, poultry and fish (organizational term) + Turkey meat (ground or minced) [FOODON:00002714]: + text: Turkey meat (ground or minced) [FOODON:00002714] + description: A food product made of ground or minced turkey meat. + meaning: FOODON:00002714 + is_a: Turkey meat [FOODON:00001286] + Turkey meat (ground or minced, lean) [FOODON:03000393]: + text: Turkey meat (ground or minced, lean) [FOODON:03000393] + description: A food product made of lean, ground or minced turkey meat. + meaning: FOODON:03000393 + is_a: Turkey meat [FOODON:00001286] + Turkey meat (ground or minced, extra lean) [FOODON:03000397]: + text: Turkey meat (ground or minced, extra lean) [FOODON:03000397] + description: A food product made of extra-lean, ground or minced turkey meat. + meaning: FOODON:03000397 + is_a: Turkey meat [FOODON:00001286] + Turkey meat (ground or minced, medium) [FOODON:03000401]: + text: Turkey meat (ground or minced, medium) [FOODON:03000401] + description: A food product made of medium, ground or minced turkey meat. + meaning: FOODON:03000401 + is_a: Turkey meat [FOODON:00001286] + Turkey meat (ground or minced, regular) [FOODON:03000405]: + text: Turkey meat (ground or minced, regular) [FOODON:03000405] + description: A food product made of regular, ground or minced turkey meat. + meaning: FOODON:03000405 + is_a: Turkey meat [FOODON:00001286] + Turkey meat (ground or minced, boneless) [FOODON:03000411]: + text: Turkey meat (ground or minced, boneless) [FOODON:03000411] + meaning: FOODON:03000411 + is_a: Turkey meat [FOODON:00001286] + Turkey thigh [FOODON:00003325]: + text: Turkey thigh [FOODON:00003325] + description: A thigh poultry cut of turkey. + meaning: FOODON:00003325 + is_a: Meat, poultry and fish (organizational term) + Turkey thigh (skinless) [FOODON:00003329]: + text: Turkey thigh (skinless) [FOODON:00003329] + description: A turkey thigh after the skin has been removed. + meaning: FOODON:00003329 + is_a: Turkey thigh [FOODON:00003325] + Turkey thigh (skinless, boneless) [FOODON:03000370]: + text: Turkey thigh (skinless, boneless) [FOODON:03000370] + meaning: FOODON:03000370 + is_a: Turkey thigh [FOODON:00003325] + Turkey thigh (with skin) [FOODON:00003328]: + text: Turkey thigh (with skin) [FOODON:00003328] + description: A turkey thigh that still contains the skin. + meaning: FOODON:00003328 + is_a: Turkey thigh [FOODON:00003325] + Turkey upper thigh [FOODON:03000382]: + text: Turkey upper thigh [FOODON:03000382] + description: Meat from the upper thigh of a turkey. + meaning: FOODON:03000382 + is_a: Turkey thigh (with skin) [FOODON:00003328] + Turkey upper thigh (with skin) [FOODON:03000384]: + text: Turkey upper thigh (with skin) [FOODON:03000384] + description: Turkey's upper thigh that contains the skin. + meaning: FOODON:03000384 + is_a: Turkey thigh (with skin) [FOODON:00003328] + Turkey wing [FOODON:03000371]: + text: Turkey wing [FOODON:03000371] + meaning: FOODON:03000371 + is_a: Meat, poultry and fish (organizational term) + Veal [FOODON:00003083]: + text: Veal [FOODON:00003083] + description: Veal is the meat of calves, in contrast to the beef from older + cattle. Veal can be produced from a calf of either sex and any breed; however, + most veal comes from young males of dairy breeds which are not used for + breeding. + meaning: FOODON:00003083 + is_a: Meat, poultry and fish (organizational term) + Formula fed veal [FOODON:000039111]: + text: Formula fed veal [FOODON:000039111] + meaning: OODON:000039111 + is_a: Veal [FOODON:00003083] + Grain-fed veal [FOODON:00004280]: + text: Grain-fed veal [FOODON:00004280] + description: Meat from a calf that is raised on grain, hay, or other solid + food, in addition to milk + meaning: FOODON:00004280 + is_a: Veal [FOODON:00003083] + FoodProductPropertiesMenu: + name: FoodProductPropertiesMenu + title: food_product_properties menu + permissible_values: + Organic food claim or use [FOODON:03510128]: + text: Organic food claim or use [FOODON:03510128] + description: 'USA: The 1990 Farm Act specifies that a food labeled ''organic'' + must meet four requirements: 1) the food must be raised by specified methods + to replenish and maintain the fertility of the soil; 2) the food must be + certified as having been produced with a nationally approved list of materials + and practices; 3) to be eligible for certification at least three years + must have elapsed between the first organic harvest and first use of nationally + approved materials on land and crops;and 4) organic foods must meet all + local, state and federal regulations governing the quality and safety of + the food supply. Europe: Foods produced in accordance with Council Regulation + (EC) No 834/2007 of 28 June 2007 on organic production and labelling of + organic products and repealing Regulation (EEC) No 2092/91. [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2007:189:0001:0023:EN:PDF]' + meaning: FOODON:03510128 + Food (raw) [FOODON:03311126]: + text: Food (raw) [FOODON:03311126] + description: A food material that has not been cooked. + meaning: FOODON:03311126 + Food (heat treated) [FOODON:03316043]: + text: Food (heat treated) [FOODON:03316043] + meaning: FOODON:03316043 + Food (pasteurized) [FOODON:00002654]: + text: Food (pasteurized) [FOODON:00002654] + meaning: FOODON:00002654 + Dairy product (no fat removed, whole): + text: Dairy product (no fat removed, whole) + Dairy product (skimmed, non-fat): + text: Dairy product (skimmed, non-fat) + Dairy product (semi-skimmed, reduced fat, 1%): + text: Dairy product (semi-skimmed, reduced fat, 1%) + Dairy product (semi-skimmed, reduced fat, 2%): + text: Dairy product (semi-skimmed, reduced fat, 2%) + FoodPackagingMenu: + name: FoodPackagingMenu + title: food_packaging menu + permissible_values: + Bottle [FOODON:03490214: + text: Bottle [FOODON:03490214 + description: A rigid or semirigid container typically of glass or plastic + having a comparatively narrow neck or mouth and usually no handle. + meaning: FOODON:03490214 + Bag [FOODON:03490197]: + text: Bag [FOODON:03490197] + description: According to FSTA Thesaurus Packaging 3.1 package types, includes + boil-in bag, carrier bag, flat bag, inner bag, retort pouch, shipping bag, + valve bag, and valve sack + meaning: FOODON:03490197 + Carton [FOODON:03490213]: + text: Carton [FOODON:03490213] + meaning: FOODON:03490213 + EnvironmentalSiteMenu: + name: EnvironmentalSiteMenu + title: environmental_site menu + permissible_values: + Abattoir [ENVO:01000925]: + text: Abattoir [ENVO:01000925] + description: A facility in which non-human animals are slaughtered and processed + for human consumption. + meaning: ENVO:01000925 + Agricultural Field [ENVO:00000114]: + text: Agricultural Field [ENVO:00000114] + description: A field which is located on land and used for agricultural purposes, + such as the grazing of livestock or the cultivation of crops. + meaning: ENVO:00000114 + Animal cage [ENVO:01000922]: + text: Animal cage [ENVO:01000922] + description: A manufactured cage which may be used to confine, contain, or + protect an animal. + meaning: ENVO:01000922 + Artificial wetland [ENVO:03501406]: + text: Artificial wetland [ENVO:03501406] + description: A wetland ecosystem which is constructed to treat municipal or + industrial wastewater, greywater or stormwater runoff. + meaning: ENVO:03501406 + Breeding ground [ENVO:03501441]: + text: Breeding ground [ENVO:03501441] + description: A place where animals breed. + meaning: ENVO:03501441 + Building [ENVO:00000073]: + text: Building [ENVO:00000073] + description: A permanent walled and roofed construction. + meaning: ENVO:00000073 + Barn [ENVO:03501257]: + text: Barn [ENVO:03501257] + description: A farm building used for housing livestock, storing machinery + or crops etc + meaning: ENVO:03501257 + Breeder barn [ENVO:03501383]: + text: Breeder barn [ENVO:03501383] + description: A barn where animals are kept for breeding purposes. + meaning: ENVO:03501383 + is_a: Barn [ENVO:03501257] + Broiler barn [ENVO:03501386]: + text: Broiler barn [ENVO:03501386] + description: A barn where broiler chickens are reared. + meaning: ENVO:03501386 + is_a: Barn [ENVO:03501257] + Sheep barn [ENVO:03501385]: + text: Sheep barn [ENVO:03501385] + description: A barn where sheep are kept. + meaning: ENVO:03501385 + is_a: Barn [ENVO:03501257] + Dairy [ENVO:00003862]: + text: Dairy [ENVO:00003862] + description: A dairy is a building in which animal milk is harvested and, + optionally, processed for human consumption. + meaning: ENVO:00003862 + Farm [ENVO:00000078]: + text: Farm [ENVO:00000078] + description: An area of land which is used for the cultivation of crops or + grazing of livestock, including any agricultural constructions therein. + meaning: ENVO:00000078 + Beef farm [ENVO:03501443]: + text: Beef farm [ENVO:03501443] + description: A farm where cows are kept for the purpose of meat production. + meaning: ENVO:03501443 + is_a: Farm [ENVO:00000078] + Breeder farm [ENVO:03501384]: + text: Breeder farm [ENVO:03501384] + description: A farm where animals are kept for breeding purposes. + meaning: ENVO:03501384 + is_a: Farm [ENVO:00000078] + Dairy farm [ENVO:03501416]: + text: Dairy farm [ENVO:03501416] + description: A farm where cows are kept for the purpose of producing milk + and other dairy products. + meaning: ENVO:03501416 + is_a: Farm [ENVO:00000078] + Feedlot [ENVO:01000627]: + text: Feedlot [ENVO:01000627] + description: A feedlot is a plot of land on which livestock are fattened for + market [URL:http://www.merriam-webster.com/dictionary/feedlot ]. + meaning: ENVO:01000627 + is_a: Farm [ENVO:00000078] + Beef cattle feedlot [ENVO:03501444]: + text: Beef cattle feedlot [ENVO:03501444] + description: A feedlot where beef cattle are kept with a focus on efficient + growth and weight gain of the animals. + meaning: ENVO:03501444 + is_a: Feedlot [ENVO:01000627] + Fish farm [ENVO:00000294]: + text: Fish farm [ENVO:00000294] + description: A facility in which fish are raised commercially in tanks or + enclosures, usually for food. + meaning: ENVO:00000294 + is_a: Farm [ENVO:00000078] + Research farm [ENVO:03501417]: + text: Research farm [ENVO:03501417] + description: A farm which is used for conducting agricultural research. + meaning: ENVO:03501417 + is_a: Farm [ENVO:00000078] + Central Experimental Farm [GAZ:00004603]: + text: Central Experimental Farm [GAZ:00004603] + description: An agricultural facility, working farm, and research centre of + the Research Branch of Agriculture and Agri-Food Canada. This farm is centrally + located in and completely surrounded by the City of Ottawa, Ontario, Canada. + The CEF is bordered by the Rideau Canal (a National Historic Site as well) + to the east, by Baseline Road to the south, by Merivale and Fisher Roads + to the west, and Carling Avenue to the north. + meaning: GAZ:00004603 + is_a: Farm [ENVO:00000078] + Freshwater environment [ENVO:01000306]: + text: Freshwater environment [ENVO:01000306] + description: An aquatic environment which is determined by freshwater. + meaning: ENVO:01000306 + Hatchery [ENVO:01001873]: + text: Hatchery [ENVO:01001873] + description: A construction in which eggs are hatched under artificial conditions. + meaning: ENVO:01001873 + Poultry hatchery [ENVO:01001874]: + text: Poultry hatchery [ENVO:01001874] + description: A hatchery in which the eggs of poultry are hatched under artificial + conditions + meaning: ENVO:01001874 + is_a: Hatchery [ENVO:01001873] + Hospital [ENVO:00002173]: + text: Hospital [ENVO:00002173] + description: A building in which health care services are provided by specialized + staff and equipment. + meaning: ENVO:00002173 + Lake [ENVO:00000020]: + text: Lake [ENVO:00000020] + description: A body of water or other liquid of considerable size contained + in a depression on a landmass. + meaning: ENVO:00000020 + Pond [ENVO:00000033]: + text: Pond [ENVO:00000033] + description: A body of water, usually of smaller size than a lake. + meaning: ENVO:00000033 + Reservoir [ENVO:00000025]: + text: Reservoir [ENVO:00000025] + description: An artificial body of water, often contained by a dam, constructed + for the purpose of water storage. + meaning: ENVO:00000025 + Irrigation reservoir [ENVO:00000450]: + text: Irrigation reservoir [ENVO:00000450] + description: A reservoir constructed for the purpose of providing water for + irrigation. + meaning: ENVO:00000450 + is_a: Reservoir [ENVO:00000025] + Retail environment [ENVO:01001448]: + text: Retail environment [ENVO:01001448] + description: A planned environmental usage process during which an environment + supports the sale of goods to ultimate consumers, usually in small quantities. + meaning: ENVO:01001448 + Shop [ENVO:00002221]: + text: Shop [ENVO:00002221] + description: A building in which a business presents a selection of goods + and offers to trade or sell them to customers for money or other goods. + meaning: ENVO:00002221 + is_a: Retail environment [ENVO:01001448] + Supermarket [ENVO:01000984]: + text: Supermarket [ENVO:01000984] + description: A food shop in which food products are the primary offer for + sale or trade. + meaning: ENVO:01000984 + is_a: Shop [ENVO:00002221] + River [ENVO:00000022]: + text: River [ENVO:00000022] + description: A stream which, through permanent or seasonal flow processes, + moves from elevated land towards lower elevations through a definite channel + and empties either into a sea, lake, or another river or ends on land as + bed seepage and evapotranspiration exceed water supply. + meaning: ENVO:00000022 + Roost (bird) [ENVO:03501439]: + text: Roost (bird) [ENVO:03501439] + description: A perch on which birds rest. + meaning: ENVO:03501439 + Wastewater treatment plant [ENVO:00002272]: + text: Wastewater treatment plant [ENVO:00002272] + description: A plant in which wastewater is treated. + meaning: ENVO:00002272 + Wetland [ENVO:00000043]: + text: Wetland [ENVO:00000043] + description: An area that is inundated or saturated by surface or ground water + at a frequency and duration sufficient to support, and that under normal + circumstances do support, a prevalence of vegetation typically adapted for + life in saturated soil conditions. + meaning: ENVO:00000043 + EnvironmentalMaterialMenu: + name: EnvironmentalMaterialMenu + title: environmental_material menu + permissible_values: + Air [ENVO:00002005]: + text: Air [ENVO:00002005] + description: 'The mixture of gases (roughly (by molar content/volume: 78% + nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts + of other gases, and a variable amount (average around 1%) of water vapor) + that surrounds the planet Earth.' + meaning: ENVO:00002005 + Animal manure [AGRO:00000079]: + text: Animal manure [AGRO:00000079] + description: Organic matter mostly derived from animal feces which can be + used as organic fertilizer in agriculture. + meaning: AGRO:00000079 + Animal feeding equipment [AGRO:00000675]: + text: Animal feeding equipment [AGRO:00000675] + description: An equipment used to feed and water livestock animals. + meaning: AGRO:00000675 + Animal feeder [AGRO:00000679]: + text: Animal feeder [AGRO:00000679] + description: An animal feeding equipment that has a food storage unit and + which enables livestock to obtain their own food. + meaning: AGRO:00000679 + is_a: Animal feeding equipment [AGRO:00000675] + Animal drinker [AGRO:00000680]: + text: Animal drinker [AGRO:00000680] + description: An animal feeding equipment that has a water storage unit which + enables livestock to obtain their own water. + meaning: AGRO:00000680 + is_a: Animal feeding equipment [AGRO:00000675] + Feed pan [AGRO:00000676]: + text: Feed pan [AGRO:00000676] + description: A bowl or pan which is used to feed livestock. + meaning: AGRO:00000676 + is_a: Animal feeding equipment [AGRO:00000675] + Watering bowl [AGRO:00000677]: + text: Watering bowl [AGRO:00000677] + description: A bowl from which animals can drink. + meaning: AGRO:00000677 + is_a: Animal feeding equipment [AGRO:00000675] + Animal transportation equipment [AGRO:00000671]: + text: Animal transportation equipment [AGRO:00000671] + description: An equipment used in the transportation of an animal + meaning: AGRO:00000671 + Dead haul trailer [GENEPIO:0100896]: + text: Dead haul trailer [GENEPIO:0100896] + description: A trailer used by a dead haul truck to transport dead animal + from an abattoir. + meaning: GENEPIO:0100896 + is_a: Animal transportation equipment [AGRO:00000671] + Dead haul truck [AGRO:00000673]: + text: Dead haul truck [AGRO:00000673] + description: A truck used to haul dead animals from an abattoir. + meaning: AGRO:00000673 + is_a: Animal transportation equipment [AGRO:00000671] + Live haul trailer [GENEPIO:0100897]: + text: Live haul trailer [GENEPIO:0100897] + description: A trailer used by a live haul truck to transport live animals. + meaning: GENEPIO:0100897 + is_a: Animal transportation equipment [AGRO:00000671] + Live haul truck [AGRO:00000674]: + text: Live haul truck [AGRO:00000674] + description: A truck used to haul live animals. + meaning: AGRO:00000674 + is_a: Animal transportation equipment [AGRO:00000671] + Belt [NCIT:C49844]: + text: Belt [NCIT:C49844] + description: A device consisting of a narrow loop of material moving over + shafts or pulleys. + meaning: NCIT:C49844 + Egg belt [AGRO:00000670]: + text: Egg belt [AGRO:00000670] + description: A conveyor belt used to collect eggs in an industrial egg production + environment. + meaning: AGRO:00000670 + is_a: Belt [NCIT:C49844] + Plucking belt [AGRO:00000669]: + text: Plucking belt [AGRO:00000669] + description: A part of the plucking machine that moves the birds through the + stages of plucking within the plucking apparatus. + meaning: AGRO:00000669 + is_a: Belt [NCIT:C49844] + Biosolids [ENVO:00002059]: + text: Biosolids [ENVO:00002059] + description: A treated form of sludge, sometimes used as a fertilizer in agriculture. + meaning: ENVO:00002059 + Boot [GSSO:012935]: + text: Boot [GSSO:012935] + description: A footwear which covers the foot, the ankle, and sometimes the + leg below the knee. + meaning: GSSO:012935 + Boot cover [OBI:0002806]: + text: Boot cover [OBI:0002806] + description: A personal protective device which is an impermiable material + which covers a shoe or boot in order to prevent spread of specific environmental + contaminants. + meaning: OBI:0002806 + is_a: Boot [GSSO:012935] + Broom [ENVO:03501431]: + text: Broom [ENVO:03501431] + description: A cleaning equipment piece which is a bundle of fibres attached + to a long handle, and is used for sweeping. + meaning: ENVO:03501431 + Bulk tank [ENVO:03501379]: + text: Bulk tank [ENVO:03501379] + description: A manufactured product which used to safely store and/or transport + solids, liquids, gases and a variety of compounds and mixtures. + meaning: ENVO:03501379 + Chick box [AGRO:00000678]: + text: Chick box [AGRO:00000678] + description: The box which is used to transport chick (juvenile chicken). + meaning: AGRO:00000678 + Chick pad [AGRO:00000672]: + text: Chick pad [AGRO:00000672] + description: The lining of a box or crate used to transport chicks (juvenile + chickens). + meaning: AGRO:00000672 + Cleaning equipment [ENVO:03501430]: + text: Cleaning equipment [ENVO:03501430] + description: An equipment piece used for cleaning a built environment or a + manufactured product. + meaning: ENVO:03501430 + Compost [ENVO:00002170]: + text: Compost [ENVO:00002170] + description: The aerobically decomposed remnants of organic materials. + meaning: ENVO:00002170 + Crate [ENVO:03501372]: + text: Crate [ENVO:03501372] + description: A manufactured product which is a container, traditionally made + of wooden slates, designed to protect transported goods from damage. + meaning: ENVO:03501372 + Dumpster [ENVO:03501400]: + text: Dumpster [ENVO:03501400] + description: A manufactured product which is a reusable container that accumulates + waste until it is periodically emptied or replaced. + meaning: ENVO:03501400 + Dust [ENVO:00002008]: + text: Dust [ENVO:00002008] + description: Minute solid particles with diameters less than 500 micrometers. + Occurs in and may be deposited from, the atmosphere. + meaning: ENVO:00002008 + Fan [NCIT:C49947]: + text: Fan [NCIT:C49947] + description: A device designed to create an air current through the rotation + of a planar surface. + meaning: NCIT:C49947 + Freezer [ENVO:03501415]: + text: Freezer [ENVO:03501415] + description: A manufactured product which is a device used to keep things + frozen by maintaining a temperature below the freezing point of water. + meaning: ENVO:03501415 + Freezer handle [ENVO:03501414]: + text: Freezer handle [ENVO:03501414] + description: A manufactured product which is the handle of a freezer door. + meaning: ENVO:03501414 + is_a: Freezer [ENVO:03501415] + Manure digester equipment [ENVO:03501424]: + text: Manure digester equipment [ENVO:03501424] + description: An equipment piece which is used in the aerobic or anaerobic + microbial digestion of manure. + meaning: ENVO:03501424 + Nest [ENVO:03501432]: + text: Nest [ENVO:03501432] + description: A structure that is built for certain animals to hold eggs or + young. + meaning: ENVO:03501432 + Bird's nest [ENVO:00005805]: + text: Bird's nest [ENVO:00005805] + description: A bird nest is the spot in which a bird lays and incubates its + eggs and raises its young. [ https://en.wikipedia.org/wiki/Bird_nest ] + meaning: ENVO:00005805 + is_a: Nest [ENVO:03501432] + Permafrost [ENVO:00000134]: + text: Permafrost [ENVO:00000134] + description: Soil or rock and included ice or organic material at or below + the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) + for two or more years. + meaning: ENVO:00000134 + Poultry fluff [UBERON:0008291]: + text: Poultry fluff [UBERON:0008291] + description: A feather lacking a vane and having a rudimentary rachis and + a tuft of non-interlocked barbs with elongated barbules extending from the + calamus. + meaning: UBERON:0008291 + Poultry litter [AGRO:00000080]: + text: Poultry litter [AGRO:00000080] + description: Manure which is primarily composed of pig feces. + meaning: AGRO:00000080 + Sediment [ENVO:00002007]: + text: Sediment [ENVO:00002007] + description: Sediment is an environmental substance comprised of any particulate + matter that can be transported by fluid flow and which eventually is deposited + as a layer of solid particles on the bedor bottom of a body of water or + other liquid. + meaning: ENVO:00002007 + Soil [ENVO:00001998]: + text: Soil [ENVO:00001998] + description: Soil is an environmental material which is primarily composed + of minerals, varying proportions of sand, silt, and clay, organic material + such as humus, gases, liquids, and a broad range of resident micro- and + macroorganisms. + meaning: ENVO:00001998 + Agricultural soil [ENVO:00002259]: + text: Agricultural soil [ENVO:00002259] + description: A type of soil used for agriculture that supports the physical, + chemical, and biological needs of the desired crop during production. + meaning: ENVO:00002259 + is_a: Soil [ENVO:00001998] + Forest soil [ENVO:00002261]: + text: Forest soil [ENVO:00002261] + description: A portion of soil which is found in a forested area. + meaning: ENVO:00002261 + is_a: Soil [ENVO:00001998] + Straw [ENVO:00003869]: + text: Straw [ENVO:00003869] + description: An agricultural byproduct, the dry stalk of a cereal plant, after + the nutrient grain or seed has been removed. + meaning: ENVO:00003869 + Water [CHEBI:15377]: + text: Water [CHEBI:15377] + description: An oxygen hydride consisting of an oxygen atom that is covalently + bonded to two hydrogen atoms. + meaning: CHEBI:15377 + Drinking water [ENVO:00003064]: + text: Drinking water [ENVO:00003064] + description: Water which is suitable for consumption by humans + meaning: ENVO:00003064 + is_a: Water [CHEBI:15377] + Fecal slurry [ENVO:03501436]: + text: Fecal slurry [ENVO:03501436] + description: A mixture of fecal material mixed, buffer, and other materials, + that is homogenized and strained and used in fecal microbiota translpantation. + meaning: ENVO:03501436 + is_a: Water [CHEBI:15377] + Fluid from meat rinse [GENEPIO:0004323]: + text: Fluid from meat rinse [GENEPIO:0004323] + meaning: GENEPIO:0004323 + is_a: Water [CHEBI:15377] + Groundwater [ENVO:01001004]: + text: Groundwater [ENVO:01001004] + description: Underground water which is located in pore spaces found in rock + or unconsolidated deposits such as soil, clay, or gravel. + meaning: ENVO:01001004 + is_a: Water [CHEBI:15377] + Poultry plucking water [AGRO_00000693]: + text: Poultry plucking water [AGRO_00000693] + description: A type of water obtained from rinsing poultry carcasses during + the feather plucking process. + meaning: AGRO:00000693 + is_a: Water [CHEBI:15377] + Surface runoff [ENVO:03501408]: + text: Surface runoff [ENVO:03501408] + description: Surface water which is 1) from some rainwater, stormwater, meltwater, + or other local source and 2) which can no longer sufficiently rapidly infiltrate + into soil, and instead flows along a drainage slope. + meaning: ENVO:03501408 + is_a: Water [CHEBI:15377] + Surface water [ENVO:00002042]: + text: Surface water [ENVO:00002042] + description: Water that is found on the surface of an astronomical object. + meaning: ENVO:00002042 + is_a: Water [CHEBI:15377] + Wastewater [ENVO:00002001]: + text: Wastewater [ENVO:00002001] + description: Water that has been adversely affected in quality by anthropogenic + influence + meaning: ENVO:00002001 + is_a: Water [CHEBI:15377] + Sludge [ENVO:00002044]: + text: Sludge [ENVO:00002044] + description: The residual semi-solid material left from domestic or industrial + processes, or wastewater treatment processes. + meaning: ENVO:00002044 + is_a: Wastewater [ENVO:00002001] + Primary sludge [ENVO:00002057]: + text: Primary sludge [ENVO:00002057] + description: Sludge generated from the initial processes (i.e., precipitation, + sedimentation) of wastewater treatment. + meaning: ENVO:00002057 + is_a: Sludge [ENVO:00002044] + Secondary sludge [ENVO:00002058]: + text: Secondary sludge [ENVO:00002058] + description: Activated waste biomass generated during wastewater treatment. + meaning: ENVO:00002058 + is_a: Sludge [ENVO:00002044] + Wastewater effluent [GENEPIO:0100891]: + text: Wastewater effluent [GENEPIO:0100891] + meaning: GENEPIO:0100891 + is_a: Wastewater [ENVO:00002001] + Primary wastewater effluent [GENEPIO:0100892]: + text: Primary wastewater effluent [GENEPIO:0100892] + description: A wastewater effluent which has been discharged from a primary + clarifier after the first stage of sedimentation. + meaning: GENEPIO:0100892 + is_a: Wastewater effluent [GENEPIO:0100891] + Secondary wastewater effluent [GENEPIO:0100893]: + text: Secondary wastewater effluent [GENEPIO:0100893] + description: A wastewater effluent which has been discharged from a secondary + clarifier after the second stage of sedimentation. + meaning: GENEPIO:0100893 + is_a: Wastewater effluent [GENEPIO:0100891] + Wastewater sediment [GENEPIO:0100890]: + text: Wastewater sediment [GENEPIO:0100890] + meaning: GENEPIO:0100890 + is_a: Wastewater [ENVO:00002001] + Weep fluid [AGRO:00000692]: + text: Weep fluid [AGRO:00000692] + description: A fluid that leaks from a bag containing an animal carcass, and + can include water, chemicals and anatomical fluids. + meaning: AGRO:00000692 + is_a: Water [CHEBI:15377] + AnatomicalMaterialMenu: + name: AnatomicalMaterialMenu + title: anatomical_material menu + permissible_values: + Blood [UBERON:0000178]: + text: Blood [UBERON:0000178] + description: A fluid that is composed of blood plasma and erythrocytes. + meaning: UBERON:0000178 + Fluid [UBERON:0006314]: + text: Fluid [UBERON:0006314] + description: Liquid components of living organisms. includes fluids that are + excreted or secreted from the body as well as body water that normally is + not. + meaning: UBERON:0006314 + Fluid (cerebrospinal (CSF)) [UBERON:0001359]: + text: Fluid (cerebrospinal (CSF)) [UBERON:0001359] + description: A clear, colorless, bodily fluid, that occupies the subarachnoid + space and the ventricular system around and inside the brain and spinal + cord. + meaning: UBERON:0001359 + is_a: Fluid [UBERON:0006314] + Fluid (amniotic) [UBERON:0000173]: + text: Fluid (amniotic) [UBERON:0000173] + description: Amniotic fluid is a bodily fluid consisting of watery liquid + surrounding and cushioning a growing fetus within the amnion. + meaning: UBERON:0000173 + is_a: Fluid [UBERON:0006314] + Saliva [UBERON:0001836]: + text: Saliva [UBERON:0001836] + description: A fluid produced in the oral cavity by salivary glands, typically + used in predigestion, but also in other functions. + meaning: UBERON:0001836 + is_a: Fluid [UBERON:0006314] + Tissue [UBERON:0000479]: + text: Tissue [UBERON:0000479] + description: Multicellular anatomical structure that consists of many cells + of one or a few types, arranged in an extracellular matrix such that their + long-range organisation is at least partly a repetition of their short-range + organisation. + meaning: UBERON:0000479 + BodyProductMenu: + name: BodyProductMenu + title: body_product menu + permissible_values: + Digestive tract substance [GENEPIO:0100898]: + text: Digestive tract substance [GENEPIO:0100898] + description: Undigested food material, microbiota, and other materials found + in the digestive tract. + meaning: GENEPIO:0100898 + Caecal content [GENEPIO:0100899]: + text: Caecal content [GENEPIO:0100899] + description: Undigested food material, microbiota, and other materials found + in the cecum + meaning: GENEPIO:0100899 + is_a: Digestive tract substance [GENEPIO:0100898] + Intestinal content [GENEPIO:0100900]: + text: Intestinal content [GENEPIO:0100900] + description: Undigested food material, microbiota, and other materials found + in the intestine + meaning: GENEPIO:0100900 + is_a: Digestive tract substance [GENEPIO:0100898] + Stomach content [GENEPIO:0100901]: + text: Stomach content [GENEPIO:0100901] + description: Undigested food material, microbiota, and other materials found + in the stomach + meaning: GENEPIO:0100901 + is_a: Digestive tract substance [GENEPIO:0100898] + Feces [UBERON:0001988]: + text: Feces [UBERON:0001988] + description: Portion of semisolid bodily waste discharged through the anus. + meaning: UBERON:0001988 + Fecal composite [GENEPIO:0004512]: + text: Fecal composite [GENEPIO:0004512] + description: A mixture of feces obtained from multiple individuals. + meaning: GENEPIO:0004512 + is_a: Feces [UBERON:0001988] + Feces (fresh) [GENEPIO:0004513]: + text: Feces (fresh) [GENEPIO:0004513] + description: Feces that was recently excreted. + meaning: GENEPIO:0004513 + is_a: Feces [UBERON:0001988] + Feces (environmental) [GENEPIO:0004514]: + text: Feces (environmental) [GENEPIO:0004514] + description: Feces which is deposited in the environment. + meaning: GENEPIO:0004514 + is_a: Feces [UBERON:0001988] + Meconium [UBERON:0007109]: + text: Meconium [UBERON:0007109] + description: A dark greenish mass that accumulates in the bowel during fetal + life and is discharged shortly after birth. + meaning: UBERON:0007109 + is_a: Feces [UBERON:0001988] + Milk [UBERON:0001913]: + text: Milk [UBERON:0001913] + description: An emulsion of fat globules within a fluid that is secreted by + the mammary gland during lactation. + meaning: UBERON:0001913 + Colostrum [UBERON:0001914]: + text: Colostrum [UBERON:0001914] + description: 'The thin, yellow, serous fluid secreted by the mammary glands + during pregnancy and immediately postpartum before lactation begins. It + consists of immunologically active substances, white blood cells, water, + protein, fat, and carbohydrates. [ MESH : A12.200.194 http://en.wikipedia.org/wiki/Colostrum + ]' + meaning: UBERON:0001914 + is_a: Milk [UBERON:0001913] + Mucus [UBERON:0000912]: + text: Mucus [UBERON:0000912] + description: Mucus is a bodily fluid consisting of a slippery secretion of + the lining of the mucous membranes in the body. It is a viscous colloid + containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus + is produced by goblet cells in the mucous membranes that cover the surfaces + of the membranes. It is made up of mucins and inorganic salts suspended + in water. + meaning: UBERON:0000912 + Urine [UBERON:0001088]: + text: Urine [UBERON:0001088] + description: Excretion that is the output of a kidney. + meaning: UBERON:0001088 + AnatomicalPartMenu: + name: AnatomicalPartMenu + title: anatomical_part menu + permissible_values: + Carcass [UBERON:0008979]: + text: Carcass [UBERON:0008979] + description: A body of a multi-cellular organism that is no longer living. + meaning: UBERON:0008979 + Digestive system [UBERON:0001007]: + text: Digestive system [UBERON:0001007] + description: Anatomical system that has as its parts the organs devoted to + the ingestion, digestion, and assimilation of food and the discharge of + residual wastes. + meaning: UBERON:0001007 + Caecum [UBERON:0001153]: + text: Caecum [UBERON:0001153] + description: pouch in the digestive tract that connects the ileum with the + ascending colon of the large intestine. It is separated from the ileum by + the ileocecal valve, and is the beginning of the large intestine. It is + also separated from the colon by the cecocolic junction. + meaning: UBERON:0001153 + is_a: Digestive system [UBERON:0001007] + Colon [UBERON:0001155]: + text: Colon [UBERON:0001155] + description: A portion of the large intestine before it becomes the rectum. + In mammals, the colon is the most part of the large intestine, excluding + the vermiform appendix, the rectum and the anal canal. + meaning: UBERON:0001155 + is_a: Digestive system [UBERON:0001007] + Digestive gland [UBERON:0006925]: + text: Digestive gland [UBERON:0006925] + description: Any gland that is part of the digestive system. + meaning: UBERON:0006925 + is_a: Digestive system [UBERON:0001007] + Foregut [UBERON:0001041]: + text: Foregut [UBERON:0001041] + description: Anterior subdivision of a digestive tract. + meaning: UBERON:0001041 + is_a: Digestive system [UBERON:0001007] + Gall bladder [UBERON:0002110]: + text: Gall bladder [UBERON:0002110] + description: An organ that aids digestion and stores bile produced by the + liver. + meaning: UBERON:0002110 + is_a: Digestive system [UBERON:0001007] + Gastrointestinal system mucosa [UBERON:0004786]: + text: Gastrointestinal system mucosa [UBERON:0004786] + description: A mucosa that is part of a gastrointestinal system. + meaning: UBERON:0004786 + is_a: Digestive system [UBERON:0001007] + Gizzard [UBERON:0005052]: + text: Gizzard [UBERON:0005052] + description: The muscular enlargement of the alimentary canal that has usually + thick muscular walls and a tough horny lining for grinding the food and + when the crop is present follows it and the proventriculus. + meaning: UBERON:0005052 + is_a: Digestive system [UBERON:0001007] + Hindgut [UBERON:0001046]: + text: Hindgut [UBERON:0001046] + description: The caudalmost subdivision of a digestive tract. + meaning: UBERON:0001046 + is_a: Digestive system [UBERON:0001007] + Intestine [UBERON:0000160]: + text: Intestine [UBERON:0000160] + description: Segment of the alimentary canal extending from the stomach to + the anus and, in humans and other mammals, consists of two segments, the + small intestine and the large intestine. + meaning: UBERON:0000160 + is_a: Digestive system [UBERON:0001007] + Small intestine [UBERON:0002108]: + text: Small intestine [UBERON:0002108] + description: 'Subdivision of digestive tract that connects the stomach to + the large intestine and is where much of the digestion and absorption of + food takes place (with the exception of ruminants). The mammalian small + intestine is long and coiled and can be differentiated histologically into: + duodenum, jejunem, ileum.' + meaning: UBERON:0002108 + is_a: Intestine [UBERON:0000160] + Duodenum [UBERON:0002114]: + text: Duodenum [UBERON:0002114] + description: The first part of the small intestine. At the junction of the + stomach and the duodenum the alimentary canal is inflected. The duodenum + first goes anteriorly for a short distance, turns dorsally, and eventually + caudally, thus it is a U-shaped structure with two horizontal sections (a + ventral and a dorsal one). + meaning: UBERON:0002114 + is_a: Small intestine [UBERON:0002108] + Ileum [UBERON:0002116]: + text: Ileum [UBERON:0002116] + description: The portion of the small intestine that extends from the jejunum + to the colon. + meaning: UBERON:0002116 + is_a: Small intestine [UBERON:0002108] + Jejunum [UBERON:0002115]: + text: Jejunum [UBERON:0002115] + description: The portion of the small intestine that extends from the duodenum + to the ileum. + meaning: UBERON:0002115 + is_a: Small intestine [UBERON:0002108] + Stomach [UBERON:0000945]: + text: Stomach [UBERON:0000945] + description: An expanded region of the vertebrate alimentary tract that serves + as a food storage compartment and digestive organ. A stomach is lined, in + whole or in part by a glandular epithelium. + meaning: UBERON:0000945 + is_a: Digestive system [UBERON:0001007] + Abomasum [UBERON:0007358]: + text: Abomasum [UBERON:0007358] + description: The fourth stomach of ruminating animals, which is an elongated + pear-shaped sac lying on the floor of the abdomen, on the right-hand side, + and roughly between the seventh and twelfth ribs. It leads to the beginning + of the small intestine. + meaning: UBERON:0007358 + is_a: Stomach [UBERON:0000945] + Rumen [UBERON:0007365]: + text: Rumen [UBERON:0007365] + description: The first compartment of the ruminant stomach. It lies on the + left side of the body, occupying the whole of the left side of the abdomen + and even stretching across the median plane of the body to the right side. + It is capacious, divided into an upper and a lower sac, each of which has + a blind sac at its posterior extremity. + meaning: UBERON:0007365 + is_a: Stomach [UBERON:0000945] + Excretory system (organizational term): + text: Excretory system (organizational term) + Anus [UBERON:0001245]: + text: Anus [UBERON:0001245] + description: 'Orifice at the opposite end of an animal''s digestive tract + from the mouth. Its function is to expel feces, unwanted semi-solid matter + produced during digestion, which, depending on the type of animal, may be + one or more of: matter which the animal cannot digest, such as bones; food + material after all the nutrients have been extracted, for example cellulose + or lignin; ingested matter which would be toxic if it remained in the digestive + tract; and dead or excess gut bacteria and other endosymbionts.' + meaning: UBERON:0001245 + is_a: Excretory system (organizational term) + Anal gland [UBERON:0011253]: + text: Anal gland [UBERON:0011253] + description: A type of gland occurring as solitary or in pairs or groups, + near the anus and sometimes opening into the rectum. + meaning: UBERON:0011253 + is_a: Excretory system (organizational term) + Cloaca [UBERON:0000162]: + text: Cloaca [UBERON:0000162] + description: Common chamber into which the intestines and excretory system + opens. Arises during development in all vertebrates, but in many it becomes + subdivided, lost or incorporated into other structures. + meaning: UBERON:0000162 + is_a: Excretory system (organizational term) + Liver [UBERON:0002107]: + text: Liver [UBERON:0002107] + description: An exocrine gland which secretes bile and functions in metabolism + of protein and carbohydrate and fat, synthesizes substances involved in + the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, + stores glycogen, and breaks down worn-out erythrocytes + meaning: UBERON:0002107 + is_a: Excretory system (organizational term) + Kidney [UBERON:0002113]: + text: Kidney [UBERON:0002113] + description: A paired organ of the urinary tract which has the production + of urine as its primary function. + meaning: UBERON:0002113 + is_a: Excretory system (organizational term) + Rectum [UBERON:0001052]: + text: Rectum [UBERON:0001052] + description: The terminal portion of the intestinal tube, terminating with + the anus. + meaning: UBERON:0001052 + is_a: Excretory system (organizational term) + Spleen [UBERON:0002106]: + text: Spleen [UBERON:0002106] + description: The organ that functions to filter blood and to store red corpuscles + and platelets. + meaning: UBERON:0002106 + is_a: Excretory system (organizational term) + Urinary bladder [UBERON:0001255]: + text: Urinary bladder [UBERON:0001255] + description: Distensible musculomembranous organ situated in the anterior + part of the pelvic cavity in which urine collects before excretion. + meaning: UBERON:0001255 + is_a: Excretory system (organizational term) + Foot [UBERON:0002387]: + text: Foot [UBERON:0002387] + description: 'The terminal part of the vertebrate leg upon which an individual + stands. 2: An invertebrate organ of locomotion or attachment; especially: + a ventral muscular surface or process of a mollusk.' + meaning: UBERON:0002387 + Head [UBERON:0000033]: + text: Head [UBERON:0000033] + description: The head is the anterior-most division of the body. + meaning: UBERON:0000033 + is_a: Foot [UBERON:0002387] + Brain [UBERON:0000955]: + text: Brain [UBERON:0000955] + description: The brain is the center of the nervous system in all vertebrate, + and most invertebrate, animals. Some primitive animals such as jellyfish + and starfish have a decentralized nervous system without a brain, while + sponges lack any nervous system at all. In vertebrates, the brain is located + in the head, protected by the skull and close to the primary sensory apparatus + of vision, hearing, balance, taste, and smell. + meaning: UBERON:0000955 + is_a: Foot [UBERON:0002387] + Ear [UBERON:0001690]: + text: Ear [UBERON:0001690] + description: Sense organ in vertebrates that is specialized for the detection + of sound, and the maintenance of balance. Includes the outer ear and middle + ear, which collect and transmit sound waves; and the inner ear, which contains + the organs of balance and (except in fish) hearing. Also includes the pinna, + the visible part of the outer ear, present in some mammals. + meaning: UBERON:0001690 + is_a: Foot [UBERON:0002387] + Eye [UBERON:0000970]: + text: Eye [UBERON:0000970] + description: An organ that detects light. + meaning: UBERON:0000970 + is_a: Foot [UBERON:0002387] + Mouth [UBERON:0000165]: + text: Mouth [UBERON:0000165] + description: The proximal portion of the digestive tract, containing the oral + cavity and bounded by the oral opening. In vertebrates, this extends to + the pharynx and includes gums, lips, tongue and parts of the palate. Typically + also includes the teeth, except where these occur elsewhere (e.g. pharyngeal + jaws) or protrude from the mouth (tusks). + meaning: UBERON:0000165 + is_a: Foot [UBERON:0002387] + Nose [UBERON:0000004]: + text: Nose [UBERON:0000004] + description: The olfactory organ of vertebrates, consisting of nares, olfactory + epithelia and the structures and skeletal framework of the nasal cavity. + meaning: UBERON:0000004 + is_a: Foot [UBERON:0002387] + Nasal turbinal [UBERON:0035612]: + text: Nasal turbinal [UBERON:0035612] + description: A skeletal element of the ethmoid region with complex morphology + that are lined with mucuous membranes involved in either olfaction or air + conditioning. + meaning: UBERON:0035612 + is_a: Nose [UBERON:0000004] + Nasopharynx (NP) [UBERON:0001728]: + text: Nasopharynx (NP) [UBERON:0001728] + description: The section of the pharynx that lies above the soft palate. + meaning: UBERON:0001728 + is_a: Nose [UBERON:0000004] + Pair of nares [UBERON:0002109]: + text: Pair of nares [UBERON:0002109] + description: Pair of nostrils. + meaning: UBERON:0002109 + is_a: Nose [UBERON:0000004] + Paranasal sinus [UBERON:0001825]: + text: Paranasal sinus [UBERON:0001825] + description: The paired air-filled cavities surrounded by the bones of the + face that are lined by mucous membranes and are continuous with the nasal + cavity. + meaning: UBERON:0001825 + is_a: Nose [UBERON:0000004] + Snout [UBERON:0006333]: + text: Snout [UBERON:0006333] + description: The projecting nose and mouth of an animal, especially a mammal. + meaning: UBERON:0006333 + is_a: Nose [UBERON:0000004] + Lymphatic system [UBERON:0006558]: + text: Lymphatic system [UBERON:0006558] + description: An organ system subdivision that is a network of vessels capable + of removing accumulating protein and fluid from the interstitial space and + returning it to the vascular space. In some species, this network is connected + to the immune system via lymph nodes and lymphocyte-producing organs, with + the whole being the lymphoid system. + meaning: UBERON:0006558 + Lymph node [UBERON:0000029]: + text: Lymph node [UBERON:0000029] + description: Any of the rounded masses of lymphoid tissue that are surrounded + by a capsule of connective tissue, are distributed along the lymphatic vessels, + and contain numerous lymphocytes which filter the flow of lymph. + meaning: UBERON:0000029 + is_a: Lymphatic system [UBERON:0006558] + Mesenteric lymph node [UBERON:0002509]: + text: Mesenteric lymph node [UBERON:0002509] + description: 'The lymph nodes located in the mesentery, of which there are + 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group.' + meaning: UBERON:0002509 + is_a: Lymph node [UBERON:0000029] + Mantle (bird) [GENEPIO:0100927]: + text: Mantle (bird) [GENEPIO:0100927] + description: The forward area of a bird's upper side that is sandwiched between + the nape and the start of the back. + meaning: GENEPIO:0100927 + Neck [UBERON:0000974]: + text: Neck [UBERON:0000974] + description: An organism subdivision that extends from the head to the pectoral + girdle, encompassing the cervical vertebral column. + meaning: UBERON:0000974 + Esophagus [UBERON:0001043]: + text: Esophagus [UBERON:0001043] + description: Tube that connects the pharynx to the stomach. In mammals, the + oesophagus connects the buccal cavity with the stomach. The stratified squamous + non-keratinised epithelium lining the buccal cavity is continued through + the pharynx down into the oesophagus. The lowest part of the oesophagus + (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main + body of the oesophagus is lined with small, simple mucous glands. Each gland + opens into the lumen by a long duct which pierces the muscularis mucosae + (Wilson and Washington, 1989). A sphincter is situated at the point where + the oesophagus enters the stomach to prevent gastro-oesophageal reflux, + i.e. to prevent acidic gastric contents from reaching stratified epithelia + of the oesophagus, where they can cause inflammation and irritation. + meaning: UBERON:0001043 + is_a: Neck [UBERON:0000974] + Trachea [UBERON:0003126]: + text: Trachea [UBERON:0003126] + description: The trachea is the portion of the airway that attaches to the + bronchi as it branches. + meaning: UBERON:0003126 + is_a: Neck [UBERON:0000974] + Nerve [UBERON:0001021]: + text: Nerve [UBERON:0001021] + description: An enclosed, cable-like bundle of axons in the peripheral nervous + system originating in a nerve root in the central nervous system (or a condensed + nervous structure) connecting with peripheral structures. + meaning: UBERON:0001021 + Spinal cord [UBERON:0002240]: + text: Spinal cord [UBERON:0002240] + description: Part of the central nervous system located in the vertebral canal + continuous with and caudal to the brain; demarcated from brain by plane + of foramen magnum. It is composed of an inner core of gray matter in which + nerve cells predominate, and an outer layer of white matter in which myelinated + nerve fibers predominate, and surrounds the central canal. + meaning: UBERON:0002240 + is_a: Nerve [UBERON:0001021] + Organs or organ parts [GENEPIO:0001117]: + text: Organs or organ parts [GENEPIO:0001117] + description: An object aggregate which has as members whole organs or parts + of organs, possibly from different organisms. + meaning: GENEPIO:0001117 + Organ [UBERON:0000062]: + text: Organ [UBERON:0000062] + description: Anatomical structure that performs a specific function or group + of functions + meaning: UBERON:0000062 + is_a: Organs or organ parts [GENEPIO:0001117] + Muscle organ [UBERON:0001630]: + text: Muscle organ [UBERON:0001630] + description: Organ consisting of a tissue made up of various elongated cells + that are specialized to contract and thus to produce movement and mechanical + work. + meaning: UBERON:0001630 + is_a: Organ [UBERON:0000062] + Skin of body [UBERON:0002097]: + text: Skin of body [UBERON:0002097] + description: The organ covering the body that consists of the dermis and epidermis. + meaning: UBERON:0002097 + is_a: Organ [UBERON:0000062] + Reproductive system [UBERON:0000990]: + text: Reproductive system [UBERON:0000990] + description: Anatomical system that has as its parts the organs concerned + with reproduction. + meaning: UBERON:0000990 + Embryo [UBERON:0000922]: + text: Embryo [UBERON:0000922] + description: Anatomical entity that comprises the organism in the early stages + of growth and differentiation that are characterized by cleavage, the laying + down of fundamental tissues, and the formation of primitive organs and organ + systems. For example, for mammals, the process would begin with zygote formation + and end with birth. For insects, the process would begin at zygote formation + and end with larval hatching. For plant zygotic embryos, this would be from + zygote formation to the end of seed dormancy. For plant vegetative embryos, + this would be from the initial determination of the cell or group of cells + to form an embryo until the point when the embryo becomes independent of + the parent plant. + meaning: UBERON:0000922 + is_a: Reproductive system [UBERON:0000990] + Fetus [UBERON:0000323]: + text: Fetus [UBERON:0000323] + description: An embryo that is at the late embryonic stage; this stage covers + late steps of the embryogenesis with a fully formed embryo still developing + before birth or egg hatching + meaning: UBERON:0000323 + is_a: Reproductive system [UBERON:0000990] + Ovary [UBERON:0000992]: + text: Ovary [UBERON:0000992] + description: The gonad of a female organism which contains germ cells. + meaning: UBERON:0000992 + is_a: Reproductive system [UBERON:0000990] + Oviduct [UBERON:0000993]: + text: Oviduct [UBERON:0000993] + description: A tube or collection of tubes in an animal from the ovaries to + the outside of the body. + meaning: UBERON:0000993 + is_a: Reproductive system [UBERON:0000990] + Placenta [UBERON:0001987]: + text: Placenta [UBERON:0001987] + description: Organ of metabolic interchange between fetus and mother, partly + of embryonic origin and partly of maternal origin[GO]. The fetal portion + of the placenta is known as the villous chorion. The maternal portion is + known as the decidua basalis. The two portions are held together by anchoring + villi that are anchored to the decidua basalis by the cytotrophoblastic + shell. + meaning: UBERON:0001987 + is_a: Reproductive system [UBERON:0000990] + Testis [UBERON:0000473]: + text: Testis [UBERON:0000473] + description: A gonad of a male animal. A gonad produces and releases sperm. + meaning: UBERON:0000473 + is_a: Reproductive system [UBERON:0000990] + Udder [UBERON:0013216]: + text: Udder [UBERON:0013216] + description: A large pendulous organ consisting of two or more mammary glands + enclosed in a common envelope and each provided with a single nipple. + meaning: UBERON:0013216 + is_a: Reproductive system [UBERON:0000990] + Uterus [UBERON:0000995]: + text: Uterus [UBERON:0000995] + description: The female muscular organ of gestation in which the developing + embryo or fetus is nourished until birth. + meaning: UBERON:0000995 + is_a: Reproductive system [UBERON:0000990] + Vagina [UBERON:0000996]: + text: Vagina [UBERON:0000996] + description: A fibromuscular tubular tract leading from the uterus to the + exterior of the body in female placental mammals and marsupials, or to the + cloaca in female birds, monotremes, and some reptiles + meaning: UBERON:0000996 + is_a: Reproductive system [UBERON:0000990] + Yolk sac [UBERON:0001040]: + text: Yolk sac [UBERON:0001040] + description: A sac-like expansion of the ventral wall of the intestine, narrowed + into a yolk stalk near the body[Hyman's]. Membranous sac attached to an + embryo, providing early nourishment in the form of yolk in bony fishes, + sharks, reptiles, birds, and primitive mammals. It functions as the developmental + circulatory system of the human embryo, before internal circulation begins. + In the mouse, the yolk sac is the first site of blood formation, generating + primitive macrophages and erythrocytes. + meaning: UBERON:0001040 + is_a: Reproductive system [UBERON:0000990] + Respiratory system [UBERON:0001004]: + text: Respiratory system [UBERON:0001004] + description: Functional system which consists of structures involved in respiration. + meaning: UBERON:0001004 + Air sac [UBERON:0009060]: + text: Air sac [UBERON:0009060] + description: Any of the membranous air-filled extensions of the lungs of birds, + which increase the efficiency of gaseous exchange in the lungs. + meaning: UBERON:0009060 + is_a: Respiratory system [UBERON:0001004] + Lung [UBERON:0002048]: + text: Lung [UBERON:0002048] + description: Respiration organ that develops as an outpocketing of the esophagus + meaning: UBERON:0002048 + is_a: Vascular system [UBERON:0007798] + Pleura [UBERON:0000977]: + text: Pleura [UBERON:0000977] + description: The invaginated serous membrane that surrounds the lungs (the + visceral portion) and lines the walls of the pleural cavity (parietal portion). + meaning: UBERON:0000977 + is_a: Respiratory system [UBERON:0001004] + Respiratory system mucosa [UBERON:0004785]: + text: Respiratory system mucosa [UBERON:0004785] + description: The mucous membrane lining the respiratory tract. + meaning: UBERON:0004785 + is_a: Respiratory system [UBERON:0001004] + Skeletal system [UBERON:0001434]: + text: Skeletal system [UBERON:0001434] + description: Anatomical system that is a multi-element, multi-tissue anatomical + cluster that consists of the skeleton and the articular system. + meaning: UBERON:0001434 + Skeletal joint [UBERON:0000982]: + text: Skeletal joint [UBERON:0000982] + description: Anatomical cluster that consists of two or more adjacent skeletal + structures, which may be interconnected by various types of tissue. + meaning: UBERON:0000982 + is_a: Skeletal system [UBERON:0001434] + Bone element [UBERON:0001474]: + text: Bone element [UBERON:0001474] + description: Skeletal element that is composed of bone tissue. + meaning: UBERON:0001474 + is_a: Skeletal system [UBERON:0001434] + Thoracic segment of trunk [UBERON:0000915]: + text: Thoracic segment of trunk [UBERON:0000915] + description: Subdivision of trunk that lies between the head and the abdomen. + meaning: UBERON:0000915 + Abdomen [UBERON:0000916]: + text: Abdomen [UBERON:0000916] + description: The subdivision of the vertebrate body between the thorax and + pelvis. The ventral part of the abdomen contains the abdominal cavity and + visceral organs. The dorsal part includes the abdominal section of the vertebral + column. + meaning: UBERON:0000916 + is_a: Thoracic segment of trunk [UBERON:0000915] + Muscle of abdomen [UBERON:0002378]: + text: Muscle of abdomen [UBERON:0002378] + description: 'Muscle (organ) which is a part of the abdomen. Examples: external + oblique, rectus abdominis.' + meaning: UBERON:0002378 + is_a: Abdomen [UBERON:0000916] + Peritoneum [UBERON:0002358]: + text: Peritoneum [UBERON:0002358] + description: 'Muscle (organ) which is a part of the abdomen. Examples: external + oblique, rectus abdominis.' + meaning: UBERON:0002358 + is_a: Abdomen [UBERON:0000916] + Vascular system [UBERON:0007798]: + text: Vascular system [UBERON:0007798] + description: Anatomical system that consists of all blood and lymph vessels. + meaning: UBERON:0007798 + Blood vessel [UBERON:0001981]: + text: Blood vessel [UBERON:0001981] + description: A vessel through which blood circulates in the body. + meaning: UBERON:0001981 + is_a: Vascular system [UBERON:0007798] + Bursa of Fabricius [UBERON:0003903]: + text: Bursa of Fabricius [UBERON:0003903] + description: An epithelial and lymphoid organ that develops as a dorsal diverticulum + of the proctodeal region of the cloaca in birds. The luminal (interior) + surface of the bursa is plicated with as many as 15 primary and 7 secondary + plicae or folds. These plicae have hundreds of bursal follicles containing + follicle-associated epithelial cells, lymphocytes, macrophages, and plasma + cells. Lymphoid stem cells migrate from the fetal liver to the bursa during + ontogeny. In the bursa, these stem cells acquire the characteristics of + mature, immunocompetent B cells. The bursa is an organ found in birds involved + in B cell differentiation. + meaning: UBERON:0003903 + is_a: Vascular system [UBERON:0007798] + Gill [UBERON:0002535]: + text: Gill [UBERON:0002535] + description: Anatomical surface structure found in many aquatic organisms. + It is a respiration organ whose function is the extraction of oxygen from + water and the excretion of carbon dioxide. The microscopic structure of + a gill is such that it presents a very large surface area to the external + environment. Gills usually consist of thin filaments of tissue, branches, + or slender tufted processes which have a highly folded surface to increase + surface area. A high surface area is crucial to the gas exchange of aquatic + organisms as water contains only 1/20 parts dissolved Oxygen compared to + air. With the exception of some aquatic insects, the filaments and lamellae + (folds) contain blood or coelomic fluid, from which gases are exchanged + through the thin walls. Oxygen is carried by the blood to other parts of + the body. Carbon dioxide passes from the blood through the thin gill tissue + into the water. Gills or gill-like organs, located in different parts of + the body, are found in various groups of aquatic animals, including mollusks, + crustaceans, insects, fish, and amphibians. [ http://en.wikipedia.org/wiki/Gill + ] + meaning: UBERON:0002535 + is_a: Vascular system [UBERON:0007798] + Heart [UBERON:0000948]: + text: Heart [UBERON:0000948] + description: A myogenic muscular circulatory organ found in the vertebrate + cardiovascular system composed of chambers of cardiac muscle. It is the + primary circulatory organ. + meaning: UBERON:0000948 + is_a: Vascular system [UBERON:0007798] + Pericardium [UBERON:0002407]: + text: Pericardium [UBERON:0002407] + description: The combination of pericardial sac (a double-walled sac containing + the heart and the roots of the great vessels) plus fibrous pericardium. + meaning: UBERON:0002407 + is_a: Vascular system [UBERON:0007798] + Vent (anatomical) [UBERON:2000298]: + text: Vent (anatomical) [UBERON:2000298] + description: The external opening of the rectum or cloaca. + meaning: UBERON:2000298 + Bird vent [UBERON:0012464]: + text: Bird vent [UBERON:0012464] + description: The opening of the cloacal chamber to the outside of the organism. + Birds maintain a single cloacal opening throughout their lives. [ http://orcid.org/0000-0002-6601-2165 + ] + meaning: UBERON:0012464 + is_a: Vent (anatomical) [UBERON:2000298] + Fish vent [GENEPIO:0100902]: + text: Fish vent [GENEPIO:0100902] + description: The external opening which opens to the reproductive and digestive + tracts of the fish. During spawning, the vent serves as an outlet for eggs + and sperm. In most fishes, the vent is in front of the anal fin. + meaning: GENEPIO:0100902 + is_a: Vent (anatomical) [UBERON:2000298] + CollectionDeviceMenu: + name: CollectionDeviceMenu + title: collection_device menu + permissible_values: + Air filter [ENVO:00003968]: + text: Air filter [ENVO:00003968] + meaning: ENVO:00003968 + Auger (earth auger) [AGRO:00000405]: + text: Auger (earth auger) [AGRO:00000405] + description: Manually operated hand tool that consists of cutter head having + semicircular blades connected to pipe with the help of clamp and flange. + The connecting pipe is further connected to a handle. + meaning: AGRO:00000405 + Bag [GSSO:008558]: + text: Bag [GSSO:008558] + description: A sac or pouch. + meaning: GSSO:008558 + Whirlpak sampling bag [GENEPIO:0002122]: + text: Whirlpak sampling bag [GENEPIO:0002122] + description: A sterilized sampling bag that is puncture proof tabs for protection + from damage due to wire-end protrusion and leak-proof closures. + meaning: GENEPIO:0002122 + is_a: Bag [GSSO:008558] + Bottle [FOODON:03490214]: + text: Bottle [FOODON:03490214] + description: A rigid or semirigid container typically of glass or plastic + having a comparatively narrow neck or mouth and usually no handle. + meaning: FOODON:03490214 + Box corer [GENEPIO:0100928]: + text: Box corer [GENEPIO:0100928] + description: A specimen collection device that is used to collect soft sediments + in lakes or oceans. + meaning: GENEPIO:0100928 + Bronchoscope [OBI:0002826]: + text: Bronchoscope [OBI:0002826] + description: A device which is a thin, tube-like instrument which includes + a light and a lens used to examine a lung. + meaning: OBI:0002826 + Collection Container [OBI:0002088]: + text: Collection Container [OBI:0002088] + description: A container with the function of containing a specimen. + meaning: OBI:0002088 + Collection Cup [GENEPIO:0100026]: + text: Collection Cup [GENEPIO:0100026] + description: A device which is used to collect liquid samples. + meaning: GENEPIO:0100026 + Culture plate [GENEPIO:0004318]: + text: Culture plate [GENEPIO:0004318] + description: A low flat-bottomed laboratory container for growing a layer + of organisms such as bacteria, molds, and cells on a thin layer of nutrient + medium. + meaning: GENEPIO:0004318 + Petri dish [NCIT:C96141]: + text: Petri dish [NCIT:C96141] + description: A shallow dish with a lid used to culture cells. + meaning: NCIT:C96141 + is_a: Culture plate [GENEPIO:0004318] + Fibrobronchoscope Brush [OBI:0002825]: + text: Fibrobronchoscope Brush [OBI:0002825] + meaning: OBI:0002825 + Filter [GENEPIO:0100103]: + text: Filter [GENEPIO:0100103] + description: A manufactured product which separates solids from fluids by + adding a medium through which only a fluid can pass. + meaning: GENEPIO:0100103 + Fine Needle [OBI:0002827]: + text: Fine Needle [OBI:0002827] + meaning: OBI:0002827 + Micropipette [OBI:0001128]: + text: Micropipette [OBI:0001128] + meaning: OBI:0001128 + Needle [OBI:0000436]: + text: Needle [OBI:0000436] + description: A needle is a sharp, hollow device used to penetrate tissue or + soft material. When attached to a syringe. it allows delivery of a specific + volume of liquid or gaseous mixture. + meaning: OBI:0000436 + PONAR grab sampler [GENEPIO:0100929]: + text: PONAR grab sampler [GENEPIO:0100929] + description: A specimen collection device that is designed to collect sediment + samples from the hard bottoms of a body of water i.e. sand, gravel, consolidated + marl or clay." + meaning: GENEPIO:0100929 + Scoop [GENEPIO:0002125]: + text: Scoop [GENEPIO:0002125] + description: A shovel-like utensil that has a deep curved dish and a short + handle and is used for digging into a soft substance for lifting out a portion. + meaning: GENEPIO:0002125 + Soil sample probe [GENEPIO:0100930]: + text: Soil sample probe [GENEPIO:0100930] + description: A specimen collection device designed to penetrate soil with + a hollow tube to collect soil sample cores. + meaning: GENEPIO:0100930 + Spatula [NCIT:C149941]: + text: Spatula [NCIT:C149941] + meaning: CIT:C149941 + Sponge [OBI:0002819]: + text: Sponge [OBI:0002819] + description: A sample collection device consisting of a soft flexible, absorbent + pad usually made from natural material such as gauze or cotton, used to + absorb specimen fluid or particulate matter. + meaning: OBI:0002819 + Suction Catheter [OBI:0002831]: + text: Suction Catheter [OBI:0002831] + description: A catheter which is used to remove mucus and other secretions + from the body. + meaning: OBI:0002831 + Swab [GENEPIO:0100027]: + text: Swab [GENEPIO:0100027] + description: A device which is a soft, absorbent material mounted on one or + both ends of a stick. + meaning: GENEPIO:0100027 + Drag swab [OBI:0002822]: + text: Drag swab [OBI:0002822] + description: A specimen collection device consisting of a specimen pad made + of sterile gauze which is aseptically attached to a pole by clips or to + a string + meaning: OBI:0002822 + is_a: Swab [GENEPIO:0100027] + Surface wipe [OBI:0002824]: + text: Surface wipe [OBI:0002824] + description: A sample collection device consisting of a thin, less absorbent + sheet, used to collect material from surfaces. + meaning: OBI:0002824 + is_a: Swab [GENEPIO:0100027] + Tube [GENEPIO:0101196]: + text: Tube [GENEPIO:0101196] + description: A sample collection device which is cylindrical shape that is + open at one end, used to collect material. + meaning: GENEPIO:0101196 + Blood Collection Tube [OBI:0002859]: + text: Blood Collection Tube [OBI:0002859] + description: 'A specimen collection tube which is designed for the collection + of whole blood. See also: https://en.wikipedia.org/wiki/Blood_culture#Collection' + meaning: OBI:0002859 + is_a: Tube [GENEPIO:0101196] + Microcapillary tube [OBI:0002858]: + text: Microcapillary tube [OBI:0002858] + meaning: OBI:0002858 + is_a: Tube [GENEPIO:0101196] + Serum Collection Tube [OBI:0002860]: + text: Serum Collection Tube [OBI:0002860] + description: A specimen collection tube which is designed for collecting whole + blood and enabling the separation of serum. + meaning: OBI:0002860 + is_a: Tube [GENEPIO:0101196] + Sputum Collection Tube [OBI:0002861]: + text: Sputum Collection Tube [OBI:0002861] + description: A specimen collection tube which is designed for collecting sputum. + meaning: OBI:0002861 + is_a: Tube [GENEPIO:0101196] + Urine Collection Tube [OBI:0002862]: + text: Urine Collection Tube [OBI:0002862] + description: A specimen container which is designed for holding urine. + meaning: OBI:0002862 + is_a: Tube [GENEPIO:0101196] + Vacuum device [GENEPIO:0002127]: + text: Vacuum device [GENEPIO:0002127] + description: A device which generates a vacuum to provide suction of material. + meaning: GENEPIO:0002127 + Vacutainer [OBIB:0000032]: + text: Vacutainer [OBIB:0000032] + description: A test tube which is either a sterile glass or plastic tube with + a closure that is evacuated to create a vacuum inside the tube facilitating + the draw of a predetermined volume of liquid. Most commonly used to draw + a blood sample directly from the vein, these also are used to collect urine + samples. Vacutainer tube may contain additives designed to stabilize and + preserve the specimen prior to analytical testing. + meaning: OBIB:0000032 + is_a: Vacuum device [GENEPIO:0002127] + CollectionMethodMenu: + name: CollectionMethodMenu + title: collection_method menu + permissible_values: + Aspiration [HP:0002835]: + text: Aspiration [HP:0002835] + description: Inspiration of a foreign object into the airway. + meaning: HP:0002835 + Biopsy [OBI:0002650]: + text: Biopsy [OBI:0002650] + description: A specimen collection that obtains a sample of tissue or cell + from a living multicellular organism body for diagnostic purposes by means + intended to be minimally invasive. + meaning: OBI:0002650 + Fecal grab [GENEPIO:0004326]: + text: Fecal grab [GENEPIO:0004326] + description: A fecal specimen collection method in which feces is obtained + by inserting the collection device into the anus of the host, or the feces + is captured as it is excreted. + meaning: GENEPIO:0004326 + Filtration [OBI:0302885]: + text: Filtration [OBI:0302885] + description: A process which separates components suspended in a fluid based + on granularity properties relying on a filter device. + meaning: OBI:0302885 + Air filtration [GENEPIO:0100031]: + text: Air filtration [GENEPIO:0100031] + description: A filtration process which removes solid particulates from the + air via an air filtration device. + meaning: GENEPIO:0100031 + is_a: Filtration [OBI:0302885] + Water filtration [GENEPIO:0100931]: + text: Water filtration [GENEPIO:0100931] + description: A filtration process which removes or reduces the concentration + of particulate matter, including suspended particles, parasites, bacteria, + algae, viruses, and fungi, as well as other undesirable chemical and biological + contaminants from contaminated water using water filters to produce safe + and clean water. + meaning: GENEPIO:0100931 + is_a: Filtration [OBI:0302885] + Lavage [OBI:0600044]: + text: Lavage [OBI:0600044] + description: A protocol application to separate cells and/or cellular secretions + from an anatomical space by the introduction and removal of fluid + meaning: OBI:0600044 + Bronchoalveolar lavage [GENEPIO:0100032]: + text: Bronchoalveolar lavage [GENEPIO:0100032] + description: The collection of bronchoalveolar lavage fluid (BAL) from the + lungs. + meaning: GENEPIO:0100032 + is_a: Lavage [OBI:0600044] + Gastric lavage [GENEPIO:0100033]: + text: Gastric lavage [GENEPIO:0100033] + description: The administration and evacuation of small volumes of liquid + through an orogastric tube to remove toxic substances within the stomach. + meaning: GENEPIO:0100033 + is_a: Lavage [OBI:0600044] + Necropsy [MMO:0000344]: + text: Necropsy [MMO:0000344] + description: A postmortem examination of the body of an animal to determine + the cause of death or the character and extent of changes produced by disease. + meaning: MMO:0000344 + Phlebotomy [NCIT:C28221]: + text: Phlebotomy [NCIT:C28221] + description: The collection of blood from a vein, most commonly via needle + venipuncture. + meaning: NCIT:C28221 + Rinsing for specimen collection [GENEPIO_0002116]: + text: Rinsing for specimen collection [GENEPIO_0002116] + description: The process of removal and collection of specimen material from + the surface of an entity by washing, or a similar application of fluids. + meaning: GENEPIO:0002116 + Scooping [GENEPIO:0100932]: + text: Scooping [GENEPIO:0100932] + description: A specimen collection process that is used to dig out an amount + of sample using a scoop. + meaning: GENEPIO:0100932 + Sediment collection [GENEPIO:0100933]: + text: Sediment collection [GENEPIO:0100933] + description: A specimen collection process that is used to collect a sediment + sample. + meaning: GENEPIO:0100933 + Soil coring [GENEPIO:0100934]: + text: Soil coring [GENEPIO:0100934] + description: A specimen collection process that is used to collect soil sample + cores. + meaning: GENEPIO:0100934 + Weep fluid collection (pouring) [GENEPIO:0101003]: + text: Weep fluid collection (pouring) [GENEPIO:0101003] + description: A specimen collection process that is used to collect weep fluid + via pouring from the source container into the sample collection device. + (e.g. bag or tube) + meaning: GENEPIO:0101003 + SampleVolumeMeasurementUnitMenu: + name: SampleVolumeMeasurementUnitMenu + title: sample_volume_measurement_unit menu + permissible_values: + microliter (uL) [UO:0000101]: + text: microliter (uL) [UO:0000101] + description: A metric unit of volume equivalent to one thousandth of a cubic + centimeter or one millionth of a liter. + meaning: UO:0000101 + milliliter (mL) [UO:0000098]: + text: milliliter (mL) [UO:0000098] + description: A metric unit of volume equivalent to one cubic centimeter or + one thousandth of a liter. + meaning: UO:0000098 + liter (L) [UO:0000099]: + text: liter (L) [UO:0000099] + description: A metric unit of volume equivalent to 1000 cubic centimeters + meaning: UO:0000099 + ResidualSampleStatusMenu: + name: ResidualSampleStatusMenu + title: residual_sample_status menu + permissible_values: + Residual sample remaining (some sample left) [GENEPIO:0101087]: + text: Residual sample remaining (some sample left) [GENEPIO:0101087] + meaning: GENEPIO:0101087 + No residual sample (sample all used) [GENEPIO:0101088]: + text: No residual sample (sample all used) [GENEPIO:0101088] + meaning: GENEPIO:0101088 + Residual sample status unkown [GENEPIO:0101089]: + text: Residual sample status unkown [GENEPIO:0101089] + meaning: GENEPIO:0101089 + PurposeOfSampling: + name: PurposeOfSampling + title: purpose of sampling + permissible_values: + Cluster/Outbreak investigation [GENEPIO:0100001]: + text: Cluster/Outbreak investigation [GENEPIO:0100001] + description: A sampling strategy in which individuals are chosen for investigation + into a disease cluster or outbreak. + meaning: GENEPIO:0100001 + Diagnostic testing [GENEPIO:0100002]: + text: Diagnostic testing [GENEPIO:0100002] + description: A sampling strategy in which individuals are sampled in the context + of diagnostic testing. + meaning: GENEPIO:0100002 + Environmental testing [GENEPIO:0100548]: + text: Environmental testing [GENEPIO:0100548] + description: A sampling strategy in which environments are sampled in the + context of testing for the presence of, or change in the levels of, chemicals, + pathogens or other phenomena. + meaning: GENEPIO:0100548 + Research [GENEPIO:0100003]: + text: Research [GENEPIO:0100003] + description: A sampling strategy in which samples are collected in order to + perform research. + meaning: GENEPIO:0100003 + Clinical trial [GENEPIO:0100549]: + text: Clinical trial [GENEPIO:0100549] + description: A sampling strategy in which individuals are sampled in the context + of experiments or observations performed as part of clinical research. + meaning: GENEPIO:0100549 + is_a: Research [GENEPIO:0100003] + Field experiment [GENEPIO:0100550]: + text: Field experiment [GENEPIO:0100550] + description: A sampling strategy in which samples are taken during real-life + experiments which test directly whether proposed interventions actually + work. + meaning: GENEPIO:0100550 + is_a: Research [GENEPIO:0100003] + Survey study [GENEPIO:0100582]: + text: Survey study [GENEPIO:0100582] + description: A sampling strategy in which individuals and/or materials are + sampled for surveillance performed for research purposes. + meaning: GENEPIO:0100582 + is_a: Research [GENEPIO:0100003] + Surveillance [GENEPIO:0100004]: + text: Surveillance [GENEPIO:0100004] + description: A sampling strategy in which individuals are sampled for surveillance + investigations. + meaning: GENEPIO:0100004 + PresamplingActivity: + name: PresamplingActivity + title: presampling activity + permissible_values: + Addition of substances to food/water [GENEPIO:0100536]: + text: Addition of substances to food/water [GENEPIO:0100536] + description: The addition of substances to food or water administered to an + individual or group of individuals. + meaning: GENEPIO:0100536 + Antimicrobial pre-treatment [GENEPIO:0100537]: + text: Antimicrobial pre-treatment [GENEPIO:0100537] + description: The administration of an antimicrobial agent to an individual + or its addition to a substance prior to some other event or activity. + meaning: GENEPIO:0100537 + Certified animal husbandry practices [GENEPIO:0100538]: + text: Certified animal husbandry practices [GENEPIO:0100538] + description: The implementation of animal husbandy practices that have been + certified by an authorized organization. + meaning: GENEPIO:0100538 + Certified humane animal husbandry practices [GENEPIO:0100894]: + text: Certified humane animal husbandry practices [GENEPIO:0100894] + description: A certification organization in Washington DC that is dedicated + to improving the lives of farm animals in food production from birth through + slaughter. + meaning: GENEPIO:0100894 + is_a: Certified animal husbandry practices [GENEPIO:0100538] + Certified organic farming practices [GENEPIO:0100539]: + text: Certified organic farming practices [GENEPIO:0100539] + description: The implementation of organic farming practices that have been + certified by an authorized organization. + meaning: GENEPIO:0100539 + Conventional farming practices [GENEPIO:0100895]: + text: Conventional farming practices [GENEPIO:0100895] + description: The implementation of farming practices that include man-made + inputs such as chemical fertilizers and genetically-modified seeds. + meaning: GENEPIO:0100895 + Change in storage conditions [GENEPIO:0100540]: + text: Change in storage conditions [GENEPIO:0100540] + description: A change in the storage conditions of a material or a substance. + meaning: GENEPIO:0100540 + Cleaning/disinfection [GENEPIO:0100541]: + text: Cleaning/disinfection [GENEPIO:0100541] + description: A process of removing unwanted substances, such as dirt, infectious + agents, and other impurities, from an object or environment. + meaning: GENEPIO:0100541 + Extended downtime between activities [GENEPIO:0100542]: + text: Extended downtime between activities [GENEPIO:0100542] + description: A prolonged period of inactivity between processes or events. + meaning: GENEPIO:0100542 + Microbial pre-treatment [GENEPIO:0100546]: + text: Microbial pre-treatment [GENEPIO:0100546] + description: The deliberate addition of microbes or a mixture of microbes + to an individual or substance prior to some other event or activity. + meaning: GENEPIO:0100546 + Probiotic pre-treatment [GENEPIO:0100547]: + text: Probiotic pre-treatment [GENEPIO:0100547] + description: The addition of a probiotic substance to an individual or material + prior to some other event or activity. + meaning: GENEPIO:0100547 + Vaccination [NCIT:C15346]: + text: Vaccination [NCIT:C15346] + description: Administration of vaccines to stimulate the host's immune response. + This includes any preparation intended for active immunological prophylaxis + or treatment. + meaning: NCIT:C15346 + SampleStorageDurationUnit: + name: SampleStorageDurationUnit + title: sample storage duration unit + permissible_values: + Second [UO:0000010]: + text: Second [UO:0000010] + description: A time unit which is equal to the duration of 9 192 631 770 periods + of the radiation corresponding to the transition between the two hyperfine + levels of the ground state of the caesium 133 atom. + meaning: UO:0000010 + Minute [UO:0000031]: + text: Minute [UO:0000031] + description: A time unit which is equal to 60 seconds. + meaning: UO:0000031 + Hour [UO:0000032]: + text: Hour [UO:0000032] + description: A time unit which is equal to 60 minutes. + meaning: UO:0000032 + Day [UO:0000033]: + text: Day [UO:0000033] + description: A time unit which is equal to 24 hours. + meaning: UO:0000033 + Week [UO:0000034]: + text: Week [UO:0000034] + description: A time unit which is equal to 7 days. + meaning: UO:0000034 + Month [UO:0000035]: + text: Month [UO:0000035] + description: A time unit which is equal to approximately 4-4.5 weeks or 28-31 + days. + meaning: UO:0000035 + Year [UO:0000036]: + text: Year [UO:0000036] + description: A time unit which is equal to 365 days, or 366 days during a + leap year. + meaning: UO:0000036 + SpecimenProcessing: + name: SpecimenProcessing + title: specimen processing + permissible_values: + Concentration [OBI:0600041]: + text: Concentration [OBI:0600041] + description: A process used to increase the density of a material of interest + by removing other materials in the entity containing the material of interest. + meaning: OBI:0600041 + Centrifugation [OBI:0302886]: + text: Centrifugation [OBI:0302886] + description: A process separating molecules by size or density using centrifugal + forces generated by a spinning rotor. + meaning: OBI:0302886 + Filtration [OBI:0302885]: + text: Filtration [OBI:0302885] + description: A process which separates components suspended in a fluid based + on granularity properties relying on a filter device. + meaning: OBI:0302885 + Pooling specimens [OBI:0600016]: + text: Pooling specimens [OBI:0600016] + description: Physical combination of several instances of like material. + meaning: OBI:0600016 + ExperimentalSpecimenRoleType: + name: ExperimentalSpecimenRoleType + title: experimental specimen role type + permissible_values: + Positive experimental control [GENEPIO:0101018]: + text: Positive experimental control [GENEPIO:0101018] + description: A control specimen that is expected to yield a positive result, + to establish a reference baseline for an experiment. + meaning: GENEPIO:0101018 + Validation strain [GENEPIO:0101123]: + text: Validation strain [GENEPIO:0101123] + meaning: GENEPIO:0101123 + is_a: Positive experimental control [GENEPIO:0101018] + Proficiency test isolate [GENEPIO:0101124]: + text: Proficiency test isolate [GENEPIO:0101124] + meaning: GENEPIO:0101124 + is_a: Positive experimental control [GENEPIO:0101018] + Negative experimental control [GENEPIO:0101019]: + text: Negative experimental control [GENEPIO:0101019] + description: A control specimen that is expected to yield a negative result, + to establish a reference baseline for an experiment + meaning: GENEPIO:0101019 + Technical replicate [EFO:0002090]: + text: Technical replicate [EFO:0002090] + description: A technical replicate is a replicate role where the same BioSample + is use e.g. the same pool of RNA used to assess technical (as opposed to + biological) variation within an experiment. + meaning: EFO:0002090 + Biological replicate [EFO:0002091]: + text: Biological replicate [EFO:0002091] + description: A biological replicate is a replicate role that consists of independent + biological replicates made from different individual biosamples. + meaning: EFO:0002091 + Synthetic lab construct [GENEPIO:0101039]: + text: Synthetic lab construct [GENEPIO:0101039] + meaning: GENEPIO:0101039 + Negative sample [GENEPIO:0101120]: + text: Negative sample [GENEPIO:0101120] + meaning: GENEPIO:0101120 + AvailableDataTypesMenu: + name: AvailableDataTypesMenu + title: available_data_types menu + permissible_values: + Documentation [GENEPIO:0100702]: + text: Documentation [GENEPIO:0100702] + description: A dataset attribute bundle which indicates the presence of documentation + data. + meaning: GENEPIO:0100702 + Experimental parameters documentation [GENEPIO:0100703]: + text: Experimental parameters documentation [GENEPIO:0100703] + description: A documentation data tag which indicates the presence of data + that describes experimental parameters. + meaning: GENEPIO:0100703 + is_a: Documentation [GENEPIO:0100702] + Feed history [GENEPIO:0100704]: + text: Feed history [GENEPIO:0100704] + description: A documentation data tag which indicates the presence of data + that describes feed history. + meaning: GENEPIO:0100704 + is_a: Documentation [GENEPIO:0100702] + Land use information [GENEPIO:0100705]: + text: Land use information [GENEPIO:0100705] + description: A documentation data tag which indicates the presence of data + that describes land use information. + meaning: GENEPIO:0100705 + is_a: Documentation [GENEPIO:0100702] + Therapeutic administration history [GENEPIO:0100706]: + text: Therapeutic administration history [GENEPIO:0100706] + description: A documentation data tag which indicates the presence of data + that describes a history of therapeutic administration. + meaning: GENEPIO:0100706 + is_a: Documentation [GENEPIO:0100702] + Chemical characterization [GENEPIO:0100707]: + text: Chemical characterization [GENEPIO:0100707] + description: A dataset attribute bundle which indicates the presence of chemical + characterization data. + meaning: GENEPIO:0100707 + Microbiological characterization [GENEPIO:0100714]: + text: Microbiological characterization [GENEPIO:0100714] + description: A dataset attribute bundle which indicates the presence of microbiological + characterization data. + meaning: GENEPIO:0100714 + Microbiological identification [GENEPIO:0100715]: + text: Microbiological identification [GENEPIO:0100715] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data. + meaning: GENEPIO:0100715 + is_a: Microbiological characterization [GENEPIO:0100714] + Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716]: + text: Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using the Beckson + Dickson BBL Crystal identification system. + meaning: GENEPIO:0100716 + is_a: Microbiological identification [GENEPIO:0100715] + "Microbiological identification (bioM\xE9rieux API) [GENEPIO:0100717]": + text: "Microbiological identification (bioM\xE9rieux API) [GENEPIO:0100717]" + description: "A microbiological characterization data tag which indicates\ + \ the presence of microbiological identification data dervied using the\ + \ bioM\xE9rieux API identification system." + meaning: GENEPIO:0100717 + is_a: Microbiological identification [GENEPIO:0100715] + Microbiological identification (Biolog) [GENEPIO:0100718]: + text: Microbiological identification (Biolog) [GENEPIO:0100718] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using the Biolog + identification system. + meaning: GENEPIO:0100718 + is_a: Microbiological identification [GENEPIO:0100715] + Microbiological identification (FAME) [GENEPIO:0100719]: + text: Microbiological identification (FAME) [GENEPIO:0100719] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using the Fatty + acid methyl esters (FAME) identification system. + meaning: GENEPIO:0100719 + is_a: Microbiological identification [GENEPIO:0100715] + Microbiological identification (Sensititre) [GENEPIO:0100720]: + text: Microbiological identification (Sensititre) [GENEPIO:0100720] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using the Sensititre + identification system. + meaning: GENEPIO:0100720 + is_a: Microbiological identification [GENEPIO:0100715] + Microbiological identification (ViTek) [GENEPIO:0100721]: + text: Microbiological identification (ViTek) [GENEPIO:0100721] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using the ViTek + identification system. + meaning: GENEPIO:0100721 + is_a: Microbiological identification [GENEPIO:0100715] + Phage type [GENEPIO:0100722]: + text: Phage type [GENEPIO:0100722] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using phage type + identification. + meaning: GENEPIO:0100722 + is_a: Microbiological identification [GENEPIO:0100715] + Serotype [GENEPIO:0100723]: + text: Serotype [GENEPIO:0100723] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using serotype identification. + meaning: GENEPIO:0100723 + is_a: Microbiological identification [GENEPIO:0100715] + Phenotypic microbiological characterization [GENEPIO:0100724]: + text: Phenotypic microbiological characterization [GENEPIO:0100724] + description: A microbiological characterization data tag which indicates the + presence of phenotypic microbiological characterization data. + meaning: GENEPIO:0100724 + is_a: Microbiological characterization [GENEPIO:0100714] + AMR phenotypic testing [GENEPIO:0100725]: + text: AMR phenotypic testing [GENEPIO:0100725] + description: A phenotypic microbiological characterization data tag which + indicates the presence of antimicrobial resistance (AMR) phenotypic testing + characterization data. + meaning: GENEPIO:0100725 + is_a: Phenotypic microbiological characterization [GENEPIO:0100724] + Biolog phenotype microarray [GENEPIO:0100726]: + text: Biolog phenotype microarray [GENEPIO:0100726] + description: A phenotypic microbiological characterization data tag which + indicates the presence of biolog phenotype microarray characterization data. + meaning: GENEPIO:0100726 + is_a: Phenotypic microbiological characterization [GENEPIO:0100724] + Microbiological quantification [GENEPIO:0100727]: + text: Microbiological quantification [GENEPIO:0100727] + description: A dataset attribute bundle which indicates the presence of microbiological + quantification data. + meaning: GENEPIO:0100727 + Colony count [GENEPIO:0100728]: + text: Colony count [GENEPIO:0100728] + description: A microbiological quantification data tag which indicates the + presence of colony count data. + meaning: GENEPIO:0100728 + is_a: Microbiological quantification [GENEPIO:0100727] + Total coliform count [GENEPIO:0100729]: + text: Total coliform count [GENEPIO:0100729] + description: A colony count microbiological quantification data tag which + indicates the presence of data that describes total colony count of coliforms. + meaning: GENEPIO:0100729 + is_a: Colony count [GENEPIO:0100728] + Total fecal coliform count [GENEPIO:0100730]: + text: Total fecal coliform count [GENEPIO:0100730] + description: A colony count microbiological quantification data tag that indicates + the presence of data which describes total colony count of fecal coliforms. + meaning: GENEPIO:0100730 + is_a: Colony count [GENEPIO:0100728] + Infectivity assay [GENEPIO:0100731]: + text: Infectivity assay [GENEPIO:0100731] + description: A microbiological quantification data tag which indicates the + presence of infectivity assay data. + meaning: GENEPIO:0100731 + is_a: Microbiological quantification [GENEPIO:0100727] + ELISA toxin binding [GENEPIO:0100732]: + text: ELISA toxin binding [GENEPIO:0100732] + description: A microbiological quantification data tag which indicates the + presence of data which describes enzyme-linked immunosorbent assay (ELISA) + toxin binding. + meaning: GENEPIO:0100732 + is_a: Microbiological quantification [GENEPIO:0100727] + Molecular characterization [GENEPIO:0100733]: + text: Molecular characterization [GENEPIO:0100733] + description: A dataset attribute bundle which indicates the presence of molecular + characterization data. + meaning: GENEPIO:0100733 + 16S rRNA Sanger sequencing [GENEPIO:0100734]: + text: 16S rRNA Sanger sequencing [GENEPIO:0100734] + description: A molecular characterization data tag which indicates the presence + of 16S rRNA Sanger sequencing characterization data. + meaning: GENEPIO:0100734 + is_a: Molecular characterization [GENEPIO:0100733] + Metagenomic sequencing [GENEPIO:0101024]: + text: Metagenomic sequencing [GENEPIO:0101024] + description: A molecular characterization data tag which indicates the presence + of metagenomic sequencing characterization data. + meaning: GENEPIO:0101024 + is_a: Molecular characterization [GENEPIO:0100733] + PCR marker detection [GENEPIO:0100735]: + text: PCR marker detection [GENEPIO:0100735] + description: A molecular characterization data tag which indicates the presence + of polymerase chain reaction (PCR) marker detection characterization data. + meaning: GENEPIO:0100735 + is_a: Molecular characterization [GENEPIO:0100733] + BOX PCR fingerprint [GENEPIO:0100736]: + text: BOX PCR fingerprint [GENEPIO:0100736] + description: A PCR marker detection characterization data tag which indicates + the presence of BOX-A1R-based repetitive extragenic palindromic (BOX) PCR + fingerprint data. + meaning: GENEPIO:0100736 + is_a: PCR marker detection [GENEPIO:0100735] + ERIC PCR fingerprint [GENEPIO:0100737]: + text: ERIC PCR fingerprint [GENEPIO:0100737] + description: A PCR marker detection characterization data tag which indicates + the presence of enterobacterial repetitive intergenic consensus (ERIC) PCR + fingerprint data. + meaning: GENEPIO:0100737 + is_a: PCR marker detection [GENEPIO:0100735] + Plasmid type [GENEPIO:0100738]: + text: Plasmid type [GENEPIO:0100738] + description: A molecular characterization data tag which indicates the presence + of plasmid type characterization data. + meaning: GENEPIO:0100738 + is_a: Molecular characterization [GENEPIO:0100733] + Ribotype [GENEPIO:0100739]: + text: Ribotype [GENEPIO:0100739] + description: A molecular characterization data tag which indicates the presence + of ribotype characterization data. + meaning: GENEPIO:0100739 + is_a: Molecular characterization [GENEPIO:0100733] + Molecular quantification [GENEPIO:0100740]: + text: Molecular quantification [GENEPIO:0100740] + description: A dataset attribute bundle which indicates the presence of molecular + quantification data. + meaning: GENEPIO:0100740 + qPCR marker organism quantification [GENEPIO:0100741]: + text: qPCR marker organism quantification [GENEPIO:0100741] + description: A molecular quantification data tag which indicates the presence + of quantitative polymerase chain reaction (qPCR) marker organism quantification + data. + meaning: GENEPIO:0100741 + is_a: Molecular quantification [GENEPIO:0100740] + Physical characterization [GENEPIO:0100742]: + text: Physical characterization [GENEPIO:0100742] + description: A dataset attribute bundle which indicates the presence of physical + characterization data. + meaning: GENEPIO:0100742 + Conductivity measurement [GENEPIO:0100743]: + text: Conductivity measurement [GENEPIO:0100743] + description: A physical characterization data tag which indicates the presence + of data that describes conductivity measurement characterization. + meaning: GENEPIO:0100743 + is_a: Physical characterization [GENEPIO:0100742] + Mollusc shell measurement [GENEPIO:0100744]: + text: Mollusc shell measurement [GENEPIO:0100744] + description: A physical characterization data tag which indicates the presence + of data that describes a measurement of a mollusc shell. + meaning: GENEPIO:0100744 + is_a: Physical characterization [GENEPIO:0100742] + Matter compostion [GENEPIO:0100746]: + text: Matter compostion [GENEPIO:0100746] + description: A physical characterization data tag which indicates the presence + of matter compostion characterization data. + meaning: GENEPIO:0100746 + is_a: Physical characterization [GENEPIO:0100742] + Dry matter composition [GENEPIO:0100747]: + text: Dry matter composition [GENEPIO:0100747] + description: A matter composition characterization data tag which indicates + the presence of data that describes dry matter composition. + meaning: GENEPIO:0100747 + is_a: Matter compostion [GENEPIO:0100746] + Organic matter composition [GENEPIO:0100748]: + text: Organic matter composition [GENEPIO:0100748] + description: A matter composition characterization data tag which indicates + the presence of data that describes organic matter composition. + meaning: GENEPIO:0100748 + is_a: Matter compostion [GENEPIO:0100746] + HostCommonNameMenu: + name: HostCommonNameMenu + title: host (common name) menu + permissible_values: + Bird [NCBITaxon:8782]: + text: Bird [NCBITaxon:8782] + description: A group of warm-blooded vertebrates in class Aves, that are characterized + by feathers, wings, toothless beaked jaws and the laying of hard-shelled + eggs and are usually able to fly. + meaning: NCBITaxon:8782 + Chicken [NCBITaxon:9031]: + text: Chicken [NCBITaxon:9031] + description: A domesticated junglefowl of the species Gallus gallus. + meaning: NCBITaxon:9031 + is_a: Bird [NCBITaxon:8782] + Seabird [FOODON:00004504]: + text: Seabird [FOODON:00004504] + description: A bird that is adapted to live within the marine environment. + meaning: FOODON:00004504 + is_a: Bird [NCBITaxon:8782] + Cormorant [NCBITaxon:9206]: + text: Cormorant [NCBITaxon:9206] + description: A family of aquatic birds (Phalacrocoracidae). + meaning: NCBITaxon:9206 + is_a: Seabird [FOODON:00004504] + Double Crested Cormorant [NCBITaxon:56069]: + text: Double Crested Cormorant [NCBITaxon:56069] + description: A species of the cormorant family of water birds (Phalacrocorax + auritus). + meaning: NCBITaxon:56069 + is_a: Cormorant [NCBITaxon:9206] + Crane [NCBITaxon:9109]: + text: Crane [NCBITaxon:9109] + description: A family of large, long-legged, and long-necked birds (Gruidae). + meaning: NCBITaxon:9109 + is_a: Seabird [FOODON:00004504] + Whooping Crane [NCBITaxon:9117]: + text: Whooping Crane [NCBITaxon:9117] + description: An endangered crane species that is native to North America and + is named for its whooping sound. + meaning: NCBITaxon:9117 + is_a: Crane [NCBITaxon:9109] + Gull (Seagull) [NCBITaxon:8911]: + text: Gull (Seagull) [NCBITaxon:8911] + description: A large genus of gulls within the family Laridae. + meaning: NCBITaxon:8911 + is_a: Seabird [FOODON:00004504] + Glaucous-winged Gull [NCBITaxon:119606]: + text: Glaucous-winged Gull [NCBITaxon:119606] + description: A species of large, white-headed gull (Larus glaucescens). + meaning: NCBITaxon:119606 + is_a: Gull (Seagull) [NCBITaxon:8911] + Great Black-backed Gull [NCBITaxon:8912]: + text: Great Black-backed Gull [NCBITaxon:8912] + description: A species of white gull that has a black back and wings (Larus + marinus). + meaning: NCBITaxon:8912 + is_a: Gull (Seagull) [NCBITaxon:8911] + Herring Gull [NCBITaxon:35669]: + text: Herring Gull [NCBITaxon:35669] + description: A species of large gull, that is up to 66 cm (26 in) long (Larus + argentatus). + meaning: NCBITaxon:35669 + is_a: Gull (Seagull) [NCBITaxon:8911] + Ring-billed Gull [NCBITaxon:126683]: + text: Ring-billed Gull [NCBITaxon:126683] + description: A species of ring-billed gull that has a black ring around its + bill (Larus delawarensis). + meaning: NCBITaxon:126683 + is_a: Gull (Seagull) [NCBITaxon:8911] + Eider [NCBITaxon:50366]: + text: Eider [NCBITaxon:50366] + description: A genus of large seaducks (Somateria). + meaning: NCBITaxon:50366 + is_a: Seabird [FOODON:00004504] + Common Eider [NCBITaxon:76058]: + text: Common Eider [NCBITaxon:76058] + description: A species of a large sea-duck that is distributed over the northern + coasts of Europe, North America and eastern Siberia (Somateria mollissima). + meaning: NCBITaxon:76058 + is_a: Eider [NCBITaxon:50366] + Turkey [NCBITaxon:9103]: + text: Turkey [NCBITaxon:9103] + description: A large, mainly domesticated game bird characterized by a bald + head and wattles (in the male) of the species Meleagris gallopavo. + meaning: NCBITaxon:9103 + is_a: Bird [NCBITaxon:8782] + Fish [FOODON:03411222]: + text: Fish [FOODON:03411222] + description: Fish are the gill-bearing aquatic craniate animals that lack + limbs with digits. Most fish are ectothermic ("cold-blooded"), allowing + their body temperatures to vary as ambient temperatures change, though some + of the large active swimmers like white shark and tuna can hold a higher + core temperature. + meaning: FOODON:03411222 + Mammal [FOODON:03411134]: + text: Mammal [FOODON:03411134] + description: Mammals (from Latin mamma "breast") are vertebrate animals constituting + the class Mammalia, and characterized by the presence of mammary glands + which in females produce milk for feeding (nursing) their young, a neocortex + (a region of the brain), fur or hair, and three middle ear bones. + meaning: FOODON:03411134 + Companion animal [FOODON:03000300]: + text: Companion animal [FOODON:03000300] + description: An animal that is kept as a companion. + meaning: FOODON:03000300 + is_a: Mammal [FOODON:03411134] + Cow [NCBITaxon:9913]: + text: Cow [NCBITaxon:9913] + description: A group of large, domesticated, cloven-hooved herbivores. + meaning: NCBITaxon:9913 + is_a: Mammal [FOODON:03411134] + Deer [NCBITaxon:9850]: + text: Deer [NCBITaxon:9850] + meaning: NCBITaxon:9850 + is_a: Mammal [FOODON:03411134] + Human [NCBITaxon:9606]: + text: Human [NCBITaxon:9606] + description: A bipedal primate mammal of the species Homo sapiens. + meaning: NCBITaxon:9606 + is_a: Mammal [FOODON:03411134] + Pig [NCBITaxon:9823]: + text: Pig [NCBITaxon:9823] + description: A stout-bodied, hooved and short-legged, omnivorous mammal from + the species Sus scofus, with thick skin usually sparsely coated with short + bristles. + meaning: NCBITaxon:9823 + is_a: Mammal [FOODON:03411134] + Sheep [NCBITaxon:9940]: + text: Sheep [NCBITaxon:9940] + description: A domesticated, even-toed, ungluate, ruminant mammal typically + kept as livestock for its wool and meat, usually of the species Ovis aries. + meaning: NCBITaxon:9940 + is_a: Mammal [FOODON:03411134] + Shellfish [FOODON:03411433]: + text: Shellfish [FOODON:03411433] + description: The term shellfish is used both broadly and specifically. For + regulatory purposes it is often narrowly defined as filter-feeding molluscs + such as clams, mussels, and oyster to the exclusion of crustaceans and all + else. Although their shells may differ, all shellfish are invertebrates. + meaning: FOODON:03411433 + HostScientificNameMenu: + name: HostScientificNameMenu + title: host (scientific name) menu + permissible_values: + Anoplopoma fimbria [NCBITaxon:229290]: + text: Anoplopoma fimbria [NCBITaxon:229290] + description: One of two members of the fish family Anoplopomatidae and the + only species in the genus Anoplopoma. + meaning: NCBITaxon:229290 + Bos taurus [NCBITaxon:9913]: + text: Bos taurus [NCBITaxon:9913] + description: A group of large, domesticated, cloven-hooved herbivores. + meaning: NCBITaxon:9913 + Crassostrea virginica [NCBITaxon:6565]: + text: Crassostrea virginica [NCBITaxon:6565] + description: A species of true oyster (Crassostrea virginica). + meaning: NCBITaxon:6565 + Gallus gallus [NCBITaxon:9031]: + text: Gallus gallus [NCBITaxon:9031] + description: A domesticated junglefowl of the species Gallus gallus. + meaning: NCBITaxon:9031 + Grus americana [NCBITaxon:9117]: + text: Grus americana [NCBITaxon:9117] + description: An endangered crane species that is native to North America and + is named for its whooping sound. + meaning: NCBITaxon:9117 + Homarus americanus [NCBITaxon:6706]: + text: Homarus americanus [NCBITaxon:6706] + description: A species of lobster that is found on the Atlantic coast of North + America (Homarus americanus). + meaning: NCBITaxon:6706 + Homo sapiens [NCBITaxon:9606]: + text: Homo sapiens [NCBITaxon:9606] + description: A bipedal primate mammal of the species Homo sapiens. + meaning: NCBITaxon:9606 + Larus argentatus [NCBITaxon:35669]: + text: Larus argentatus [NCBITaxon:35669] + description: A species of large gull, that is up to 66 cm (26 in) long (Larus + argentatus). + meaning: NCBITaxon:35669 + Larus delawarensis [NCBITaxon:126683]: + text: Larus delawarensis [NCBITaxon:126683] + description: A species of ring-billed gull that has a black ring around its + bill (Larus delawarensis). + meaning: NCBITaxon:126683 + Larus glaucescens [NCBITaxon:119606]: + text: Larus glaucescens [NCBITaxon:119606] + description: A species of large, white-headed gull (Larus glaucescens). + meaning: NCBITaxon:119606 + Larus marinus [NCBITaxon:8912]: + text: Larus marinus [NCBITaxon:8912] + description: A species of white gull that has a black back and wings (Larus + marinus). + meaning: NCBITaxon:8912 + Meleagris gallopavo [NCBITaxon:9103]: + text: Meleagris gallopavo [NCBITaxon:9103] + description: A large, mainly domesticated game bird characterized by a bald + head and wattles (in the male) of the species Meleagris gallopavo. + meaning: NCBITaxon:9103 + Mytilus edulis [NCBITaxon:6550]: + text: Mytilus edulis [NCBITaxon:6550] + description: A medium-sized edible marine bivalve mollusc in the family Mytilidae, + the mussels. + meaning: NCBITaxon:6550 + Oncorhynchus kisutch [NCBITaxon:8019]: + text: Oncorhynchus kisutch [NCBITaxon:8019] + description: A species of pacific salmon in North America, that is commonly + called as coho salmon. + meaning: NCBITaxon:8019 + Oncorhynchus mykiss [NCBITaxon:8022]: + text: Oncorhynchus mykiss [NCBITaxon:8022] + description: A species of trout native to cold-water tributaries of the Pacific + Ocean in Asia and North America (Oncorhynchus mykiss). + meaning: NCBITaxon:8022 + Oncorhynchus tshawytscha [NCBITaxon:74940]: + text: Oncorhynchus tshawytscha [NCBITaxon:74940] + description: The largest species of pacific salmon in North America (Oncorhynchus + tshawytscha). + meaning: NCBITaxon:74940 + Ovis aries [NCBITaxon:9940]: + text: Ovis aries [NCBITaxon:9940] + description: A domesticated, even-toed, ungluate, ruminant mammal typically + kept as livestock for its wool and meat, usually of the species Ovis aries. + meaning: NCBITaxon:9940 + Phalacrocorax auritus [NCBITaxon:56069]: + text: Phalacrocorax auritus [NCBITaxon:56069] + description: A species of the cormorant family of water birds (Phalacrocorax + auritus). + meaning: NCBITaxon:56069 + Salmo salar [NCBITaxon:8030]: + text: Salmo salar [NCBITaxon:8030] + description: A species of ray-finned fish in the family Salmonidae (Salmo + salar). + meaning: NCBITaxon:8030 + Somateria mollissima [NCBITaxon:76058]: + text: Somateria mollissima [NCBITaxon:76058] + description: A species of a large sea-duck that is distributed over the northern + coasts of Europe, North America and eastern Siberia (Somateria mollissima). + meaning: NCBITaxon:76058 + Sus scrofa domesticus [NCBITaxon:9825]: + text: Sus scrofa domesticus [NCBITaxon:9825] + description: A stout-bodied, hooved and short-legged, omnivorous mammal, with + thick skin usually sparsely coated with short bristles raised for its meat. + meaning: NCBITaxon:9825 + HostFoodProductionNameMenu: + name: HostFoodProductionNameMenu + title: host (food production name) menu + permissible_values: + Cow (by age/production stage) (organizational term): + text: Cow (by age/production stage) (organizational term) + Calf [FOODON:03411349]: + text: Calf [FOODON:03411349] + description: Calves are the young of domestic cattle. Calves are reared to + become adult cattle, or are slaughtered for their meat, called veal. + meaning: FOODON:03411349 + is_a: Cow (by age/production stage) (organizational term) + Dry cow [FOODON:00004411]: + text: Dry cow [FOODON:00004411] + description: A cow that is in a stage of its lactation cycle where milk production + ceases prior to calving. + meaning: FOODON:00004411 + is_a: Cow (by age/production stage) (organizational term) + Feeder cow [FOODON:00004292]: + text: Feeder cow [FOODON:00004292] + description: A young cow mature enough either to undergo backgrounding or + to be fattened in preparation for slaughter. + meaning: FOODON:00004292 + is_a: Cow (by age/production stage) (organizational term) + Finisher cow [FOODON:00004293]: + text: Finisher cow [FOODON:00004293] + meaning: FOODON:00004293 + is_a: Cow (by age/production stage) (organizational term) + Milker cow [FOODON:03411201]: + text: Milker cow [FOODON:03411201] + description: A cow that is bred specifically for milk production. + meaning: FOODON:03411201 + is_a: Cow (by age/production stage) (organizational term) + Stocker cow [FOODON:00004294]: + text: Stocker cow [FOODON:00004294] + description: A type of cow that has been weaned and is being fed in a way + to add physical bulk to its body. + meaning: FOODON:00004294 + is_a: Cow (by age/production stage) (organizational term) + Weanling cow [FOODON:00004295]: + text: Weanling cow [FOODON:00004295] + description: A type of young cow that has been weaned and consumes solid food. + meaning: FOODON:00004295 + is_a: Cow (by age/production stage) (organizational term) + Cow (by sex/reproductive stage) (organizational term): + text: Cow (by sex/reproductive stage) (organizational term) + Bull [FOODON:00000015]: + text: Bull [FOODON:00000015] + description: A cattle bull is an adult "intact" (i.e. not castrated) male + of a cattle species. + meaning: FOODON:00000015 + is_a: Cow (by sex/reproductive stage) (organizational term) + Cow [NCBITaxon:9913]: + text: Cow [NCBITaxon:9913] + description: A group of large, domesticated, cloven-hooved herbivores. + meaning: NCBITaxon:9913 + is_a: Cow (by sex/reproductive stage) (organizational term) + Freemartin [FOODON:00004296]: + text: Freemartin [FOODON:00004296] + description: A cow that is genetically female, but has many characteristics + of a male and is usually infertile. + meaning: FOODON:00004296 + is_a: Cow (by sex/reproductive stage) (organizational term) + Heifer [FOODON:00002518]: + text: Heifer [FOODON:00002518] + description: A heifer is a young female, under three years of age, of a cattle + species before she has had a calf of her own. + meaning: FOODON:00002518 + is_a: Cow (by sex/reproductive stage) (organizational term) + Steer [FOODON:00002531]: + text: Steer [FOODON:00002531] + description: A cattle steer is an adult castrated male of a cattle species. + meaning: FOODON:00002531 + is_a: Cow (by sex/reproductive stage) (organizational term) + Pig (by age/production stage) (organizational term): + text: Pig (by age/production stage) (organizational term) + Finisher pig [FOODON:00003371]: + text: Finisher pig [FOODON:00003371] + description: A grower pig over 70 kg (150 lb) liveweight. + meaning: FOODON:00003371 + is_a: Pig (by age/production stage) (organizational term) + Grower pig [FOODON:00003370]: + text: Grower pig [FOODON:00003370] + description: A pig between weaning and sale or transfer to the breeding herd, + sold for slaughter or killed for rations. + meaning: FOODON:00003370 + is_a: Pig (by age/production stage) (organizational term) + Nursing pig [FOODON:00004297 ]: + text: Nursing pig [FOODON:00004297 ] + meaning: OODON:00004297 + is_a: Pig (by age/production stage) (organizational term) + Pig [NCBITaxon:9823]: + text: Pig [NCBITaxon:9823] + description: A stout-bodied, hooved and short-legged, omnivorous mammal from + the species Sus scofus, with thick skin usually sparsely coated with short + bristles. + meaning: NCBITaxon:9823 + is_a: Pig (by age/production stage) (organizational term) + Piglet [FOODON:00003952]: + text: Piglet [FOODON:00003952] + description: An unweaned or immature pig. + meaning: FOODON:00003952 + is_a: Pig (by age/production stage) (organizational term) + Weanling (weaner) pig [FOODON:00003373]: + text: Weanling (weaner) pig [FOODON:00003373] + description: A young pig recently separated from the sow + meaning: FOODON:00003373 + is_a: Pig (by age/production stage) (organizational term) + Pig (by sex/reproductive stage) (organizational term): + text: Pig (by sex/reproductive stage) (organizational term) + Barrow [FOODON:03411280]: + text: Barrow [FOODON:03411280] + description: A male swine castrated before sexual maturity. + meaning: FOODON:03411280 + is_a: Pig (by sex/reproductive stage) (organizational term) + Boar [FOODON:03412248]: + text: Boar [FOODON:03412248] + description: An adult male swine. + meaning: FOODON:03412248 + is_a: Pig (by sex/reproductive stage) (organizational term) + Gilt [FOODON:00003369]: + text: Gilt [FOODON:00003369] + description: A female pig under the age of 1 year. The term is also often + used to refer to a pig who has not farrowed, or given birth to a litter. + meaning: FOODON:00003369 + is_a: Pig (by sex/reproductive stage) (organizational term) + Sow [FOODON:00003333]: + text: Sow [FOODON:00003333] + description: An adult female swine. + meaning: FOODON:00003333 + is_a: Pig (by sex/reproductive stage) (organizational term) + Poultry or game bird [FOODON:03411563]: + text: Poultry or game bird [FOODON:03411563] + description: Domesticated birds kept by humans for their eggs, their meat + or their feathers. + meaning: FOODON:03411563 + Broiler or fryer chicken [FOODON:03411198]: + text: Broiler or fryer chicken [FOODON:03411198] + description: A chicken younger than 10 weeks old (previously younger than + 13 weeks), of either sex, that is tender-meated with soft, pliable, smooth-textured + skin and flexible breastbone cartilage. + meaning: FOODON:03411198 + is_a: Poultry or game bird [FOODON:03411563] + Capon [FOODON:03411711]: + text: Capon [FOODON:03411711] + description: A surgically neutered male chicken younger than four months old + (previously younger than eight months) that is tender-meated with soft, + pliable, smooth-textured skin. + meaning: FOODON:03411711 + is_a: Poultry or game bird [FOODON:03411563] + Chick [FOODON:00004299]: + text: Chick [FOODON:00004299] + description: A young offspring of any bird. + meaning: FOODON:00004299 + is_a: Poultry or game bird [FOODON:03411563] + Chicken [NCBITaxon:9031]: + text: Chicken [NCBITaxon:9031] + description: A domesticated junglefowl of the species Gallus gallus. + meaning: NCBITaxon:9031 + is_a: Poultry or game bird [FOODON:03411563] + Egg [UBERON:0007379]: + text: Egg [UBERON:0007379] + description: 'The hard-shelled reproductive body produced by a bird (especially + by the common domestic chicken) or a reptile; also: its contents used as + food.' + meaning: UBERON:0007379 + is_a: Poultry or game bird [FOODON:03411563] + Hatchling [FOODON:00004300]: + text: Hatchling [FOODON:00004300] + description: A young animal that has recently emerged from its egg. + meaning: FOODON:00004300 + is_a: Poultry or game bird [FOODON:03411563] + Hen [FOODON:00003282]: + text: Hen [FOODON:00003282] + description: An adult female chicken. + meaning: FOODON:00003282 + is_a: Poultry or game bird [FOODON:03411563] + Layer chicken [FOODON:00004301]: + text: Layer chicken [FOODON:00004301] + description: A type of chicken kept for laying eggs. + meaning: FOODON:00004301 + is_a: Poultry or game bird [FOODON:03411563] + Layer turkey [FOODON:00004302]: + text: Layer turkey [FOODON:00004302] + description: A type of turkey kept for laying eggs. + meaning: FOODON:00004302 + is_a: Poultry or game bird [FOODON:03411563] + Poult [FOODON:00002962]: + text: Poult [FOODON:00002962] + description: A poult is a young domestic chicken, turkey, pheasant, or other + fowl being raised for food. + meaning: FOODON:00002962 + is_a: Poultry or game bird [FOODON:03411563] + Pullet [FOODON:00004303]: + text: Pullet [FOODON:00004303] + description: A young hen, especially one less than one year old. + meaning: FOODON:00004303 + is_a: Poultry or game bird [FOODON:03411563] + Rooster [FOODON:03411714]: + text: Rooster [FOODON:03411714] + description: A mature male chicken with coarse skin, toughened and darkened + meat, and hardened breastbone tip. + meaning: FOODON:03411714 + is_a: Poultry or game bird [FOODON:03411563] + Tom (Gobbler) [FOODON:00004304 ]: + text: Tom (Gobbler) [FOODON:00004304 ] + meaning: OODON:00004304 + is_a: Poultry or game bird [FOODON:03411563] + Turkey [NCBITaxon:9103]: + text: Turkey [NCBITaxon:9103] + description: A large, mainly domesticated game bird characterized by a bald + head and wattles (in the male) of the species Meleagris gallopavo. + meaning: NCBITaxon:9103 + is_a: Poultry or game bird [FOODON:03411563] + Sheep [NCBITaxon:9940]: + text: Sheep [NCBITaxon:9940] + description: A domesticated, even-toed, ungluate, ruminant mammal typically + kept as livestock for its wool and meat, usually of the species Ovis aries. + meaning: NCBITaxon:9940 + Ram [FOODON:00004305]: + text: Ram [FOODON:00004305] + description: An adult male sheep kept for breeding and for wool production. + meaning: FOODON:00004305 + is_a: Sheep [NCBITaxon:9940] + Wether sheep [FOODON:00004306]: + text: Wether sheep [FOODON:00004306] + description: A castrated male sheep. + meaning: FOODON:00004306 + is_a: Sheep [NCBITaxon:9940] + Ewe [FOODON:03412610]: + text: Ewe [FOODON:03412610] + description: A ewe is a female sheep. + meaning: FOODON:03412610 + is_a: Sheep [NCBITaxon:9940] + Lamb [FOODON:03411669]: + text: Lamb [FOODON:03411669] + description: A whole lamb or some material processed from a lamb. + meaning: FOODON:03411669 + is_a: Sheep [NCBITaxon:9940] + Fish [FOODON:03411222]: + text: Fish [FOODON:03411222] + description: Fish are the gill-bearing aquatic craniate animals that lack + limbs with digits. Most fish are ectothermic ("cold-blooded"), allowing + their body temperatures to vary as ambient temperatures change, though some + of the large active swimmers like white shark and tuna can hold a higher + core temperature. + meaning: FOODON:03411222 + Fish egg [FOODON_00004319]: + text: Fish egg [FOODON_00004319] + description: An egg or spawn of a fish that is contained within or separated + from the ovary. + meaning: FOODON:00004319 + is_a: Fish [FOODON:03411222] + Fry (fish) [FOODON_00004318]: + text: Fry (fish) [FOODON_00004318] + description: A fish that is recently hatched and has reached the stage where + its yolk-sac has almost disappeared and its swim bladder is operational + to the point where the fish can actively feed for itself. + meaning: FOODON:00004318 + is_a: Fish [FOODON:03411222] + Juvenile fish [FOODON_00004317]: + text: Juvenile fish [FOODON_00004317] + description: A fish that has not reached to sexual maturity. + meaning: FOODON:00004317 + is_a: Fish [FOODON:03411222] + HostAgeUnitMenu: + name: HostAgeUnitMenu + title: host_age_unit menu + permissible_values: + month [UO:0000035]: + text: month [UO:0000035] + description: A time unit which is equal to approximately 4-4.5 weeks or 28-31 + days. + meaning: UO:0000035 + year [UO:0000036]: + text: year [UO:0000036] + description: A time unit which is equal to 365 days, or 366 days during a + leap year. + meaning: UO:0000036 + HostAgeBinMenu: + name: HostAgeBinMenu + title: host_age_bin menu + permissible_values: + First winter [GENEPIO:0100684]: + text: First winter [GENEPIO:0100684] + description: An age group used to classify birds identified by their first + winter nonbreeding plumage, generally indicating a juvenile bird. + meaning: GENEPIO:0100684 + First summer [GENEPIO:0100685]: + text: First summer [GENEPIO:0100685] + description: An age group used to classify birds identified by their first + summer nonbreeding plumage, generally indicating a juvenile bird. + meaning: GENEPIO:0100685 + Second winter [GENEPIO:0100686]: + text: Second winter [GENEPIO:0100686] + description: An age group used to classify birds identified by their second + winter plumage (many types of birds molt several times during the same season). + meaning: GENEPIO:0100686 + Second summer [GENEPIO:0100687]: + text: Second summer [GENEPIO:0100687] + description: An age group used to classify birds identified by their second + summer plumage (many types of birds molt several times during the same season). + meaning: GENEPIO:0100687 + Third winter [GENEPIO:0100688]: + text: Third winter [GENEPIO:0100688] + description: An age group used to classify birds identified by their third + winter plumage (many types of birds molt several times during the same season). + meaning: GENEPIO:0100688 + Third summer [GENEPIO:0100689]: + text: Third summer [GENEPIO:0100689] + description: An age group used to classify birds identified by their third + summer plumage (many types of birds molt several times during the same season). + meaning: GENEPIO:0100689 + 0 - 9 [GENEPIO:0100049]]: + text: 0 - 9 [GENEPIO:0100049]] + meaning: ENEPIO:0100049 + 10 - 19 [GENEPIO:0100050]: + text: 10 - 19 [GENEPIO:0100050] + description: An age group that stratifies the age of a case to be between + 10 to 19 years old (inclusive). + meaning: GENEPIO:0100050 + 20 - 29 [GENEPIO:0100051]: + text: 20 - 29 [GENEPIO:0100051] + description: An age group that stratifies the age of a case to be between + 20 to 29 years old (inclusive). + meaning: GENEPIO:0100051 + 30 - 39 [GENEPIO:0100052]: + text: 30 - 39 [GENEPIO:0100052] + description: An age group that stratifies the age of a case to be between + 30 to 39 years old (inclusive). + meaning: GENEPIO:0100052 + 40 - 49 [GENEPIO:0100053]: + text: 40 - 49 [GENEPIO:0100053] + description: An age group that stratifies the age of a case to be between + 40 to 49 years old (inclusive). + meaning: GENEPIO:0100053 + 50 - 59 [GENEPIO:0100054]: + text: 50 - 59 [GENEPIO:0100054] + description: An age group that stratifies the age of a case to be between + 50 to 59 years old (inclusive). + meaning: GENEPIO:0100054 + 60 - 69 [GENEPIO:0100055]: + text: 60 - 69 [GENEPIO:0100055] + description: An age group that stratifies the age of a case to be between + 60 to 69 years old (inclusive). + meaning: GENEPIO:0100055 + 70 - 79 [GENEPIO:0100056]: + text: 70 - 79 [GENEPIO:0100056] + description: An age group that stratifies the age of a case to be between + 70 to 79 years old (inclusive). + meaning: GENEPIO:0100056 + 80 - 89 [GENEPIO:0100057]: + text: 80 - 89 [GENEPIO:0100057] + description: An age group that stratifies the age of a case to be between + 80 to 89 years old (inclusive). + meaning: GENEPIO:0100057 + 90 - 99 [GENEPIO:0100058]: + text: 90 - 99 [GENEPIO:0100058] + description: An age group that stratifies the age of a case to be between + 90 to 99 years old (inclusive). + meaning: GENEPIO:0100058 + 100+ [GENEPIO:0100059]: + text: 100+ [GENEPIO:0100059] + description: An age group that stratifies the age of a case to be greater + than or equal to 100 years old. + meaning: GENEPIO:0100059 + HostGender: + name: HostGender + title: host_gender + permissible_values: + Female [NCIT:C46110]: + text: Female [NCIT:C46110] + description: An individual who reports belonging to the cultural gender role + distinction of female. + meaning: NCIT:C46110 + Male [NCIT:C46109]: + text: Male [NCIT:C46109] + description: An individual who reports belonging to the cultural gender role + distinction of male. + meaning: NCIT:C46109 + Non-binary gender [GSSO:000132]: + text: Non-binary gender [GSSO:000132] + description: Either, a specific gender identity which is not male or female; + or, more broadly, an umbrella term for gender identities not considered + male or female. + meaning: GSSO:000132 + Transgender (assigned male at birth) [GSSO:004004]: + text: Transgender (assigned male at birth) [GSSO:004004] + description: Having a feminine gender (identity) which is different from the + sex one was assigned at birth. + meaning: GSSO:004004 + Transgender (assigned female at birth) [GSSO:004005]: + text: Transgender (assigned female at birth) [GSSO:004005] + description: Having a masculine gender (identity) which is different from + the sex one was assigned at birth. + meaning: GSSO:004005 + Undeclared [NCIT:C110959]: + text: Undeclared [NCIT:C110959] + meaning: CIT:C110959 + HostDiseaseMenu: + name: HostDiseaseMenu + title: host_disease menu + permissible_values: + Highly pathogenic avian influenza A (HPAI): + text: Highly pathogenic avian influenza A (HPAI) + HostHealthStateMenu: + name: HostHealthStateMenu + title: host_health_state menu + permissible_values: + Asymptomatic [NCIT:C3833]: + text: Asymptomatic [NCIT:C3833] + description: Without clinical signs or indications that raise the possibility + of a particular disorder or dysfunction. + meaning: NCIT:C3833 + Deceased [NCIT:C28554]: + text: Deceased [NCIT:C28554] + description: The cessation of life. + meaning: NCIT:C28554 + Healthy [NCIT:C115935]: + text: Healthy [NCIT:C115935] + meaning: CIT:C115935 + Recovered [NCIT:C49498]: + text: Recovered [NCIT:C49498] + description: One of the possible results of an adverse event outcome that + indicates that the event has improved or recuperated. + meaning: NCIT:C49498 + Symptomatic [NCIT:C25269]: + text: Symptomatic [NCIT:C25269] + description: Exhibiting the symptoms of a particular disease. + meaning: NCIT:C25269 + HostHealthStatusDetailsMenu: + name: HostHealthStatusDetailsMenu + title: host_health_status_details menu + permissible_values: + Hospitalized [NCIT:C25179]: + text: Hospitalized [NCIT:C25179] + description: The condition of being treated as a patient in a hospital. + meaning: NCIT:C25179 + Hospitalized (Non-ICU) [GENEPIO:0100045]: + text: Hospitalized (Non-ICU) [GENEPIO:0100045] + description: The condition of being treated as a patient in a hospital without + admission to an intensive care unit (ICU). + meaning: GENEPIO:0100045 + is_a: Hospitalized [NCIT:C25179] + Hospitalized (ICU) [GENEPIO:0100046]: + text: Hospitalized (ICU) [GENEPIO:0100046] + description: The condition of being treated as a patient in a hospital intensive + care unit (ICU). + meaning: GENEPIO:0100046 + is_a: Hospitalized [NCIT:C25179] + Mechanical Ventilation [NCIT:C70909]: + text: Mechanical Ventilation [NCIT:C70909] + meaning: NCIT:C70909 + Medically Isolated [GENEPIO:0100047]: + text: Medically Isolated [GENEPIO:0100047] + description: Separation of people with a contagious disease from population + to reduce the spread of the disease. + meaning: GENEPIO:0100047 + Medically Isolated (Negative Pressure) [GENEPIO:0100048]: + text: Medically Isolated (Negative Pressure) [GENEPIO:0100048] + description: 'Medical isolation in a negative pressure environment: 6 to 12 + air exchanges per hour, and direct exhaust to the outside or through a high + efficiency particulate air filter.' + meaning: GENEPIO:0100048 + is_a: Medically Isolated [GENEPIO:0100047] + Self-quarantining [NCIT:C173768]: + text: Self-quarantining [NCIT:C173768] + meaning: CIT:C173768 + HostHealthOutcomeMenu: + name: HostHealthOutcomeMenu + title: host_health_outcome menu + permissible_values: + Deceased [NCIT:C28554]: + text: Deceased [NCIT:C28554] + description: The cessation of life. + meaning: NCIT:C28554 + Deteriorating [NCIT:C25254]: + text: Deteriorating [NCIT:C25254] + description: Advancing in extent or severity. + meaning: NCIT:C25254 + Recovered [NCIT:C49498]: + text: Recovered [NCIT:C49498] + description: One of the possible results of an adverse event outcome that + indicates that the event has improved or recuperated. + meaning: NCIT:C49498 + Stable [NCIT:C30103]: + text: Stable [NCIT:C30103] + description: Subject to little fluctuation; showing little if any change. + meaning: NCIT:C30103 + SignsAndSymptomsMenu: + name: SignsAndSymptomsMenu + title: signs_and_symptoms menu + permissible_values: + Abnormal lung auscultation [HP:0030829]: + text: Abnormal lung auscultation [HP:0030829] + meaning: HP:0030829 + Acute Respiratory Distress Syndrome [HP:0033677]: + text: Acute Respiratory Distress Syndrome [HP:0033677] + meaning: HP:0033677 + Altered mental status [HP:0011446]: + text: Altered mental status [HP:0011446] + meaning: HP:0011446 + Cognitive impairment [HP:0100543]: + text: Cognitive impairment [HP:0100543] + meaning: HP:0100543 + is_a: Altered mental status [HP:0011446] + Coma [HP:0001259]: + text: Coma [HP:0001259] + meaning: HP:0001259 + is_a: Altered mental status [HP:0011446] + Confusion [HP:0001289]: + text: Confusion [HP:0001289] + meaning: HP:0001289 + is_a: Altered mental status [HP:0011446] + Delirium (sudden severe confusion) [HP:0031258]: + text: Delirium (sudden severe confusion) [HP:0031258] + meaning: HP:0031258 + is_a: Confusion [HP:0001289] + Arrhythmia [HP:0011675]: + text: Arrhythmia [HP:0011675] + meaning: HP:0011675 + Asthenia (generalized weakness) [HP:0025406]: + text: Asthenia (generalized weakness) [HP:0025406] + meaning: HP:0025406 + Bleeding gums [GENEPIO:0101182]: + text: Bleeding gums [GENEPIO:0101182] + meaning: GENEPIO:0101182 + Chest tightness or pressure [HP:0031352]: + text: Chest tightness or pressure [HP:0031352] + meaning: HP:0031352 + Rigors (fever shakes) [HP:0025145]: + text: Rigors (fever shakes) [HP:0025145] + meaning: HP:0025145 + is_a: Chest tightness or pressure [HP:0031352] + Chills (sudden cold sensation) [HP:0025143]: + text: Chills (sudden cold sensation) [HP:0025143] + description: A sudden sensation of feeling cold. + meaning: HP:0025143 + Conjunctivitis (pink eye) [HP:0000509]: + text: Conjunctivitis (pink eye) [HP:0000509] + description: Inflammation of the conjunctiva. + meaning: HP:0000509 + Coryza (rhinitis) [MP:0001867]: + text: Coryza (rhinitis) [MP:0001867] + meaning: MP:0001867 + Cough [HP:0012735]: + text: Cough [HP:0012735] + description: A sudden, audible expulsion of air from the lungs through a partially + closed glottis, preceded by inhalation. + meaning: HP:0012735 + Nonproductive cough (dry cough) [HP:0031246]: + text: Nonproductive cough (dry cough) [HP:0031246] + meaning: HP:0031246 + is_a: Cough [HP:0012735] + Productive cough (wet cough) [HP:0031245]: + text: Productive cough (wet cough) [HP:0031245] + meaning: HP:0031245 + is_a: Cough [HP:0012735] + Diarrhea [DOID:13250]: + text: Diarrhea [DOID:13250] + meaning: DOID:13250 + Dyspnea (breathing difficulty) [HP:0002094]: + text: Dyspnea (breathing difficulty) [HP:0002094] + meaning: HP:0002094 + Fatigue (tiredness) [HP:0012378]: + text: Fatigue (tiredness) [HP:0012378] + description: A subjective feeling of tiredness characterized by a lack of + energy and motivation. + meaning: HP:0012378 + Fever [HP:0001945]: + text: Fever [HP:0001945] + description: Body temperature elevated above the normal range. + meaning: HP:0001945 + "Fever (>=38\xB0C) [GENEPIO:0100066]": + text: "Fever (>=38\xB0C) [GENEPIO:0100066]" + meaning: GENEPIO:0100066 + is_a: Fever [HP:0001945] + Headache [HP:0002315]: + text: Headache [HP:0002315] + description: Cephalgia, or pain sensed in various parts of the head, not confined + to the area of distribution of any nerve. + meaning: HP:0002315 + Hypoxemia (low blood oxygen) [HP:0012418]: + text: Hypoxemia (low blood oxygen) [HP:0012418] + meaning: HP:0012418 + Silent hypoxemia [GENEPIO:0100068]: + text: Silent hypoxemia [GENEPIO:0100068] + meaning: GENEPIO:0100068 + is_a: Hypoxemia (low blood oxygen) [HP:0012418] + Malaise (general discomfort/unease) [HP:0033834]: + text: Malaise (general discomfort/unease) [HP:0033834] + meaning: HP:0033834 + Muscle weakness [HP:0001324]: + text: Muscle weakness [HP:0001324] + meaning: HP:0001324 + Nasal obstruction (stuffy nose) [HP:0001742]: + text: Nasal obstruction (stuffy nose) [HP:0001742] + meaning: HP:0001742 + Nausea [HP:0002018]: + text: Nausea [HP:0002018] + description: A sensation of unease in the stomach together with an urge to + vomit. + meaning: HP:0002018 + Pain [HP:0012531]: + text: Pain [HP:0012531] + meaning: HP:0012531 + Arthralgia (painful joints) [HP:0002829]: + text: Arthralgia (painful joints) [HP:0002829] + meaning: HP:0002829 + is_a: Pain [HP:0012531] + Myalgia (muscle pain) [HP:0003326]: + text: Myalgia (muscle pain) [HP:0003326] + description: Pain in muscle. + meaning: HP:0003326 + is_a: Pain [HP:0012531] + Pharyngitis (sore throat) [HP:0025439]: + text: Pharyngitis (sore throat) [HP:0025439] + meaning: HP:0025439 + Rhinorrhea (runny nose) [HP:0031417]: + text: Rhinorrhea (runny nose) [HP:0031417] + meaning: HP:0031417 + Shivering (involuntary muscle twitching) [HP:0025144]: + text: Shivering (involuntary muscle twitching) [HP:0025144] + meaning: HP:0025144 + Sneezing [HP:0025095]: + text: Sneezing [HP:0025095] + meaning: HP:0025095 + Sputum Production [HP:0033709]: + text: Sputum Production [HP:0033709] + meaning: HP:0033709 + Swollen Lymph Nodes [HP:0002716]: + text: Swollen Lymph Nodes [HP:0002716] + description: Enlargment (swelling) of a lymph node. + meaning: HP:0002716 + Tachypnea (accelerated respiratory rate) [HP:0002789]: + text: Tachypnea (accelerated respiratory rate) [HP:0002789] + meaning: HP:0002789 + Vomiting (throwing up) [HP:0002013]: + text: Vomiting (throwing up) [HP:0002013] + description: Forceful ejection of the contents of the stomach through the + mouth by means of a series of involuntary spasmic contractions. + meaning: HP:0002013 + PreExistingConditionsAndRiskFactorsMenu: + name: PreExistingConditionsAndRiskFactorsMenu + title: pre-existing_conditions_and_risk_factors menu + permissible_values: + Age 60+ [VO:0004925]: + text: Age 60+ [VO:0004925] + meaning: VO:0004925 + Anemia [DOID:2355]: + text: Anemia [DOID:2355] + meaning: DOID:2355 + Hemoglobinopathy [DOID:2860]: + text: Hemoglobinopathy [DOID:2860] + meaning: DOID:2860 + is_a: Anemia [DOID:2355] + Anorexia [HP:0002039]: + text: Anorexia [HP:0002039] + meaning: HP:0002039 + Birthing labor [NCIT:C92743]: + text: Birthing labor [NCIT:C92743] + meaning: NCIT:C92743 + Bone marrow failure [NCIT:C80693]: + text: Bone marrow failure [NCIT:C80693] + meaning: NCIT:C80693 + Cancer [MONDO:0004992]: + text: Cancer [MONDO:0004992] + description: A tumor composed of atypical neoplastic, often pleomorphic cells + that invade other tissues. Malignant neoplasms often metastasize to distant + anatomic sites and may recur after excision. The most common malignant neoplasms + are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and + non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas. + meaning: MONDO:0004992 + Breast cancer [MONDO:0007254]: + text: Breast cancer [MONDO:0007254] + meaning: MONDO:0007254 + is_a: Cancer [MONDO:0004992] + Colorectal cancer [MONDO:0005575]: + text: Colorectal cancer [MONDO:0005575] + meaning: MONDO:0005575 + is_a: Cancer [MONDO:0004992] + Hematologic malignancy (cancer of the blood) [DOID:2531]: + text: Hematologic malignancy (cancer of the blood) [DOID:2531] + meaning: DOID:2531 + is_a: Cancer [MONDO:0004992] + Lung cancer [MONDO:0008903]: + text: Lung cancer [MONDO:0008903] + meaning: MONDO:0008903 + is_a: Cancer [MONDO:0004992] + Metastatic disease [MONDO:0024880]: + text: Metastatic disease [MONDO:0024880] + meaning: MONDO:0024880 + is_a: Cancer [MONDO:0004992] + Cancer treatment [NCIT:C16212]: + text: Cancer treatment [NCIT:C16212] + description: Any intervention for management of a malignant neoplasm. + meaning: NCIT:C16212 + Cancer surgery [NCIT:C157740]: + text: Cancer surgery [NCIT:C157740] + meaning: NCIT:C157740 + is_a: Cancer treatment [NCIT:C16212] + Chemotherapy [NCIT:C15632]: + text: Chemotherapy [NCIT:C15632] + description: The use of synthetic or naturally-occurring chemicals for the + treatment of diseases. + meaning: NCIT:C15632 + is_a: Cancer treatment [NCIT:C16212] + Adjuvant chemotherapy [NCIT:C15360]: + text: Adjuvant chemotherapy [NCIT:C15360] + meaning: NCIT:C15360 + is_a: Chemotherapy [NCIT:C15632] + Cardiac disorder [NCIT:C3079]: + text: Cardiac disorder [NCIT:C3079] + meaning: NCIT:C3079 + Arrhythmia [HP:0011675]: + text: Arrhythmia [HP:0011675] + meaning: HP:0011675 + is_a: Cardiac disorder [NCIT:C3079] + Cardiac disease [MONDO:0005267]: + text: Cardiac disease [MONDO:0005267] + meaning: MONDO:0005267 + is_a: Cardiac disorder [NCIT:C3079] + Cardiomyopathy [HP:0001638]: + text: Cardiomyopathy [HP:0001638] + meaning: HP:0001638 + is_a: Cardiac disorder [NCIT:C3079] + Cardiac injury [GENEPIO:0100074]: + text: Cardiac injury [GENEPIO:0100074] + meaning: GENEPIO:0100074 + is_a: Cardiac disorder [NCIT:C3079] + Hypertension (high blood pressure) [HP:0000822]: + text: Hypertension (high blood pressure) [HP:0000822] + meaning: HP:0000822 + is_a: Cardiac disorder [NCIT:C3079] + Hypotension (low blood pressure) [HP:0002615]: + text: Hypotension (low blood pressure) [HP:0002615] + meaning: HP:0002615 + is_a: Cardiac disorder [NCIT:C3079] + Cesarean section [HP:0011410]: + text: Cesarean section [HP:0011410] + meaning: HP:0011410 + Chronic cough [GENEPIO:0100075]: + text: Chronic cough [GENEPIO:0100075] + meaning: GENEPIO:0100075 + Chronic gastrointestinal disease [GENEPIO:0100076]: + text: Chronic gastrointestinal disease [GENEPIO:0100076] + meaning: GENEPIO:0100076 + Corticosteroids [NCIT:C211]: + text: Corticosteroids [NCIT:C211] + meaning: NCIT:C211 + Diabetes mellitus (diabetes) [HP:0000819]: + text: Diabetes mellitus (diabetes) [HP:0000819] + description: A group of abnormalities characterized by hyperglycemia and glucose + intolerance. + meaning: HP:0000819 + Type I diabetes mellitus (T1D) [HP:0100651]: + text: Type I diabetes mellitus (T1D) [HP:0100651] + description: A chronic condition in which the pancreas produces little or + no insulin. Type I diabetes mellitus is manifested by the sudden onset of + severe hyperglycemia with rapid progression to diabetic ketoacidosis unless + treated with insulin. + meaning: HP:0100651 + is_a: Diabetes mellitus (diabetes) [HP:0000819] + Type II diabetes mellitus (T2D) [HP:0005978]: + text: Type II diabetes mellitus (T2D) [HP:0005978] + description: A type of diabetes mellitus initially characterized by insulin + resistance and hyperinsulinemia and subsequently by glucose interolerance + and hyperglycemia. + meaning: HP:0005978 + is_a: Diabetes mellitus (diabetes) [HP:0000819] + Eczema [HP:0000964]: + text: Eczema [HP:0000964] + meaning: HP:0000964 + Electrolyte disturbance [HP:0003111]: + text: Electrolyte disturbance [HP:0003111] + meaning: HP:0003111 + Hypocalcemia [HP:0002901]: + text: Hypocalcemia [HP:0002901] + meaning: HP:0002901 + is_a: Electrolyte disturbance [HP:0003111] + Hypokalemia [HP:0002900]: + text: Hypokalemia [HP:0002900] + meaning: HP:0002900 + is_a: Electrolyte disturbance [HP:0003111] + Hypomagnesemia [HP:0002917]: + text: Hypomagnesemia [HP:0002917] + meaning: HP:0002917 + is_a: Electrolyte disturbance [HP:0003111] + Encephalitis (brain inflammation) [HP:0002383]: + text: Encephalitis (brain inflammation) [HP:0002383] + meaning: HP:0002383 + Epilepsy [MONDO:0005027]: + text: Epilepsy [MONDO:0005027] + meaning: MONDO:0005027 + Hemodialysis [NCIT:C15248]: + text: Hemodialysis [NCIT:C15248] + meaning: NCIT:C15248 + Hemoglobinopathy [MONDO:0044348]: + text: Hemoglobinopathy [MONDO:0044348] + meaning: MONDO:0044348 + Human immunodeficiency virus (HIV) [MONDO:0005109]: + text: Human immunodeficiency virus (HIV) [MONDO:0005109] + description: An infection caused by the human immunodeficiency virus. + meaning: MONDO:0005109 + Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]: + text: Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268] + description: A syndrome resulting from the acquired deficiency of cellular + immunity caused by the human immunodeficiency virus (HIV). It is characterized + by the reduction of the Helper T-lymphocytes in the peripheral blood and + the lymph nodes. + meaning: MONDO:0012268 + is_a: Human immunodeficiency virus (HIV) [MONDO:0005109] + HIV and antiretroviral therapy (ART) [NCIT:C16118]: + text: HIV and antiretroviral therapy (ART) [NCIT:C16118] + description: Treatment of human immunodeficiency virus (HIV) infections with + medications that target the virus directly, limiting the ability of infected + cells to produce new HIV particles. + meaning: NCIT:C16118 + is_a: Human immunodeficiency virus (HIV) [MONDO:0005109] + Immunocompromised [NCIT:C14139]: + text: Immunocompromised [NCIT:C14139] + description: A loss of any arm of immune functions, resulting in potential + or actual increase in infections. This state may be reached secondary to + specific genetic lesions, syndromes with unidentified or polygenic causes, + acquired deficits from other disease states, or as result of therapy for + other diseases or conditions. + meaning: NCIT:C14139 + Lupus [MONDO:0004670]: + text: Lupus [MONDO:0004670] + description: An autoimmune, connective tissue chronic inflammatory disorder + affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood + cells. It is more commonly seen in women than men. Variants include discoid + and systemic lupus erythematosus. + meaning: MONDO:0004670 + is_a: Immunocompromised [NCIT:C14139] + Inflammatory bowel disease (IBD) [MONDO:0005265]: + text: Inflammatory bowel disease (IBD) [MONDO:0005265] + meaning: MONDO:0005265 + Colitis [HP:0002583]: + text: Colitis [HP:0002583] + meaning: HP:0002583 + is_a: Inflammatory bowel disease (IBD) [MONDO:0005265] + Ulcerative colitis [HP:0100279]: + text: Ulcerative colitis [HP:0100279] + meaning: HP:0100279 + is_a: Colitis [HP:0002583] + Crohn's disease [HP:0100280]: + text: Crohn's disease [HP:0100280] + meaning: HP:0100280 + is_a: Inflammatory bowel disease (IBD) [MONDO:0005265] + Renal disorder [NCIT:C3149]: + text: Renal disorder [NCIT:C3149] + meaning: NCIT:C3149 + Renal disease [MONDO:0005240]: + text: Renal disease [MONDO:0005240] + meaning: MONDO:0005240 + is_a: Renal disorder [NCIT:C3149] + Chronic renal disease [HP:0012622]: + text: Chronic renal disease [HP:0012622] + meaning: HP:0012622 + is_a: Renal disease [MONDO:0005240] + Renal failure [HP:0000083]: + text: Renal failure [HP:0000083] + meaning: HP:0000083 + is_a: Renal disorder [NCIT:C3149] + Liver disease [MONDO:0005154]: + text: Liver disease [MONDO:0005154] + meaning: MONDO:0005154 + Chronic liver disease [NCIT:C113609]: + text: Chronic liver disease [NCIT:C113609] + meaning: NCIT:C113609 + is_a: Liver disease [MONDO:0005154] + Fatty liver disease (FLD) [HP:0001397]: + text: Fatty liver disease (FLD) [HP:0001397] + meaning: HP:0001397 + is_a: Chronic liver disease [NCIT:C113609] + Myalgia (muscle pain) [HP:0003326]: + text: Myalgia (muscle pain) [HP:0003326] + description: Pain in muscle. + meaning: HP:0003326 + Myalgic encephalomyelitis (ME) [MONDO:0005404]: + text: Myalgic encephalomyelitis (ME) [MONDO:0005404] + meaning: MONDO:0005404 + Neurological disorder [MONDO:0005071]: + text: Neurological disorder [MONDO:0005071] + meaning: MONDO:0005071 + Neuromuscular disorder [MONDO:0019056]: + text: Neuromuscular disorder [MONDO:0019056] + meaning: MONDO:0019056 + is_a: Neurological disorder [MONDO:0005071] + Obesity [HP:0001513]: + text: Obesity [HP:0001513] + meaning: HP:0001513 + Severe obesity [MONDO:0005139]: + text: Severe obesity [MONDO:0005139] + meaning: MONDO:0005139 + is_a: Obesity [HP:0001513] + Respiratory disorder [MONDO:0005087]: + text: Respiratory disorder [MONDO:0005087] + meaning: MONDO:0005087 + Asthma [HP:0002099]: + text: Asthma [HP:0002099] + meaning: HP:0002099 + is_a: Respiratory disorder [MONDO:0005087] + Chronic bronchitis [HP:0004469]: + text: Chronic bronchitis [HP:0004469] + meaning: HP:0004469 + is_a: Respiratory disorder [MONDO:0005087] + Chronic obstructive pulmonary disease [HP:0006510]: + text: Chronic obstructive pulmonary disease [HP:0006510] + meaning: HP:0006510 + is_a: Respiratory disorder [MONDO:0005087] + Emphysema [HP:0002097]: + text: Emphysema [HP:0002097] + meaning: HP:0002097 + is_a: Respiratory disorder [MONDO:0005087] + Lung disease [MONDO:0005275]: + text: Lung disease [MONDO:0005275] + meaning: MONDO:0005275 + is_a: Respiratory disorder [MONDO:0005087] + Chronic lung disease [HP:0006528]: + text: Chronic lung disease [HP:0006528] + meaning: HP:0006528 + is_a: Lung disease [MONDO:0005275] + Pulmonary fibrosis [HP:0002206]: + text: Pulmonary fibrosis [HP:0002206] + meaning: HP:0002206 + is_a: Lung disease [MONDO:0005275] + Pneumonia [HP:0002090]: + text: Pneumonia [HP:0002090] + meaning: HP:0002090 + is_a: Respiratory disorder [MONDO:0005087] + Respiratory failure [HP:0002878]: + text: Respiratory failure [HP:0002878] + meaning: HP:0002878 + is_a: Respiratory disorder [MONDO:0005087] + Adult respiratory distress syndrome [HP:0033677]: + text: Adult respiratory distress syndrome [HP:0033677] + meaning: HP:0033677 + is_a: Respiratory failure [HP:0002878] + Newborn respiratory distress syndrome [MONDO:0009971]: + text: Newborn respiratory distress syndrome [MONDO:0009971] + meaning: MONDO:0009971 + is_a: Respiratory failure [HP:0002878] + Tuberculosis [MONDO:0018076]: + text: Tuberculosis [MONDO:0018076] + meaning: MONDO:0018076 + is_a: Respiratory disorder [MONDO:0005087] + "Postpartum (\u22646 weeks) [GENEPIO:0100077]": + text: "Postpartum (\u22646 weeks) [GENEPIO:0100077]" + meaning: GENEPIO:0100077 + Pregnancy [NCIT:C25742]: + text: Pregnancy [NCIT:C25742] + description: The state or condition of having a developing embryo or fetus + in the body (uterus), after union of an ovum and spermatozoon, during the + period from conception to birth. + meaning: NCIT:C25742 + Reye syndrome [DOID:14525]: + text: Reye syndrome [DOID:14525] + meaning: DOID:14525 + Rheumatic disease [MONDO:0005554]: + text: Rheumatic disease [MONDO:0005554] + meaning: MONDO:0005554 + Sickle cell disease [MONDO:0011382]: + text: Sickle cell disease [MONDO:0011382] + meaning: MONDO:0011382 + Substance use [NBO:0001845]: + text: Substance use [NBO:0001845] + meaning: NBO:0001845 + Alcohol abuse [MONDO:0002046]: + text: Alcohol abuse [MONDO:0002046] + meaning: MONDO:0002046 + is_a: Substance use [NBO:0001845] + Drug abuse [GENEPIO:0100078]: + text: Drug abuse [GENEPIO:0100078] + meaning: GENEPIO:0100078 + is_a: Substance use [NBO:0001845] + Injection drug abuse [GENEPIO:0100079]: + text: Injection drug abuse [GENEPIO:0100079] + meaning: GENEPIO:0100079 + is_a: Drug abuse [GENEPIO:0100078] + Smoking [NBO:0015005]: + text: Smoking [NBO:0015005] + meaning: NBO:0015005 + is_a: Substance use [NBO:0001845] + Vaping [NCIT:C173621]: + text: Vaping [NCIT:C173621] + meaning: NCIT:C173621 + is_a: Substance use [NBO:0001845] + Tachypnea (accelerated respiratory rate) [HP:0002789]: + text: Tachypnea (accelerated respiratory rate) [HP:0002789] + meaning: HP:0002789 + Transplant [NCIT:C159659]: + text: Transplant [NCIT:C159659] + meaning: CIT:C159659 + Cardiac transplant [NCIT:C131759]: + text: Cardiac transplant [NCIT:C131759] + meaning: NCIT:C131759 + is_a: Transplant [NCIT:C159659] + Hematopoietic stem cell transplant (bone marrow transplant) [GENEPIO:0100080]: + text: Hematopoietic stem cell transplant (bone marrow transplant) [GENEPIO:0100080] + meaning: GENEPIO:0100080 + is_a: Transplant [NCIT:C159659] + Kidney transplant [NCIT:C157332]: + text: Kidney transplant [NCIT:C157332] + meaning: NCIT:C157332 + is_a: Transplant [NCIT:C159659] + Liver transplant [GENEPIO:0100081]: + text: Liver transplant [GENEPIO:0100081] + meaning: GENEPIO:0100081 + is_a: Transplant [NCIT:C159659] + ComplicationsMenu: + name: ComplicationsMenu + title: complications menu + permissible_values: + Abnormal blood oxygen level [HP:0500165]: + text: Abnormal blood oxygen level [HP:0500165] + meaning: HP:0500165 + Acute lung injury [MONDO:0015796]: + text: Acute lung injury [MONDO:0015796] + meaning: MONDO:0015796 + Ventilation induced lung injury (VILI) [GENEPIO:0100092]: + text: Ventilation induced lung injury (VILI) [GENEPIO:0100092] + meaning: GENEPIO:0100092 + is_a: Acute lung injury [MONDO:0015796] + Acute respiratory failure [MONDO:0001208]: + text: Acute respiratory failure [MONDO:0001208] + meaning: MONDO:0001208 + Arrhythmia (complication) [HP:0011675]: + text: Arrhythmia (complication) [HP:0011675] + meaning: HP:0011675 + Tachycardia [HP:0001649]: + text: Tachycardia [HP:0001649] + meaning: HP:0001649 + is_a: Arrhythmia (complication) [HP:0011675] + Cardiac injury [GENEPIO:0100074]: + text: Cardiac injury [GENEPIO:0100074] + meaning: GENEPIO:0100074 + Cardiac arrest [HP:0001695]: + text: Cardiac arrest [HP:0001695] + meaning: HP:0001695 + Blood clot [HP:0001977]: + text: Blood clot [HP:0001977] + meaning: HP:0001977 + Arterial clot [HP:0004420]: + text: Arterial clot [HP:0004420] + meaning: HP:0004420 + is_a: Blood clot [HP:0001977] + Deep vein thrombosis (DVT) [HP:0002625]: + text: Deep vein thrombosis (DVT) [HP:0002625] + meaning: HP:0002625 + is_a: Blood clot [HP:0001977] + Pulmonary embolism (PE) [HP:0002204]: + text: Pulmonary embolism (PE) [HP:0002204] + meaning: HP:0002204 + is_a: Blood clot [HP:0001977] + Cardiomyopathy [HP:0001638]: + text: Cardiomyopathy [HP:0001638] + meaning: HP:0001638 + Central nervous system invasion [MONDO:0024619]: + text: Central nervous system invasion [MONDO:0024619] + meaning: MONDO:0024619 + Stroke (complication) [HP:0001297]: + text: Stroke (complication) [HP:0001297] + meaning: HP:0001297 + Central Nervous System Vasculitis [MONDO:0003346]: + text: Central Nervous System Vasculitis [MONDO:0003346] + meaning: MONDO:0003346 + is_a: Stroke (complication) [HP:0001297] + Acute ischemic stroke [HP:0002140]: + text: Acute ischemic stroke [HP:0002140] + meaning: HP:0002140 + is_a: Stroke (complication) [HP:0001297] + Coma [HP:0001259]: + text: Coma [HP:0001259] + meaning: HP:0001259 + Convulsions [HP:0011097]: + text: Convulsions [HP:0011097] + meaning: HP:0011097 + Cystic fibrosis [MONDO:0009061]: + text: Cystic fibrosis [MONDO:0009061] + meaning: MONDO:0009061 + Cytokine release syndrome [MONDO:0600008]: + text: Cytokine release syndrome [MONDO:0600008] + meaning: MONDO:0600008 + Disseminated intravascular coagulation (DIC) [MPATH:108]: + text: Disseminated intravascular coagulation (DIC) [MPATH:108] + meaning: MPATH:108 + Encephalopathy [HP:0001298]: + text: Encephalopathy [HP:0001298] + meaning: HP:0001298 + Fulminant myocarditis [GENEPIO:0100088]: + text: Fulminant myocarditis [GENEPIO:0100088] + meaning: GENEPIO:0100088 + "Guillain-Barr\xE9 syndrome [MONDO:0016218]": + text: "Guillain-Barr\xE9 syndrome [MONDO:0016218]" + meaning: MONDO:0016218 + Internal hemorrhage (complication; internal bleeding) [HP:0011029]: + text: Internal hemorrhage (complication; internal bleeding) [HP:0011029] + meaning: HP:0011029 + Intracerebral haemorrhage [MONDO:0013792]: + text: Intracerebral haemorrhage [MONDO:0013792] + meaning: MONDO:0013792 + is_a: Internal hemorrhage (complication; internal bleeding) [HP:0011029] + Kawasaki disease [MONDO:0012727]: + text: Kawasaki disease [MONDO:0012727] + meaning: MONDO:0012727 + Complete Kawasaki disease [GENEPIO:0100089]: + text: Complete Kawasaki disease [GENEPIO:0100089] + meaning: GENEPIO:0100089 + is_a: Kawasaki disease [MONDO:0012727] + Incomplete Kawasaki disease [GENEPIO:0100090]: + text: Incomplete Kawasaki disease [GENEPIO:0100090] + meaning: GENEPIO:0100090 + is_a: Kawasaki disease [MONDO:0012727] + Liver dysfunction [HP:0001410]: + text: Liver dysfunction [HP:0001410] + meaning: HP:0001410 + Acute liver injury [GENEPIO:0100091]: + text: Acute liver injury [GENEPIO:0100091] + meaning: GENEPIO:0100091 + is_a: Liver dysfunction [HP:0001410] + Long COVID-19 [MONDO:0100233]: + text: Long COVID-19 [MONDO:0100233] + meaning: MONDO:0100233 + Meningitis [HP:0001287]: + text: Meningitis [HP:0001287] + meaning: HP:0001287 + Migraine [HP:0002076]: + text: Migraine [HP:0002076] + meaning: HP:0002076 + Miscarriage [HP:0005268]: + text: Miscarriage [HP:0005268] + meaning: HP:0005268 + Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163]: + text: Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163] + meaning: MONDO:0100163 + Multisystem inflammatory syndrome in adults (MIS-A) [MONDO:0100319]: + text: Multisystem inflammatory syndrome in adults (MIS-A) [MONDO:0100319] + meaning: MONDO:0100319 + Muscle injury [GENEPIO:0100093]: + text: Muscle injury [GENEPIO:0100093] + meaning: GENEPIO:0100093 + Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404]: + text: Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404] + meaning: MONDO:0005404 + Myocardial infarction (heart attack) [MONDO:0005068]: + text: Myocardial infarction (heart attack) [MONDO:0005068] + meaning: MONDO:0005068 + Myocardial injury [HP:0001700]: + text: Myocardial injury [HP:0001700] + meaning: HP:0001700 + Neonatal complications [NCIT:C168498]: + text: Neonatal complications [NCIT:C168498] + meaning: CIT:C168498 + Noncardiogenic pulmonary edema [GENEPIO:0100085]: + text: Noncardiogenic pulmonary edema [GENEPIO:0100085] + meaning: GENEPIO:0100085 + Acute respiratory distress syndrome (ARDS) [HP:0033677]: + text: Acute respiratory distress syndrome (ARDS) [HP:0033677] + meaning: HP:0033677 + is_a: Noncardiogenic pulmonary edema [GENEPIO:0100085] + Organ failure [GENEPIO:0100094]: + text: Organ failure [GENEPIO:0100094] + meaning: GENEPIO:0100094 + Paralysis [HP:0003470]: + text: Paralysis [HP:0003470] + meaning: HP:0003470 + Pneumothorax (collapsed lung) [HP:0002107]: + text: Pneumothorax (collapsed lung) [HP:0002107] + meaning: HP:0002107 + Pneumonia (complication) [HP:0002090]: + text: Pneumonia (complication) [HP:0002090] + meaning: HP:0002090 + Pregancy complications [HP:0001197]: + text: Pregancy complications [HP:0001197] + meaning: HP:0001197 + Rhabdomyolysis [HP:0003201]: + text: Rhabdomyolysis [HP:0003201] + meaning: HP:0003201 + Secondary infection [IDO:0000567]: + text: Secondary infection [IDO:0000567] + description: An infection bearing the secondary infection role. + meaning: IDO:0000567 + Seizure (complication) [HP:0001250]: + text: Seizure (complication) [HP:0001250] + meaning: HP:0001250 + Sepsis/Septicemia [HP:0100806]: + text: Sepsis/Septicemia [HP:0100806] + description: Systemic inflammatory response to infection. + meaning: HP:0100806 + Sepsis (systemic inflammatory response to infection) [IDO:0000636]: + text: Sepsis (systemic inflammatory response to infection) [IDO:0000636] + meaning: IDO:0000636 + is_a: Sepsis/Septicemia [HP:0100806] + Septicemia (bloodstream infection) [NCIT:C3364]: + text: Septicemia (bloodstream infection) [NCIT:C3364] + meaning: NCIT:C3364 + is_a: Sepsis/Septicemia [HP:0100806] + Shock [HP:0031273]: + text: Shock [HP:0031273] + meaning: HP:0031273 + Hyperinflammatory shock [GENEPIO:0100097]: + text: Hyperinflammatory shock [GENEPIO:0100097] + meaning: GENEPIO:0100097 + is_a: Shock [HP:0031273] + Septic shock [NCIT:C35018]: + text: Septic shock [NCIT:C35018] + meaning: NCIT:C35018 + is_a: Shock [HP:0031273] + Vasculitis [HP:0002633]: + text: Vasculitis [HP:0002633] + meaning: HP:0002633 + ExposureEventMenu: + name: ExposureEventMenu + title: exposure_event menu + permissible_values: + Mass Gathering [GENEPIO:0100237]: + text: Mass Gathering [GENEPIO:0100237] + description: A gathering or event attended by a sufficient number of people + to strain the planning and response resources of the host community, state/province, + nation, or region where it is being held. + meaning: GENEPIO:0100237 + Convention [GENEPIO:0100238]: + text: Convention [GENEPIO:0100238] + description: A gathering of individuals who meet at an arranged place and + time in order to discuss or engage in some common interest. The most common + conventions are based upon industry, profession, and fandom. + meaning: GENEPIO:0100238 + is_a: Mass Gathering [GENEPIO:0100237] + Convocation [GENEPIO:0100239]: + text: Convocation [GENEPIO:0100239] + meaning: GENEPIO:0100239 + is_a: Mass Gathering [GENEPIO:0100237] + Agricultural Event [GENEPIO:0100240]: + text: Agricultural Event [GENEPIO:0100240] + description: A gathering exhibiting the equipment, animals, sports and recreation + associated with agriculture and animal husbandry. + meaning: GENEPIO:0100240 + is_a: Mass Gathering [GENEPIO:0100237] + Religious Gathering [GENEPIO:0100241]: + text: Religious Gathering [GENEPIO:0100241] + meaning: GENEPIO:0100241 + Mass [GENEPIO:0100242]: + text: Mass [GENEPIO:0100242] + meaning: GENEPIO:0100242 + is_a: Religious Gathering [GENEPIO:0100241] + Social Gathering [PCO:0000033]: + text: Social Gathering [PCO:0000033] + description: A type of social behavior in which a collection of humans intentionally + gathers together on a temporary basis to engage socially. + meaning: PCO:0000033 + Baby Shower [PCO:0000039]: + text: Baby Shower [PCO:0000039] + meaning: PCO:0000039 + is_a: Social Gathering [PCO:0000033] + Community Event [PCO:0000034]: + text: Community Event [PCO:0000034] + meaning: PCO:0000034 + is_a: Social Gathering [PCO:0000033] + Family Gathering [GENEPIO:0100243]: + text: Family Gathering [GENEPIO:0100243] + meaning: GENEPIO:0100243 + is_a: Social Gathering [PCO:0000033] + Family Reunion [GENEPIO:0100244]: + text: Family Reunion [GENEPIO:0100244] + meaning: GENEPIO:0100244 + is_a: Family Gathering [GENEPIO:0100243] + Funeral [GENEPIO:0100245]: + text: Funeral [GENEPIO:0100245] + meaning: GENEPIO:0100245 + is_a: Social Gathering [PCO:0000033] + Party [PCO:0000035]: + text: Party [PCO:0000035] + meaning: PCO:0000035 + is_a: Social Gathering [PCO:0000033] + Potluck [PCO:0000037]: + text: Potluck [PCO:0000037] + meaning: PCO:0000037 + is_a: Social Gathering [PCO:0000033] + Wedding [PCO:0000038]: + text: Wedding [PCO:0000038] + meaning: PCO:0000038 + is_a: Social Gathering [PCO:0000033] + Animal contact event [GENEPIO:0101183]: + text: Animal contact event [GENEPIO:0101183] + meaning: GENEPIO:0101183 + Trip to a live animal market [GENEPIO:0101185]: + text: Trip to a live animal market [GENEPIO:0101185] + meaning: GENEPIO:0101185 + is_a: Animal contact event [GENEPIO:0101183] + Trip to a farm [GENEPIO:0101186]: + text: Trip to a farm [GENEPIO:0101186] + meaning: GENEPIO:0101186 + is_a: Animal contact event [GENEPIO:0101183] + Wildlife encounter [GENEPIO:0101188]: + text: Wildlife encounter [GENEPIO:0101188] + meaning: GENEPIO:0101188 + is_a: Animal contact event [GENEPIO:0101183] + Hunting trip [GENEPIO:0101184]: + text: Hunting trip [GENEPIO:0101184] + meaning: GENEPIO:0101184 + is_a: Wildlife encounter [GENEPIO:0101188] + Animal transportation event [GENEPIO:0101187]: + text: Animal transportation event [GENEPIO:0101187] + meaning: GENEPIO:0101187 + Other exposure event: + text: Other exposure event + ExposureContactLevelMenu: + name: ExposureContactLevelMenu + title: exposure_contact_level menu + permissible_values: + Contact with infected animal [GENEPIO:0101189]: + text: Contact with infected animal [GENEPIO:0101189] + meaning: GENEPIO:0101189 + Direct (host-to-animal contact) [GENEPIO:0101190]: + text: Direct (host-to-animal contact) [GENEPIO:0101190] + meaning: GENEPIO:0101190 + is_a: Contact with infected animal [GENEPIO:0101189] + Indirect contact (host-to-animal) [GENEPIO:0101191]: + text: Indirect contact (host-to-animal) [GENEPIO:0101191] + meaning: GENEPIO:0101191 + is_a: Contact with infected animal [GENEPIO:0101189] + Close animal contact (face-to-face contact) [GENEPIO:0101192]: + text: Close animal contact (face-to-face contact) [GENEPIO:0101192] + meaning: GENEPIO:0101192 + is_a: Indirect contact (host-to-animal) [GENEPIO:0101191] + Casual animal contact [GENEPIO:0101193]: + text: Casual animal contact [GENEPIO:0101193] + meaning: GENEPIO:0101193 + is_a: Indirect contact (host-to-animal) [GENEPIO:0101191] + Contact with infected individual: + text: Contact with infected individual + Direct (human-to-human contact) [TRANS:0000001]: + text: Direct (human-to-human contact) [TRANS:0000001] + description: Direct and essentially immediate transfer of infectious agents + to a receptive portal of entry through which human or animal infection may + take place. This may be by direct contact such as touching, kissing, biting, + or sexual intercourse or by the direct projection (droplet spread) of droplet + spray onto the conjunctiva or the mucous membranes of the eyes, nose, or + mouth. It may also be by direct exposure of susceptible tissue to an agent + in soil, compost, or decaying vegetable matter or by the bite of a rabid + animal. Transplacental transmission is another form of direct transmission. + meaning: TRANS:0000001 + is_a: Contact with infected individual + Indirect contact [GENEPIO:0100246]: + text: Indirect contact [GENEPIO:0100246] + description: A type of contact in which an individual does not come in direct + contact with a source of infection e.g. through airborne transmission, contact + with contaminated surfaces. + meaning: GENEPIO:0100246 + is_a: Contact with infected individual + Close contact (face-to-face contact) [GENEPIO:0100247]: + text: Close contact (face-to-face contact) [GENEPIO:0100247] + description: A type of indirect contact where an individual sustains unprotected + exposure by being within 6 feet of an infected individual over a sustained + period of time. + meaning: GENEPIO:0100247 + is_a: Indirect contact [GENEPIO:0100246] + Casual contact [GENEPIO:0100248]: + text: Casual contact [GENEPIO:0100248] + description: A type of indirect contact where an individual may at the same + location at the same time as a positive case; however, they may have been + there only briefly, or it may have been a location that carries a lower + risk of transmission. + meaning: GENEPIO:0100248 + is_a: Indirect contact [GENEPIO:0100246] + HostRoleMenu: + name: HostRoleMenu + title: host_role menu + permissible_values: + Attendee [GENEPIO:0100249]: + text: Attendee [GENEPIO:0100249] + description: A role inhering in a person that is realized when the bearer + is present on a given occasion or at a given place. + meaning: GENEPIO:0100249 + Student [OMRSE:00000058]: + text: Student [OMRSE:00000058] + description: A human social role that, if realized, is realized by the process + of formal education that the bearer undergoes. + meaning: OMRSE:00000058 + is_a: Attendee [GENEPIO:0100249] + Patient [OMRSE:00000030]: + text: Patient [OMRSE:00000030] + description: A patient role that inheres in a human being. + meaning: OMRSE:00000030 + Inpatient [NCIT:C25182]: + text: Inpatient [NCIT:C25182] + description: A patient who is residing in the hospital where he is being treated. + meaning: NCIT:C25182 + is_a: Patient [OMRSE:00000030] + Outpatient [NCIT:C28293]: + text: Outpatient [NCIT:C28293] + description: A patient who comes to a healthcare facility for diagnosis or + treatment but is not admitted for an overnight stay. + meaning: NCIT:C28293 + is_a: Patient [OMRSE:00000030] + Passenger [GENEPIO:0100250]: + text: Passenger [GENEPIO:0100250] + description: A role inhering in a person that is realized when the bearer + travels in a vehicle but bears little to no responsibility for vehicle operation + nor arrival at its destination. + meaning: GENEPIO:0100250 + Resident [GENEPIO:0100251]: + text: Resident [GENEPIO:0100251] + description: A role inhering in a person that is realized when the bearer + maintains residency in a given place. + meaning: GENEPIO:0100251 + Visitor [GENEPIO:0100252]: + text: Visitor [GENEPIO:0100252] + description: A role inhering in a person that is realized when the bearer + pays a visit to a specific place or event. + meaning: GENEPIO:0100252 + Volunteer [GENEPIO:0100253]: + text: Volunteer [GENEPIO:0100253] + description: A role inhering in a person that is realized when the bearer + enters into any service of their own free will. + meaning: GENEPIO:0100253 + Work [GENEPIO:0100254]: + text: Work [GENEPIO:0100254] + description: A role inhering in a person that is realized when the bearer + performs labor for a living. + meaning: GENEPIO:0100254 + Administrator [GENEPIO:0100255]: + text: Administrator [GENEPIO:0100255] + description: A role inhering in a person that is realized when the bearer + is engaged in administration or administrative work. + meaning: GENEPIO:0100255 + is_a: Work [GENEPIO:0100254] + First Responder [GENEPIO:0100256]: + text: First Responder [GENEPIO:0100256] + description: A role inhering in a person that is realized when the bearer + is among the first to arrive at the scene of an emergency and has specialized + training to provide assistance. + meaning: GENEPIO:0100256 + is_a: Work [GENEPIO:0100254] + Firefighter [GENEPIO:0100257]: + text: Firefighter [GENEPIO:0100257] + meaning: GENEPIO:0100257 + is_a: First Responder [GENEPIO:0100256] + Paramedic [GENEPIO:0100258]: + text: Paramedic [GENEPIO:0100258] + meaning: GENEPIO:0100258 + is_a: First Responder [GENEPIO:0100256] + Police Officer [GENEPIO:0100259]: + text: Police Officer [GENEPIO:0100259] + meaning: GENEPIO:0100259 + is_a: First Responder [GENEPIO:0100256] + Housekeeper [GENEPIO:0100260]: + text: Housekeeper [GENEPIO:0100260] + description: A role inhering in a person that is realized when the bearer + is an individual who performs cleaning duties and/or is responsible for + the supervision of cleaning staff. + meaning: GENEPIO:0100260 + is_a: Work [GENEPIO:0100254] + Kitchen Worker [GENEPIO:0100261]: + text: Kitchen Worker [GENEPIO:0100261] + description: A role inhering in a person that is realized when the bearer + is an employee that performs labor in a kitchen. + meaning: GENEPIO:0100261 + is_a: Work [GENEPIO:0100254] + Healthcare Worker [GENEPIO:0100334]: + text: Healthcare Worker [GENEPIO:0100334] + description: A role inhering in a person that is realized when the bearer + is an employee that performs labor in a healthcare setting. + meaning: GENEPIO:0100334 + is_a: Work [GENEPIO:0100254] + Community Healthcare Worker [GENEPIO:0100420]: + text: Community Healthcare Worker [GENEPIO:0100420] + description: A role inhering in a person that is realized when the bearer + a professional caregiver that provides health care or supportive care in + the individual home where the patient or client is living, as opposed to + care provided in group accommodations like clinics or nursing home. + meaning: GENEPIO:0100420 + is_a: Healthcare Worker [GENEPIO:0100334] + Laboratory Worker [GENEPIO:0100262]: + text: Laboratory Worker [GENEPIO:0100262] + description: A role inhering in a person that is realized when the bearer + is an employee that performs labor in a laboratory. + meaning: GENEPIO:0100262 + is_a: Healthcare Worker [GENEPIO:0100334] + Nurse [OMRSE:00000014]: + text: Nurse [OMRSE:00000014] + description: A health care role borne by a human being and realized by the + care of individuals, families, and communities so they may attain, maintain, + or recover optimal health and quality of life. + meaning: OMRSE:00000014 + is_a: Healthcare Worker [GENEPIO:0100334] + Personal Care Aid [GENEPIO:0100263]: + text: Personal Care Aid [GENEPIO:0100263] + description: A role inhering in a person that is realized when the bearer + works to help another person complete their daily activities. + meaning: GENEPIO:0100263 + is_a: Healthcare Worker [GENEPIO:0100334] + Pharmacist [GENEPIO:0100264]: + text: Pharmacist [GENEPIO:0100264] + description: A role inhering in a person that is realized when the bearer + is a health professional who specializes in dispensing prescription drugs + at a healthcare facility. + meaning: GENEPIO:0100264 + is_a: Healthcare Worker [GENEPIO:0100334] + Physician [OMRSE:00000013]: + text: Physician [OMRSE:00000013] + description: A health care role borne by a human being and realized by promoting, + maintaining or restoring human health through the study, diagnosis, and + treatment of disease, injury and other physical and mental impairments. + meaning: OMRSE:00000013 + is_a: Healthcare Worker [GENEPIO:0100334] + Rotational Worker [GENEPIO:0100354]: + text: Rotational Worker [GENEPIO:0100354] + description: A role inhering in a person that is realized when the bearer + performs labor on a regular schedule, often requiring travel to geographic + locations other than where they live. + meaning: GENEPIO:0100354 + is_a: Work [GENEPIO:0100254] + Seasonal Worker [GENEPIO:0100355]: + text: Seasonal Worker [GENEPIO:0100355] + description: A role inhering in a person that is realized when the bearer + performs labor for a particular period of the year, such as harvest, or + Christmas. + meaning: GENEPIO:0100355 + is_a: Work [GENEPIO:0100254] + Veterinarian [GENEPIO:0100265]: + text: Veterinarian [GENEPIO:0100265] + description: A role inhering in a person that is realized when the bearer + is a professional who practices veterinary medicine. + meaning: GENEPIO:0100265 + is_a: Work [GENEPIO:0100254] + Social role [OMRSE:00000001]: + text: Social role [OMRSE:00000001] + description: A social role inhering in a human being. + meaning: OMRSE:00000001 + Acquaintance of case [GENEPIO:0100266]: + text: Acquaintance of case [GENEPIO:0100266] + description: A role inhering in a person that is realized when the bearer + is in a state of being acquainted with a person. + meaning: GENEPIO:0100266 + is_a: Social role [OMRSE:00000001] + Relative of case [GENEPIO:0100267]: + text: Relative of case [GENEPIO:0100267] + description: A role inhering in a person that is realized when the bearer + is a relative of the case. + meaning: GENEPIO:0100267 + is_a: Social role [OMRSE:00000001] + Child of case [GENEPIO:0100268]: + text: Child of case [GENEPIO:0100268] + description: A role inhering in a person that is realized when the bearer + is a person younger than the age of majority. + meaning: GENEPIO:0100268 + is_a: Relative of case [GENEPIO:0100267] + Parent of case [GENEPIO:0100269]: + text: Parent of case [GENEPIO:0100269] + description: A role inhering in a person that is realized when the bearer + is a caregiver of the offspring of their own species. + meaning: GENEPIO:0100269 + is_a: Relative of case [GENEPIO:0100267] + Father of case [GENEPIO:0100270]: + text: Father of case [GENEPIO:0100270] + description: A role inhering in a person that is realized when the bearer + is the male parent of a child. + meaning: GENEPIO:0100270 + is_a: Parent of case [GENEPIO:0100269] + Mother of case [GENEPIO:0100271]: + text: Mother of case [GENEPIO:0100271] + description: A role inhering in a person that is realized when the bearer + is the female parent of a child. + meaning: GENEPIO:0100271 + is_a: Parent of case [GENEPIO:0100269] + Spouse of case [GENEPIO:0100272]: + text: Spouse of case [GENEPIO:0100272] + description: A role inhering in a person that is realized when the bearer + is a significant other in a marriage, civil union, or common-law marriage. + meaning: GENEPIO:0100272 + is_a: Social role [OMRSE:00000001] + Other Host Role: + text: Other Host Role + ExposureSettingMenu: + name: ExposureSettingMenu + title: exposure_setting menu + permissible_values: + Human Exposure [ECTO:3000005]: + text: Human Exposure [ECTO:3000005] + description: A history of exposure to Homo sapiens. + meaning: ECTO:3000005 + Contact with Patient [GENEPIO:0100185]: + text: Contact with Patient [GENEPIO:0100185] + description: A process occuring within or in the vicinity of a human patient + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100185 + is_a: Human Exposure [ECTO:3000005] + Contact with Person with Acute Respiratory Illness [GENEPIO:0100187]: + text: Contact with Person with Acute Respiratory Illness [GENEPIO:0100187] + meaning: GENEPIO:0100187 + is_a: Human Exposure [ECTO:3000005] + Contact with Person with Fever and/or Cough [GENEPIO:0100188]: + text: Contact with Person with Fever and/or Cough [GENEPIO:0100188] + meaning: GENEPIO:0100188 + is_a: Human Exposure [ECTO:3000005] + Occupational, Residency or Patronage Exposure [GENEPIO:0100190]: + text: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + description: A process occuring within or in the vicinity of a human residential + environment that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100190 + Abbatoir [ECTO:1000033]: + text: Abbatoir [ECTO:1000033] + description: A exposure event involving the interaction of an exposure receptor + to abattoir. + meaning: ECTO:1000033 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Animal Rescue [GENEPIO:0100191]: + text: Animal Rescue [GENEPIO:0100191] + description: A process occuring within or in the vicinity of an animal rescue + facility that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100191 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Childcare [GENEPIO:0100192]: + text: Childcare [GENEPIO:0100192] + description: A process occuring within or in the vicinity of a human childcare + environment that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100192 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Daycare [GENEPIO:0100193]: + text: Daycare [GENEPIO:0100193] + description: A process occuring within or in the vicinity of a human daycare + environment that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100193 + is_a: Childcare [GENEPIO:0100192] + Nursery [GENEPIO:0100194]: + text: Nursery [GENEPIO:0100194] + description: A process occuring within or in the vicinity of a human nursery + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100194 + is_a: Childcare [GENEPIO:0100192] + Community Service Centre [GENEPIO:0100195]: + text: Community Service Centre [GENEPIO:0100195] + description: A process occuring within or in the vicinity of a community service + centre that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100195 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Correctional Facility [GENEPIO:0100196]: + text: Correctional Facility [GENEPIO:0100196] + description: A process occuring within or in the vicinity of a correctional + facility that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100196 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Dormitory [GENEPIO:0100197]: + text: Dormitory [GENEPIO:0100197] + description: A process occuring within or in the vicinity of a dormitory that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100197 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Farm [ECTO:1000034]: + text: Farm [ECTO:1000034] + description: A exposure event involving the interaction of an exposure receptor + to farm + meaning: ECTO:1000034 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + First Nations Reserve [GENEPIO:0100198]: + text: First Nations Reserve [GENEPIO:0100198] + description: A process occuring within or in the vicinity of a first nations + reserve that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100198 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Funeral Home [GENEPIO:0100199]: + text: Funeral Home [GENEPIO:0100199] + description: A process occuring within or in the vicinity of a group home + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100199 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Group Home [GENEPIO:0100200]: + text: Group Home [GENEPIO:0100200] + description: A process occuring within or in the vicinity of a group home + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100200 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Healthcare Setting [GENEPIO:0100201]: + text: Healthcare Setting [GENEPIO:0100201] + description: A process occuring within or in the vicinity of a healthcare + environment that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100201 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Ambulance [GENEPIO:0100202]: + text: Ambulance [GENEPIO:0100202] + description: A process occuring within or in the vicinity of an ambulance + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100202 + is_a: Healthcare Setting [GENEPIO:0100201] + Acute Care Facility [GENEPIO:0100203]: + text: Acute Care Facility [GENEPIO:0100203] + description: A process occuring within or in the vicinity of an acute care + facility that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100203 + is_a: Healthcare Setting [GENEPIO:0100201] + Clinic [GENEPIO:0100204]: + text: Clinic [GENEPIO:0100204] + description: A process occuring within or in the vicinity of a medical clinic + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100204 + is_a: Healthcare Setting [GENEPIO:0100201] + Community Healthcare (At-Home) Setting [GENEPIO:0100415]: + text: Community Healthcare (At-Home) Setting [GENEPIO:0100415] + description: A process occuring within or in the vicinty of a the individual + home where the patient or client is living and health care or supportive + care is being being delivered, as opposed to care provided in group accommodations + like clinics or nursing home. + meaning: GENEPIO:0100415 + is_a: Healthcare Setting [GENEPIO:0100201] + Community Health Centre [GENEPIO:0100205]: + text: Community Health Centre [GENEPIO:0100205] + description: A process occuring within or in the vicinity of a community health + centre that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100205 + is_a: Healthcare Setting [GENEPIO:0100201] + Hospital [ECTO:1000035]: + text: Hospital [ECTO:1000035] + description: A exposure event involving the interaction of an exposure receptor + to hospital. + meaning: ECTO:1000035 + is_a: Healthcare Setting [GENEPIO:0100201] + Emergency Department [GENEPIO:0100206]: + text: Emergency Department [GENEPIO:0100206] + description: A process occuring within or in the vicinity of an emergency + department that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100206 + is_a: Hospital [ECTO:1000035] + ICU [GENEPIO:0100207]: + text: ICU [GENEPIO:0100207] + description: A process occuring within or in the vicinity of an ICU that exposes + the recipient organism to a material entity. + meaning: GENEPIO:0100207 + is_a: Hospital [ECTO:1000035] + Ward [GENEPIO:0100208]: + text: Ward [GENEPIO:0100208] + description: A process occuring within or in the vicinity of a hospital ward + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100208 + is_a: Hospital [ECTO:1000035] + Laboratory [ECTO:1000036]: + text: Laboratory [ECTO:1000036] + description: A exposure event involving the interaction of an exposure receptor + to laboratory facility. + meaning: ECTO:1000036 + is_a: Healthcare Setting [GENEPIO:0100201] + Long-Term Care Facility [GENEPIO:0100209]: + text: Long-Term Care Facility [GENEPIO:0100209] + description: A process occuring within or in the vicinity of a long-term care + facility that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100209 + is_a: Healthcare Setting [GENEPIO:0100201] + Pharmacy [GENEPIO:0100210]: + text: Pharmacy [GENEPIO:0100210] + description: A process occuring within or in the vicinity of a pharmacy that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100210 + is_a: Healthcare Setting [GENEPIO:0100201] + Physician's Office [GENEPIO:0100211]: + text: Physician's Office [GENEPIO:0100211] + description: A process occuring within or in the vicinity of a physician's + office that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100211 + is_a: Healthcare Setting [GENEPIO:0100201] + Household [GENEPIO:0100212]: + text: Household [GENEPIO:0100212] + description: A process occuring within or in the vicinity of a household that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100212 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Insecure Housing (Homeless) [GENEPIO:0100213]: + text: Insecure Housing (Homeless) [GENEPIO:0100213] + description: A process occuring that exposes the recipient organism to a material + entity as a consequence of said organism having insecure housing. + meaning: GENEPIO:0100213 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Occupational Exposure [GENEPIO:0100214]: + text: Occupational Exposure [GENEPIO:0100214] + description: A process occuring within or in the vicinity of a human occupational + environment that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100214 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Worksite [GENEPIO:0100215]: + text: Worksite [GENEPIO:0100215] + description: A process occuring within or in the vicinity of an office that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100215 + is_a: Occupational Exposure [GENEPIO:0100214] + Office [ECTO:1000037]: + text: Office [ECTO:1000037] + description: A exposure event involving the interaction of an exposure receptor + to office. + meaning: ECTO:1000037 + is_a: Worksite [GENEPIO:0100215] + Outdoors [GENEPIO:0100216]: + text: Outdoors [GENEPIO:0100216] + description: A process occuring outdoors that exposes the recipient organism + to a material entity. + meaning: GENEPIO:0100216 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Camp/camping [ECTO:5000009]: + text: Camp/camping [ECTO:5000009] + description: A exposure event involving the interaction of an exposure receptor + to campground. + meaning: ECTO:5000009 + is_a: Outdoors [GENEPIO:0100216] + Hiking Trail [GENEPIO:0100217]: + text: Hiking Trail [GENEPIO:0100217] + description: A process that exposes the recipient organism to a material entity + as a consequence of hiking. + meaning: GENEPIO:0100217 + is_a: Outdoors [GENEPIO:0100216] + Hunting Ground [ECTO:6000030]: + text: Hunting Ground [ECTO:6000030] + description: An exposure event involving hunting behavior + meaning: ECTO:6000030 + is_a: Outdoors [GENEPIO:0100216] + Petting zoo [ECTO:5000008]: + text: Petting zoo [ECTO:5000008] + description: A exposure event involving the interaction of an exposure receptor + to petting zoo. + meaning: ECTO:5000008 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Place of Worship [GENEPIO:0100220]: + text: Place of Worship [GENEPIO:0100220] + description: A process occuring within or in the vicinity of a place of worship + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100220 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Church [GENEPIO:0100221]: + text: Church [GENEPIO:0100221] + description: A process occuring within or in the vicinity of a church that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100221 + is_a: Place of Worship [GENEPIO:0100220] + Mosque [GENEPIO:0100222]: + text: Mosque [GENEPIO:0100222] + description: A process occuring within or in the vicinity of a mosque that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100222 + is_a: Place of Worship [GENEPIO:0100220] + Temple [GENEPIO:0100223]: + text: Temple [GENEPIO:0100223] + description: A process occuring within or in the vicinity of a temple that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100223 + is_a: Place of Worship [GENEPIO:0100220] + Restaurant [ECTO:1000040]: + text: Restaurant [ECTO:1000040] + description: A exposure event involving the interaction of an exposure receptor + to restaurant. + meaning: ECTO:1000040 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Retail Store [ECTO:1000041]: + text: Retail Store [ECTO:1000041] + description: A exposure event involving the interaction of an exposure receptor + to shop. + meaning: ECTO:1000041 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + School [GENEPIO:0100224]: + text: School [GENEPIO:0100224] + description: A process occuring within or in the vicinity of a school that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100224 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Temporary Residence [GENEPIO:0100225]: + text: Temporary Residence [GENEPIO:0100225] + description: A process occuring within or in the vicinity of a temporary residence + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100225 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Homeless Shelter [GENEPIO:0100226]: + text: Homeless Shelter [GENEPIO:0100226] + description: A process occuring within or in the vicinity of a homeless shelter + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100226 + is_a: Temporary Residence [GENEPIO:0100225] + Hotel [GENEPIO:0100227]: + text: Hotel [GENEPIO:0100227] + description: A process occuring within or in the vicinity of a hotel exposure + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100227 + is_a: Temporary Residence [GENEPIO:0100225] + Veterinary Care Clinic [GENEPIO:0100228]: + text: Veterinary Care Clinic [GENEPIO:0100228] + description: A process occuring within or in the vicinity of a veterinary + facility that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100228 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Travel Exposure [GENEPIO:0100229]: + text: Travel Exposure [GENEPIO:0100229] + description: A process occuring as a result of travel that exposes the recipient + organism to a material entity. + meaning: GENEPIO:0100229 + Travelled on a Cruise Ship [GENEPIO:0100230]: + text: Travelled on a Cruise Ship [GENEPIO:0100230] + description: A process occuring within or in the vicinity of a cruise ship + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100230 + is_a: Travel Exposure [GENEPIO:0100229] + Travelled on a Plane [GENEPIO:0100231]: + text: Travelled on a Plane [GENEPIO:0100231] + description: A process occuring within or in the vicinity of an airplane that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100231 + is_a: Travel Exposure [GENEPIO:0100229] + Travelled on Ground Transport [GENEPIO:0100232]: + text: Travelled on Ground Transport [GENEPIO:0100232] + description: A process occuring within or in the vicinity of ground transport + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100232 + is_a: Travel Exposure [GENEPIO:0100229] + Travelled outside Province/Territory [GENEPIO:0001118]: + text: Travelled outside Province/Territory [GENEPIO:0001118] + meaning: GENEPIO:0001118 + is_a: Travel Exposure [GENEPIO:0100229] + Travelled outside Canada [GENEPIO:0001119]: + text: Travelled outside Canada [GENEPIO:0001119] + meaning: GENEPIO:0001119 + is_a: Travel Exposure [GENEPIO:0100229] + Other Exposure Setting [GENEPIO:0100235]: + text: Other Exposure Setting [GENEPIO:0100235] + description: A process occuring that exposes the recipient organism to a material + entity. + meaning: GENEPIO:0100235 + HostVaccinationStatusMenu: + name: HostVaccinationStatusMenu + title: host_vaccination_status menu + permissible_values: + Fully Vaccinated [GENEPIO:0100100]: + text: Fully Vaccinated [GENEPIO:0100100] + description: Completed a full series of an authorized vaccine according to + the regional health institutional guidance. + meaning: GENEPIO:0100100 + Not Vaccinated [GENEPIO:0100102]: + text: Not Vaccinated [GENEPIO:0100102] + description: Have not completed or initiated a vaccine series authorized and + administered according to the regional health institutional guidance. + meaning: GENEPIO:0100102 + InfluenzaAntiviralTreatmentAdministrationMenu: + name: InfluenzaAntiviralTreatmentAdministrationMenu + title: influenza_antiviral_treatment_administration menu + permissible_values: + Influenza antiviral treatment administered [GENEPIO:0101194]: + text: Influenza antiviral treatment administered [GENEPIO:0101194] + meaning: GENEPIO:0101194 + No influenza antiviral treatment administered [GENEPIO:0101195]: + text: No influenza antiviral treatment administered [GENEPIO:0101195] + meaning: GENEPIO:0101195 + WaterCatchmentAreaHumanPopulationRangeMenu: + name: WaterCatchmentAreaHumanPopulationRangeMenu + title: water_catchment_area_human_population_range menu + permissible_values: + <10 people: + text: <10 people + 10 - 100 people: + text: 10 - 100 people + 100 - 1,000 people: + text: 100 - 1,000 people + 1,000 - 10,000 people: + text: 1,000 - 10,000 people + 10,000 - 100,000 people: + text: 10,000 - 100,000 people + 100,000 - 1,000,000 people: + text: 100,000 - 1,000,000 people + 1,000,000+ people: + text: 1,000,000+ people + WaterCatchmentAreaHumanPopulationDensityUnitMenu: + name: WaterCatchmentAreaHumanPopulationDensityUnitMenu + title: water_catchment_area_human_population_density_unit menu + permissible_values: + persons per square mile [GENEPIO:0100989]: + text: persons per square mile [GENEPIO:0100989] + description: A unit of population density that describes the average number + of people in a square mile of a given area. + meaning: GENEPIO:0100989 + persons per square kilometer [GENEPIO:0100990]: + text: persons per square kilometer [GENEPIO:0100990] + description: A unit of population density that describes the average number + of people in a square kilometer of a given area. + meaning: GENEPIO:0100990 + residents per square mile [GENEPIO:0100991]: + text: residents per square mile [GENEPIO:0100991] + description: A unit of population density that describes the average number + of registered residents in a square mile of a given area. + meaning: GENEPIO:0100991 + residents per square kilometer [GENEPIO:0100992]: + text: residents per square kilometer [GENEPIO:0100992] + description: A unit of population density that describes the average number + of registered residents in a square kilometer of a given area. + meaning: GENEPIO:0100992 + PopulatedAreaTypeMenu: + name: PopulatedAreaTypeMenu + title: populated_area_type menu + permissible_values: + Suburban [GSSO:011077]: + text: Suburban [GSSO:011077] + description: A mixed-use or residential area, existing either as part of a + city/urban area, or as a separate residential community within commuting + distance of one. Suburbs might have their own political or legal jurisdiction, + especially in the United States, but this is not always the case, especially + in the United Kingdom where most suburbs are located within the administrative + boundaries of cities. + meaning: GSSO:011077 + Rural [GSSO:011078]: + text: Rural [GSSO:011078] + description: A geographic area that is located outside towns and cities. Rural + areas are primarily used for agriculture or pastoralism and may contain + rural settlements. + meaning: GSSO:011078 + Urban [GSSO:011080]: + text: Urban [GSSO:011080] + description: A human settlement with a high population density and infrastructure + of built environment. Urban areas are created through urbanization and are + categorized by urban morphology as cities, towns, conurbations or suburbs. + In urbanism, the term contrasts to rural areas such as villages and hamlets; + in urban sociology or urban anthropology it contrasts with natural environment. + meaning: GSSO:011080 + SamplingWeatherConditionsMenu: + name: SamplingWeatherConditionsMenu + title: sampling_weather_conditions menu + permissible_values: + Cloudy/Overcast [ENVO:03501418]: + text: Cloudy/Overcast [ENVO:03501418] + description: Atmospheric weather in which the sky is mostly or completely + obscured by clouds. + meaning: ENVO:03501418 + Partially cloudy [ENVO:03501419]: + text: Partially cloudy [ENVO:03501419] + description: Atmospheric weather in which the sky is partially obscured by + clouds. + meaning: ENVO:03501419 + is_a: Cloudy/Overcast [ENVO:03501418] + Drizzle [ENVO:03501420]: + text: Drizzle [ENVO:03501420] + description: An aggregate of water drops smaller than those of rain which + falls on a planetary surface during a precipitation process. + meaning: ENVO:03501420 + Fog [ENVO:01000844]: + text: Fog [ENVO:01000844] + description: A visible mass of cloud water droplets or ice crystals suspended + in the air at or near the surface of an astronomical body. + meaning: ENVO:01000844 + Rain [ENVO:01001564]: + text: Rain [ENVO:01001564] + description: An aggregate of raindrops falling to a planetary surface during + a precipitation process. + meaning: ENVO:01001564 + Snow [ENVO:01000406]: + text: Snow [ENVO:01000406] + description: Snow is an environmental material which is primarily composed + of flakes of crystalline water ice. + meaning: ENVO:01000406 + Storm [ENVO:01000876]: + text: Storm [ENVO:01000876] + description: A storm is an environmental process in which an environmental + system and the processes it participates in are strongly perturbed by external + forcings. These forcings typically increase the rates of processes unfolding + in the system, relative to their normal rates. + meaning: ENVO:01000876 + Sunny/Clear [ENVO:03501421]: + text: Sunny/Clear [ENVO:03501421] + description: Atmospheric weather in which the sun can be seen to shine brightly. + meaning: ENVO:03501421 + PresamplingWeatherConditionsMenu: + name: PresamplingWeatherConditionsMenu + title: presampling_weather_conditions menu + permissible_values: + Cloudy/Overcast [ENVO:03501418]: + text: Cloudy/Overcast [ENVO:03501418] + description: Atmospheric weather in which the sky is mostly or completely + obscured by clouds. + meaning: ENVO:03501418 + Partially cloudy [ENVO:03501419]: + text: Partially cloudy [ENVO:03501419] + description: Atmospheric weather in which the sky is partially obscured by + clouds. + meaning: ENVO:03501419 + is_a: Cloudy/Overcast [ENVO:03501418] + Drizzle [ENVO:03501420]: + text: Drizzle [ENVO:03501420] + description: An aggregate of water drops smaller than those of rain which + falls on a planetary surface during a precipitation process. + meaning: ENVO:03501420 + Fog [ENVO:01000844]: + text: Fog [ENVO:01000844] + description: A visible mass of cloud water droplets or ice crystals suspended + in the air at or near the surface of an astronomical body. + meaning: ENVO:01000844 + Rain [ENVO:01001564]: + text: Rain [ENVO:01001564] + description: An aggregate of raindrops falling to a planetary surface during + a precipitation process. + meaning: ENVO:01001564 + Snow [ENVO:01000406]: + text: Snow [ENVO:01000406] + description: Snow is an environmental material which is primarily composed + of flakes of crystalline water ice. + meaning: ENVO:01000406 + Storm [ENVO:01000876]: + text: Storm [ENVO:01000876] + description: A storm is an environmental process in which an environmental + system and the processes it participates in are strongly perturbed by external + forcings. These forcings typically increase the rates of processes unfolding + in the system, relative to their normal rates. + meaning: ENVO:01000876 + Sunny/Clear [ENVO:03501421]: + text: Sunny/Clear [ENVO:03501421] + description: Atmospheric weather in which the sun can be seen to shine brightly. + meaning: ENVO:03501421 + PrecipitationMeasurementUnitMenu: + name: PrecipitationMeasurementUnitMenu + title: precipitation_measurement_unit menu + permissible_values: + millimeter (mm) [UO:0000016]: + text: millimeter (mm) [UO:0000016] + description: A length unit which is defined as one thousandth of a meter. + meaning: UO:0000016 + centimeter (cm) [UO:0000015]: + text: centimeter (cm) [UO:0000015] + description: A length unit which is equal to one hundredth of a meter or 10^[-2] + m + meaning: UO:0000015 + meter (m) [UO:0000008]: + text: meter (m) [UO:0000008] + description: An SI unit of length defined as the length of the path travelled + by light in a vacuum in 1/299792458th of a second. + meaning: UO:0000008 + inch (in) [UO:0010011]: + text: inch (in) [UO:0010011] + description: A non-SI unit of length defined as one twelfth of a foot. + meaning: UO:0010011 + foot (ft) [UO:0010013]: + text: foot (ft) [UO:0010013] + description: A non-SI unit of length which is approximately 0.3048 meters. + meaning: UO:0010013 + AirPressureMeasurementUnitMenu: + name: AirPressureMeasurementUnitMenu + title: air_pressure_measurement_unit menu + permissible_values: + atmosphere (atm) [EFO:0005212]: + text: atmosphere (atm) [EFO:0005212] + description: A non-SI unit of pressure defined as 101,325 pascals (Pa). + meaning: EFO:0005212 + bar: + text: bar + pascal [UO:0000110]: + text: pascal [UO:0000110] + description: An SI unit of pressure defined as one newton per square meter + (N/m^2). + meaning: UO:0000110 + AmbientTemperatureMeasurementUnitMenu: + name: AmbientTemperatureMeasurementUnitMenu + title: ambient_temperature_measurement_unit menu + permissible_values: + degree Fahrenheit (F) [UO:0000195]: + text: degree Fahrenheit (F) [UO:0000195] + description: A unit of temperature on a scale where water freezes at 32 degrees + and boils at 212 degrees under standard conditions. + meaning: UO:0000195 + degree Celsius (C) [UO:0000027]: + text: degree Celsius (C) [UO:0000027] + description: A unit of temperature on a scale where water freezes at 0 degrees + and boils at 100 degrees under standard conditions. + meaning: UO:0000027 + TotalDailyFlowRateMeasurementUnitMenu: + name: TotalDailyFlowRateMeasurementUnitMenu + title: total_daily_flow_rate_measurement_unit menu + permissible_values: + cubic meter per second (m^3/s): + text: cubic meter per second (m^3/s) + cubic meter per minute (m^3/min): + text: cubic meter per minute (m^3/min) + cubic meter per hour (m^3/h): + text: cubic meter per hour (m^3/h) + liter per second (L/s): + text: liter per second (L/s) + liter per minute (L/min): + text: liter per minute (L/min) + liter per hour (L/h): + text: liter per hour (L/h) + liter per day (L/day): + text: liter per day (L/day) + million gallons per day (MGD): + text: million gallons per day (MGD) + InstantaneousFlowRateMeasurementUnitMenu: + name: InstantaneousFlowRateMeasurementUnitMenu + title: instantaneous_flow_rate_measurement_unit menu + permissible_values: + cubic meter per second (m^3/s): + text: cubic meter per second (m^3/s) + cubic meter per minute (m^3/min): + text: cubic meter per minute (m^3/min) + cubic meter per hour (m^3/h): + text: cubic meter per hour (m^3/h) + liter per second (L/s): + text: liter per second (L/s) + liter per minute (L/min): + text: liter per minute (L/min) + liter per hour (L/h): + text: liter per hour (L/h) + liter per day (L/day): + text: liter per day (L/day) + million gallons per day (MGD): + text: million gallons per day (MGD) + TurbidityMeasurementUnitMenu: + name: TurbidityMeasurementUnitMenu + title: turbidity_measurement_unit menu + permissible_values: + nephelometric turbidity unit (NTU): + text: nephelometric turbidity unit (NTU) + formazin nephelometric unit (FNU) [UO:0000318]: + text: formazin nephelometric unit (FNU) [UO:0000318] + description: A measure of turbidity calculated by comparing how infrared light + is scattered in a water sample against the amount of infrared light scattered + in a reference solution containing formazin. + meaning: UO:0000318 + DissolvedOxygenMeasurementUnitMenu: + name: DissolvedOxygenMeasurementUnitMenu + title: dissolved_oxygen_measurement_unit menu + permissible_values: + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. + meaning: UO:0000273 + kilogram per cubic meter (kg/m^3) [UO:0000083]: + text: kilogram per cubic meter (kg/m^3) [UO:0000083] + description: An SI unit of density that is one thousandth of the density of + water. + meaning: UO:0000083 + part per million (ppm) [UO:0000169]: + text: part per million (ppm) [UO:0000169] + description: A unitless measure of density that represents one item out of + a million. + meaning: UO:0000169 + OxygenReductionPotentialOrpMeasurementUnitMenu: + name: OxygenReductionPotentialOrpMeasurementUnitMenu + title: oxygen_reduction_potential_(ORP)_measurement_unit menu + permissible_values: + milliVolt (mV) [UO:0000247]: + text: milliVolt (mV) [UO:0000247] + description: A non-SI unit of electromotive force that is one thousandth of + a volt. + meaning: UO:0000247 + ChemicalOxygenDemandCodMeasurementUnitMenu: + name: ChemicalOxygenDemandCodMeasurementUnitMenu + title: chemical_oxygen_demand_(COD)_measurement_unit menu + permissible_values: + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. + meaning: UO:0000273 + CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu: + name: CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu + title: carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_unit menu + permissible_values: + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. + meaning: UO:0000273 + TotalSuspendedSolidsTssMeasurementUnitMenu: + name: TotalSuspendedSolidsTssMeasurementUnitMenu + title: total_suspended_solids_(TSS)_measurement_unit menu + permissible_values: + percent (%) [UO:0000187]: + text: percent (%) [UO:0000187] + description: A unitless measure that represents one in a hundred. + meaning: UO:0000187 + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. + meaning: UO:0000175 + TotalDissolvedSolidsTdsMeasurementUnitMenu: + name: TotalDissolvedSolidsTdsMeasurementUnitMenu + title: total_dissolved_solids_(TDS)_measurement_unit menu + permissible_values: + percent (%) [UO:0000187]: + text: percent (%) [UO:0000187] + description: A unitless measure that represents one in a hundred. + meaning: UO:0000187 + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. + meaning: UO:0000175 + TotalSolidsTsMeasurementUnitMenu: + name: TotalSolidsTsMeasurementUnitMenu + title: total_solids_(TS)_measurement_unit menu + permissible_values: + percent (%) [UO:0000187]: + text: percent (%) [UO:0000187] + description: A unitless measure that represents one in a hundred. + meaning: UO:0000187 + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. + meaning: UO:0000175 + AlkalinityMeasurementUnitMenu: + name: AlkalinityMeasurementUnitMenu + title: alkalinity_measurement_unit menu + permissible_values: + milliequivalent per liter (meq/L): + text: milliequivalent per liter (meq/L) + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. + meaning: UO:0000273 + parts per million [UO:0000169]: + text: parts per million [UO:0000169] + description: A unitless measure of density that represents one item out of + a million. + meaning: UO:0000169 + ConductivityMeasurementUnitMenu: + name: ConductivityMeasurementUnitMenu + title: conductivity_measurement_unit menu + permissible_values: + milliSiemen per centimeter (mS/cm): + text: milliSiemen per centimeter (mS/cm) + "microSiemen per centimeter (\u03BCS/cm)": + text: "microSiemen per centimeter (\u03BCS/cm)" + Siemen per meter (S/m): + text: Siemen per meter (S/m) + SalinityMeasurementUnitMenu: + name: SalinityMeasurementUnitMenu + title: salinity_measurement_unit menu + permissible_values: + practical salinity unit (PSU): + text: practical salinity unit (PSU) + weight for weight (% w/w): + text: weight for weight (% w/w) + parts per thousand [UO:0000168]: + text: parts per thousand [UO:0000168] + description: A dimensionless concentration notation which denotes the amount + of a given substance in a total amount of 1000 regardless of the units of + measure as long as they are the same. + meaning: UO:0000168 + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. + meaning: UO:0000175 + TotalNitrogenTnMeasurementUnitMenu: + name: TotalNitrogenTnMeasurementUnitMenu + title: total_nitrogen_(TN)_measurement_unit menu + permissible_values: + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. + meaning: UO:0000273 + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. + meaning: UO:0000175 + gram per total solids (g/gTS): + text: gram per total solids (g/gTS) + TotalPhosphorpusTpMeasurementUnitMenu: + name: TotalPhosphorpusTpMeasurementUnitMenu + title: total_phosphorpus_(TP)_measurement_unit menu + permissible_values: + gram per total solids (g/gTS): + text: gram per total solids (g/gTS) + orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]: + text: orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998] + description: A substance unit which describes the weight of orthophosphate + as phosphorus (gPO4-P) within a sample to the weight of total solids. + meaning: GENEPIO:0100998 + milligrams per liter (mg/L) [UO:0000273]: + text: milligrams per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. + meaning: UO:0000273 + milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999]: + text: milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999] + description: A density unit comparing the weight of orthophosphate as phosphorus + (PO4-P) in milligrams within a standard liter volume. + meaning: GENEPIO:0100999 + FecalContaminationIndicatorMenu: + name: FecalContaminationIndicatorMenu + title: fecal contamination indicator menu + permissible_values: + crAssphage [NCBITaxon:1211417]: + text: crAssphage [NCBITaxon:1211417] + description: CrAss-like phage, a bacteriophage discovered in 2014 in the human + fecal metagenome. + meaning: NCBITaxon:1211417 + PMMoV / pepper mild mottle virus [NCBITaxon:12239]: + text: PMMoV / pepper mild mottle virus [NCBITaxon:12239] + description: A plant RNA virus that is abundant in human feces. + meaning: NCBITaxon:12239 + Bacteroides HF183: + text: Bacteroides HF183 + description: A fecal indicator which is the most commonly used sewage-associated + marker gene, belonging to the Bacteroides genus. + meaning: GENEPIO:0101000 + Lachnospiraceae Lachno3: + text: Lachnospiraceae Lachno3 + description: A fecal indicator which is a human-associated genetic marker + in the Lachnospiraceae family of bacteria. + meaning: GENEPIO:0101001 + F+ (male specific) coliphages: + text: F+ (male specific) coliphages + description: A fecal indicator which is a bacteriophage that infects coliform + bacteria and is used in water assessment. + meaning: GENEPIO:0101002 + Stercobilin: + text: Stercobilin + description: Bile pigment found in fecal material. + meaning: CHEBI:26756 + FecalContaminationUnitMenu: + name: FecalContaminationUnitMenu + title: fecal_contamination_unit menu + permissible_values: + log10 gene copies per 100 milliliter (log10 GC/100 mL): + text: log10 gene copies per 100 milliliter (log10 GC/100 mL) + gene copies per liter (GC/L): + text: gene copies per liter (GC/L) + PCR quantification cycle [UO:0010077]: + text: PCR quantification cycle [UO:0010077] + description: A count unit of how many Polymerase Chain Reaction (PCR) cycles + it took to detect a real signal from a sample. Equivalent to the PCR cycle + number at which a sample's reaction curve intersects the threshold line. + meaning: UO:0010077 + log10 gene copies per nanogram total DNA: + text: log10 gene copies per nanogram total DNA + UrinaryContaminationIndicatorMenu: + name: UrinaryContaminationIndicatorMenu + title: urinary_contamination_indicator menu + permissible_values: + Urobilin [CHEBI:36378]: + text: Urobilin [CHEBI:36378] + description: A tetrapyrroledicarboxylic acid that causes the yellow color + in urine. Also known as urochrome. + meaning: CHEBI:36378 + UrinaryContaminationUnitMenu: + name: UrinaryContaminationUnitMenu + title: urinary_contamination_unit menu + permissible_values: + nanograms per liter (ng/L) [EFO:0004382]: + text: nanograms per liter (ng/L) [EFO:0004382] + description: A mass unit density which is equal to mass of an object in nanograms + divided by the volume in liters. + meaning: EFO:0004382 + FecalColiformCountUnitMenu: + name: FecalColiformCountUnitMenu + title: fecal_coliform_count_unit menu + permissible_values: + colony forming units per milliliter (CFU/mL) [UO:0000213]: + text: colony forming units per milliliter (CFU/mL) [UO:0000213] + description: A unit of microbial density that describes the number of colony + forming units within a milliliter of material. + meaning: UO:0000213 + colony forming units per 100 milliliter (CFU/100 mL): + text: colony forming units per 100 milliliter (CFU/100 mL) + colony forming units per grams total solids (CFU/gTS): + text: colony forming units per grams total solids (CFU/gTS) + most probable number per milliliter (MPN/mL): + text: most probable number per milliliter (MPN/mL) + most probable number per 100 milliliter (MPN/100 mL): + text: most probable number per 100 milliliter (MPN/100 mL) + SampleTemperatureUnitAtCollectionMenu: + name: SampleTemperatureUnitAtCollectionMenu + title: sample_temperature_unit_(at collection) menu + permissible_values: + degree Fahrenheit (F) [UO:0000195]: + text: degree Fahrenheit (F) [UO:0000195] + description: A unit of temperature on a scale where water freezes at 32 degrees + and boils at 212 degrees under standard conditions. + meaning: UO:0000195 + degree Celsius (C) [UO:0000027]: + text: degree Celsius (C) [UO:0000027] + description: A unit of temperature on a scale where water freezes at 0 degrees + and boils at 100 degrees under standard conditions. + meaning: UO:0000027 + SampleTemperatureUnitWhenReceivedMenu: + name: SampleTemperatureUnitWhenReceivedMenu + title: sample_temperature_unit_(when received) menu + permissible_values: + degree Fahrenheit (F) [UO:0000195]: + text: degree Fahrenheit (F) [UO:0000195] + description: A unit of temperature on a scale where water freezes at 32 degrees + and boils at 212 degrees under standard conditions. + meaning: UO:0000195 + degree Celsius (C) [UO:0000027]: + text: degree Celsius (C) [UO:0000027] + description: A unit of temperature on a scale where water freezes at 0 degrees + and boils at 100 degrees under standard conditions. + meaning: UO:0000027 + SequencingAssayTypeMenu: + name: SequencingAssayTypeMenu + title: sequencing_assay_type menu + permissible_values: + Amplicon sequencing assay [OBI:0002767]: + text: Amplicon sequencing assay [OBI:0002767] + description: A sequencing assay in which a DNA or RNA input molecule is amplified + by PCR and the product sequenced. + meaning: OBI:0002767 + 16S ribosomal gene sequencing assay [OBI:0002763]: + text: 16S ribosomal gene sequencing assay [OBI:0002763] + description: An amplicon sequencing assay in which the amplicon is derived + from universal primers used to amplify the 16S ribosomal RNA gene from isolate + bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting + sequences are compared to reference 16S sequence databases to identify or + classify bacteria present within a given sample. + meaning: OBI:0002763 + is_a: Amplicon sequencing assay [OBI:0002767] + CRISPR amplicon sequencing assay [GENEPIO:0101128]: + text: CRISPR amplicon sequencing assay [GENEPIO:0101128] + meaning: GENEPIO:0101128 + is_a: Amplicon sequencing assay [OBI:0002767] + Primal tiling amplicon sequencing assay [GENEPIO:0101129]: + text: Primal tiling amplicon sequencing assay [GENEPIO:0101129] + meaning: GENEPIO:0101129 + is_a: Amplicon sequencing assay [OBI:0002767] + Whole genome sequencing assay [OBI:0002117]: + text: Whole genome sequencing assay [OBI:0002117] + description: A DNA sequencing assay that intends to provide information about + the sequence of an entire genome of an organism. + meaning: OBI:0002117 + Whole metagenome sequencing assay [OBI:0002623]: + text: Whole metagenome sequencing assay [OBI:0002623] + description: A DNA sequencing assay that intends to provide information on + the DNA sequences of multiple genomes (a metagenome) from different organisms + present in the same input sample. + meaning: OBI:0002623 + Whole virome sequencing assay [OBI:0002768]: + text: Whole virome sequencing assay [OBI:0002768] + description: A whole metagenome sequencing assay that intends to provide information + on multiple genome sequences from different viruses present in the same + input sample. + meaning: OBI:0002768 + is_a: Whole metagenome sequencing assay [OBI:0002623] + PurposeOfSequencingMenu: + name: PurposeOfSequencingMenu + title: purpose_of_sequencing menu + permissible_values: + Baseline surveillance (random sampling) [GENEPIO:0100005]: + text: Baseline surveillance (random sampling) [GENEPIO:0100005] + description: A surveillance sampling strategy in which baseline is established + at the beginning of a study or project by the selection of sample units + via random sampling. + meaning: GENEPIO:0100005 + Targeted surveillance (non-random sampling) [GENEPIO:0100006]: + text: Targeted surveillance (non-random sampling) [GENEPIO:0100006] + description: A surveillance sampling strategy in which an aspired outcome + is explicitly stated. + meaning: GENEPIO:0100006 + Priority surveillance project [GENEPIO:0100007]: + text: Priority surveillance project [GENEPIO:0100007] + description: A targeted surveillance strategy which is considered important + and/or urgent. + meaning: GENEPIO:0100007 + is_a: Targeted surveillance (non-random sampling) [GENEPIO:0100006] + Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]: + text: Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009] + description: A surveillance strategy in which an individual or site is selected + to undergo repeat sampling over a defined period of time. + meaning: GENEPIO:0100009 + is_a: Priority surveillance project [GENEPIO:0100007] + Cluster/Outbreak investigation [GENEPIO:0100019]: + text: Cluster/Outbreak investigation [GENEPIO:0100019] + description: A sampling strategy in which individuals are chosen for investigation + into a disease cluster or outbreak. + meaning: GENEPIO:0100019 + Multi-jurisdictional outbreak investigation [GENEPIO:0100020]: + text: Multi-jurisdictional outbreak investigation [GENEPIO:0100020] + description: An outbreak investigation sampling strategy in which individuals + are chosen for investigation into a disease outbreak that has connections + to two or more jurisdictions. + meaning: GENEPIO:0100020 + is_a: Cluster/Outbreak investigation [GENEPIO:0100019] + Intra-jurisdictional outbreak investigation [GENEPIO:0100021]: + text: Intra-jurisdictional outbreak investigation [GENEPIO:0100021] + description: An outbreak investigation sampling strategy in which individuals + are chosen for investigation into a disease outbreak that only has connections + within a single jurisdiction. + meaning: GENEPIO:0100021 + is_a: Cluster/Outbreak investigation [GENEPIO:0100019] + Research [GENEPIO:0100022]: + text: Research [GENEPIO:0100022] + description: A sampling strategy in which sites are sampled in order to perform + research. + meaning: GENEPIO:0100022 + Viral passage experiment [GENEPIO:0100023]: + text: Viral passage experiment [GENEPIO:0100023] + description: A research sampling strategy in which samples are selected in + order to perform a viral passage experiment. + meaning: GENEPIO:0100023 + is_a: Research [GENEPIO:0100022] + Protocol testing experiment [GENEPIO:0100024]: + text: Protocol testing experiment [GENEPIO:0100024] + description: A research sampling strategy in which samples are collected in + order to test a method or protocol. + meaning: GENEPIO:0100024 + is_a: Research [GENEPIO:0100022] + Retrospective sequencing [GENEPIO:0100356]: + text: Retrospective sequencing [GENEPIO:0100356] + description: A sampling strategy in which stored samples from past events + are sequenced. + meaning: GENEPIO:0100356 + GeoLocNameCountryMenu: + name: GeoLocNameCountryMenu + title: geo_loc_name_(country) menu + permissible_values: + Afghanistan [GAZ:00006882]: + text: Afghanistan [GAZ:00006882] + description: A landlocked country that is located approximately in the center + of Asia. It is bordered by Pakistan in the south and east Iran in the west, + Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far + northeast. Afghanistan is administratively divided into thirty-four (34) + provinces (welayats). Each province is then divided into many provincial + districts, and each district normally covers a city or several townships. + [ url:http://en.wikipedia.org/wiki/Afghanistan ] + meaning: GAZ:00006882 + Albania [GAZ:00002953]: + text: Albania [GAZ:00002953] + description: 'A country in South Eastern Europe. Albania is bordered by Greece + to the south-east, Montenegro to the north, Kosovo to the northeast, and + the Republic of Macedonia to the east. It has a coast on the Adriatic Sea + to the west, and on the Ionian Sea to the southwest. From the Strait of + Otranto, Albania is less than 100 km from Italy. Albania is divided into + 12 administrative divisions called (Albanian: official qark/qarku, but often + prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities + (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania + ]' + meaning: GAZ:00002953 + Algeria [GAZ:00000563]: + text: Algeria [GAZ:00000563] + description: A country in North Africa. It is bordered by Tunisia in the northeast, + Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, + a few km of the Western Sahara in the west, Morocco in the northwest, and + the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), + 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). + [ url:http://en.wikipedia.org/wiki/Algeria ] + meaning: GAZ:00000563 + American Samoa [GAZ:00003957]: + text: American Samoa [GAZ:00003957] + description: An unincorporated territory of the United States located in the + South Pacific Ocean, southeast of the sovereign State of Samoa. The main + (largest and most populous) island is Tutuila, with the Manu'a Islands, + Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa + ] + meaning: GAZ:00003957 + Andorra [GAZ:00002948]: + text: Andorra [GAZ:00002948] + description: 'A small landlocked country in western Europe, located in the + eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. + Andorra consists of seven communities known as parishes (Catalan: parroquies, + singular - parroquia). Until relatively recently, it had only six parishes; + the seventh, Escaldes-Engordany, was created in 1978. Some parishes have + a further territorial subdivision. Ordino, La Massana and Sant Julia de + Loria are subdivided into quarts (quarters), while Canillo is subdivided + into veinats (neighborhoods). Those mostly coincide with villages, which + are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ]' + meaning: GAZ:00002948 + Angola [GAZ:00001095]: + text: Angola [GAZ:00001095] + description: A country in south-central Africa bordering Namibia to the south, + Democratic Republic of the Congo to the north, and Zambia to the east, and + with a west coast along the Atlantic Ocean. The exclave province Cabinda + has a border with the Republic of the Congo and the Democratic Republic + of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ] + meaning: GAZ:00001095 + Anguilla [GAZ:00009159]: + text: Anguilla [GAZ:00009159] + description: A British overseas territory in the Caribbean, one of the most + northerly of the Leeward Islands in the Lesser Antilles. It consists of + the main island of Anguilla itself, approximately 26 km long by 5 km wide + at its widest point, together with a number of much smaller islands and + cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila + ] + meaning: GAZ:00009159 + Antarctica [GAZ:00000462]: + text: Antarctica [GAZ:00000462] + description: The Earth's southernmost continent, overlying the South Pole. + It is situated in the southern hemisphere, almost entirely south of the + Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica + ] + meaning: GAZ:00000462 + Antigua and Barbuda [GAZ:00006883]: + text: Antigua and Barbuda [GAZ:00006883] + description: An island nation located on the eastern boundary of the Caribbean + Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda + ] + meaning: GAZ:00006883 + Argentina [GAZ:00002928]: + text: Argentina [GAZ:00002928] + description: 'A South American country, constituted as a federation of twenty-three + provinces and an autonomous city. It is bordered by Paraguay and Bolivia + in the north, Brazil and Uruguay in the northeast, and Chile in the west + and south. The country claims the British controlled territories of the + Falkland Islands and South Georgia and the South Sandwich Islands. Argentina + also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping + other claims made by Chile and the United Kingdom. Argentina is subdivided + into twenty-three provinces (Spanish: provincias, singular provincia) and + one federal district (Capital de la Republica or Capital de la Nacion, informally + the Capital Federal). The federal district and the provinces have their + own constitutions, but exist under a federal system. Provinces are then + divided into departments (Spanish: departamentos, singular departamento), + except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina + ]' + meaning: GAZ:00002928 + Armenia [GAZ:00004094]: + text: Armenia [GAZ:00004094] + description: A landlocked mountainous country in Eurasia between the Black + Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the + west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan + exclave of Azerbaijan to the south. A transcontinental country at the juncture + of Eastern Europe and Western Asia. A former republic of the Soviet Union. + Armenia is divided into ten marzes (provinces, singular marz), with the + city (kaghak) of Yerevan having special administrative status as the country's + capital. [ url:http://en.wikipedia.org/wiki/Armenia ] + meaning: GAZ:00004094 + Aruba [GAZ:00004025]: + text: Aruba [GAZ:00004025] + description: An autonomous region within the Kingdom of the Netherlands, Aruba + has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba + ] + meaning: GAZ:00004025 + Ashmore and Cartier Islands [GAZ:00005901]: + text: Ashmore and Cartier Islands [GAZ:00005901] + description: A Territory of Australia that includes two groups of small low-lying + uninhabited tropical islands in the Indian Ocean situated on the edge of + the continental shelf north-west of Australia and south of the Indonesian + island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands + ] + meaning: GAZ:00005901 + Australia [GAZ:00000463]: + text: Australia [GAZ:00000463] + description: A country in the southern hemisphere comprising the mainland + of the world's smallest continent, the major island of Tasmania, and a number + of other islands in the Indian and Pacific Oceans. The neighbouring countries + are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon + Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to + the south-east. Australia has six states, two major mainland territories, + and other minor territories. + meaning: GAZ:00000463 + Austria [GAZ:00002942]: + text: Austria [GAZ:00002942] + description: A landlocked country in Central Europe. It borders both Germany + and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia + and Italy to the south, and Switzerland and Liechtenstein to the west. The + capital is the city of Vienna on the Danube River. Austria is divided into + nine states (Bundeslander). These states are then divided into districts + (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities + (Gemeinden). Cities have the competencies otherwise granted to both districts + and municipalities. + meaning: GAZ:00002942 + Azerbaijan [GAZ:00004941]: + text: Azerbaijan [GAZ:00004941] + description: A country in the he South Caucasus region of Eurasia, it is bounded + by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, + Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan + is bordered by Armenia to the north and east, Iran to the south and west, + and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts + in Azerbaijan's southwest, have been controlled by Armenia since the end + of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons + 11 city districts (saharlar), and one autonomous republic (muxtar respublika). + meaning: GAZ:00004941 + Bahamas [GAZ:00002733]: + text: Bahamas [GAZ:00002733] + description: A country consisting of two thousand cays and seven hundred islands + that form an archipelago. It is located in the Atlantic Ocean, southeast + of Florida and the United States, north of Cuba, the island of Hispanola + and the Caribbean, and northwest of the British overseas territory of the + Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, + whose affairs are handled directly by the central government. + meaning: GAZ:00002733 + Bahrain [GAZ:00005281]: + text: Bahrain [GAZ:00005281] + description: A borderless island country in the Persian Gulf. Saudi Arabia + lies to the west and is connected to Bahrain by the King Fahd Causeway, + and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into + five governorates. + meaning: GAZ:00005281 + Baker Island [GAZ:00007117]: + text: Baker Island [GAZ:00007117] + description: An uninhabited atoll located just north of the equator in the + central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island + is an unincorporated and unorganized territory of the US. + meaning: GAZ:00007117 + Bangladesh [GAZ:00003750]: + text: Bangladesh [GAZ:00003750] + description: A country in South Asia. It is bordered by India on all sides + except for a small border with Myanmar to the far southeast and by the Bay + of Bengal to the south. Bangladesh is divided into six administrative divisions. + Divisions are subdivided into districts (zila). There are 64 districts in + Bangladesh, each further subdivided into upazila (subdistricts) or thana + ("police stations"). + meaning: GAZ:00003750 + Barbados [GAZ:00001251]: + text: Barbados [GAZ:00001251] + description: "An island country in the Lesser Antilles of the West Indies,\ + \ in the Caribbean region of the Americas, and the most easterly of the\ + \ Caribbean Islands. It is 34 kilometres (21 miles) in length and up to\ + \ 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is\ + \ in the western part of the North Atlantic, 100 km (62 mi) east of the\ + \ Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards,\ + \ part of the Lesser Antilles, at roughly 13\xB0N of the equator. It is\ + \ about 168 km (104 mi) east of both the countries of Saint Lucia and Saint\ + \ Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique\ + \ and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside\ + \ the principal Atlantic hurricane belt. Its capital and largest city is\ + \ Bridgetown." + meaning: GAZ:00001251 + Bassas da India [GAZ:00005810]: + text: Bassas da India [GAZ:00005810] + description: A roughly circular atoll about 10 km in diameter, which corresponds + to a total size (including lagoon) of 80 km2. It is located in the southern + Mozambique Channel, about half-way between Madagascar (which is 385 km to + the east) and Mozambique, and 110 km northwest of Europa Island. It rises + steeply from the seabed 3000 m below. + meaning: GAZ:00005810 + Belarus [GAZ:00006886]: + text: Belarus [GAZ:00006886] + description: A landlocked country in Eastern Europe, that borders Russia to + the north and east, Ukraine to the south, Poland to the west, and Lithuania + and Latvia to the north. Its capital is Minsk. Belarus is divided into six + voblasts, or provinces. Voblasts are further subdivided into raions (commonly + translated as districts or regions). As of 2002, there are six voblasts, + 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special + status, due to the city serving as the national capital. + meaning: GAZ:00006886 + Belgium [GAZ:00002938]: + text: Belgium [GAZ:00002938] + description: A country in northwest Europe. Belgium shares borders with France + (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 + km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each + comprise five provinces; the third region, Brussels-Capital Region, is not + a province, nor does it contain any Together, these comprise 589 municipalities, + which in general consist of several sub-municipalities (which were independent + municipalities before the municipal merger operation mainly in 1977). + meaning: GAZ:00002938 + Belize [GAZ:00002934]: + text: Belize [GAZ:00002934] + description: A country in Central America. It is the only officially English + speaking country in the region. Belize was a British colony for more than + a century and was known as British Honduras until 1973. It became an independent + nation within The Commonwealth in 1981. Belize is divided into 6 districts, + which are further divided into 31 constituencies. + meaning: GAZ:00002934 + Benin [GAZ:00000904]: + text: Benin [GAZ:00000904] + description: A country in Western Africa. It borders Togo to the west, Nigeria + to the east and Burkina Faso and Niger to the north; its short coastline + to the south leads to the Bight of Benin. Its capital is Porto Novo, but + the seat of government is Cotonou. Benin is divided into 12 departments + and subdivided into 77 communes. + meaning: GAZ:00000904 + Bermuda [GAZ:00001264]: + text: Bermuda [GAZ:00001264] + description: A British overseas territory in the North Atlantic Ocean. Located + off the east coast of the United States, it is situated around 1770 km NE + of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately + 138 islands. + meaning: GAZ:00001264 + Bhutan [GAZ:00003920]: + text: Bhutan [GAZ:00003920] + description: A landlocked nation in South Asia. It is located amidst the eastern + end of the Himalaya Mountains and is bordered to the south, east and west + by India and to the north by Tibet. Bhutan is separated from Nepal by the + Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative + zones). Each dzongdey is further divided into dzongkhag (districts). There + are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into + subdistricts known as dungkhag. At the basic level, groups of villages form + a constituency called gewog. + meaning: GAZ:00003920 + Bolivia [GAZ:00002511]: + text: Bolivia [GAZ:00002511] + description: 'A landlocked country in central South America. It is bordered + by Brazil on the north and east, Paraguay and Argentina on the south, and + Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: + departamentos). Each of the departments is subdivided into provinces (provincias), + which are further subdivided into municipalities (municipios).' + meaning: GAZ:00002511 + Borneo [GAZ:00025355]: + text: Borneo [GAZ:00025355] + description: 'An island at the grographic centre of Maritime Southeast Adia, + in relation to major Indonesian islands, it is located north of Java, west + of Sulawesi, and east of Sumatra. It is the third-largest island in the + world and the larest in Asia. The island is politically divided among three + countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] + Approximately 73% of the island is Indonesian territory. In the north, the + East Malaysian states of Sabah and Sarawak make up about 26% of the island. + Additionally, the Malaysian federal territory of Labuan is situated on a + small island just off the coast of Borneo. The sovereign state of Brunei, + located on the north coast, comprises about 1% of Borneo''s land area. A + little more than half of the island is in the Northern Hemisphere, including + Brunei and the Malaysian portion, while the Indonesian portion spans the + Northern and Southern hemispheres.' + meaning: GAZ:00025355 + Bosnia and Herzegovina [GAZ:00006887]: + text: Bosnia and Herzegovina [GAZ:00006887] + description: A country on the Balkan peninsula of Southern Europe. Bordered + by Croatia to the north, west and south, Serbia to the east, and Montenegro + to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 + km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided + into three political regions of which one, the Brcko District is part of + the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. + All three have an equal constitutional status on the whole territory of + Bosnia and Herzegovina. + meaning: GAZ:00006887 + Botswana [GAZ:00001097]: + text: Botswana [GAZ:00001097] + description: A landlocked nation in Southern Africa. It is bordered by South + Africa to the south and southeast, Namibia to the west, Zambia to the north, + and Zimbabwe to the northeast. Botswana is divided into nine districts, + which are subdivided into a total twenty-eight subdistricts. + meaning: GAZ:00001097 + Bouvet Island [GAZ:00001453]: + text: Bouvet Island [GAZ:00001453] + description: A sub-antarctic volcanic island in the South Atlantic Ocean, + south-southwest of the Cape of Good Hope (South Africa). It is a dependent + area of Norway and is not subject to the Antarctic Treaty, as it is north + of the latitude south of which claims are suspended. + meaning: GAZ:00001453 + Brazil [GAZ:00002828]: + text: Brazil [GAZ:00002828] + description: 'A country in South America. Bordered by the Atlantic Ocean and + by Venezuela, Suriname, Guyana and the department of French Guiana to the + north, Colombia to the northwest, Bolivia and Peru to the west, Argentina + and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six + states (estados) and one federal district (Distrito Federal). The states + are subdivided into municipalities. For statistical purposes, the States + are grouped into five main regions: North, Northeast, Central-West, Southeast + and South.' + meaning: GAZ:00002828 + British Virgin Islands [GAZ:00003961]: + text: British Virgin Islands [GAZ:00003961] + description: A British overseas territory, located in the Caribbean to the + east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, + the remaining islands constituting the US Virgin Islands. The British Virgin + Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and + Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately + fifteen of the islands are inhabited. + meaning: GAZ:00003961 + Brunei [GAZ:00003901]: + text: Brunei [GAZ:00003901] + description: A country located on the north coast of the island of Borneo, + in Southeast Asia. Apart from its coastline with the South China Sea it + is completely surrounded by the State of Sarawak, Malaysia, and in fact + it is separated into two parts by Limbang, which is part of Sarawak. Brunei + is divided into four districts (daerah), the districts are subdivided into + thirty-eight mukims, which are then divided into kampong (villages). + meaning: GAZ:00003901 + Bulgaria [GAZ:00002950]: + text: Bulgaria [GAZ:00002950] + description: A country in Southeastern Europe, borders five other countries; + Romania to the north (mostly along the Danube), Serbia and the Republic + of Macedonia to the west, and Greece and Turkey to the south. The Black + Sea defines the extent of the country to the east. Since 1999, it has consisted + of twenty-eight provinces. The provinces subdivide into 264 municipalities. + meaning: GAZ:00002950 + Burkina Faso [GAZ:00000905]: + text: Burkina Faso [GAZ:00000905] + description: 'A landlocked nation in West Africa. It is surrounded by six + countries: Mali to the north, Niger to the east, Benin to the south east, + Togo and Ghana to the south, and Cote d''Ivoire to the south west. Burkina + Faso is divided into thirteen regions, forty-five provinces, and 301 departments + (communes).' + meaning: GAZ:00000905 + Burundi [GAZ:00001090]: + text: Burundi [GAZ:00001090] + description: A small country in the Great Lakes region of Africa. It is bordered + by Rwanda on the north, Tanzania on the south and east, and the Democratic + Republic of the Congo on the west. Although the country is landlocked, much + of its western border is adjacent to Lake Tanganyika. Burundi is divided + into 17 provinces, 117 communes, and 2,638 collines. + meaning: GAZ:00001090 + Cambodia [GAZ:00006888]: + text: Cambodia [GAZ:00006888] + description: A country in Southeast Asia. The country borders Thailand to + its west and northwest, Laos to its northeast, and Vietnam to its east and + southeast. In the south it faces the Gulf of Thailand. + meaning: GAZ:00006888 + Cameroon [GAZ:00001093]: + text: Cameroon [GAZ:00001093] + description: A country of central and western Africa. It borders Nigeria to + the west; Chad to the northeast; the Central African Republic to the east; + and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. + Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea + and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces + and 58 divisions or departments. The divisions are further sub-divided into + sub-divisions (arrondissements) and districts. + meaning: GAZ:00001093 + Canada [GAZ:00002560]: + text: Canada [GAZ:00002560] + description: A country occupying most of northern North America, extending + from the Atlantic Ocean in the east to the Pacific Ocean in the west and + northward into the Arctic Ocean. Canada is a federation composed of ten + provinces and three territories; in turn, these may be grouped into regions. + Western Canada consists of British Columbia and the three Prairie provinces + (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec + and Ontario. Atlantic Canada consists of the three Maritime provinces (New + Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland + and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada + together. Three territories (Yukon, Northwest Territories, and Nunavut) + make up Northern Canada. + meaning: GAZ:00002560 + Cape Verde [GAZ:00001227]: + text: Cape Verde [GAZ:00001227] + description: A republic located on an archipelago in the Macaronesia ecoregion + of the North Atlantic Ocean, off the western coast of Africa. Cape Verde + is divided into 22 municipalities (concelhos), and subdivided into 32 parishes + (freguesias). + meaning: GAZ:00001227 + Cayman Islands [GAZ:00003986]: + text: Cayman Islands [GAZ:00003986] + description: A British overseas territory located in the western Caribbean + Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. + The Cayman Islands are divided into seven districts. + meaning: GAZ:00003986 + Central African Republic [GAZ:00001089]: + text: Central African Republic [GAZ:00001089] + description: A landlocked country in Central Africa. It borders Chad in the + north, Sudan in the east, the Republic of the Congo and the Democratic Republic + of the Congo in the south, and Cameroon in the west. The Central African + Republic is divided into 14 administrative prefectures (prefectures), along + with 2 economic prefectures (prefectures economiques) and one autonomous + commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures). + meaning: GAZ:00001089 + Chad [GAZ:00000586]: + text: Chad [GAZ:00000586] + description: A landlocked country in central Africa. It is bordered by Libya + to the north, Sudan to the east, the Central African Republic to the south, + Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided + into 18 regions. The departments are divided into 200 sub-prefectures, which + are in turn composed of 446 cantons. This is due to change. + meaning: GAZ:00000586 + Chile [GAZ:00002825]: + text: Chile [GAZ:00002825] + description: 'A country in South America occupying a long and narrow coastal + strip wedged between the Andes mountains and the Pacific Ocean. The Pacific + forms the country''s entire western border, with Peru to the north, Bolivia + to the northeast, Argentina to the east, and the Drake Passage at the country''s + southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. + Chile is divided into 15 regions. Every region is further divided into provinces. + Finally each province is divided into communes. Each region is designated + by a name and a Roman numeral, assigned from north to south. The only exception + is the region housing the nation''s capital, which is designated RM, that + stands for Region Metropolitana (Metropolitan Region). Two new regions were + created in 2006: Arica-Parinacota in the north, and Los Rios in the south. + Both became operative in 2007-10.' + meaning: GAZ:00002825 + China [GAZ:00002845]: + text: China [GAZ:00002845] + description: 'A large country in Northeast Asia. China borders 14 nations + (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, + Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia + and North Korea. Additionally the border between PRC and ROC is located + in territorial waters. The People''s Republic of China has administrative + control over twenty-two provinces and considers Taiwan to be its twenty-third + province. There are also five autonomous regions, each with a designated + minority group; four municipalities; and two Special Administrative Regions + that enjoy considerable autonomy. The People''s Republic of China administers + 33 province-level regions, 333 prefecture-level regions, 2,862 county-level + regions, 41,636 township-level regions, and several village-level regions.' + meaning: GAZ:00002845 + Christmas Island [GAZ:00005915]: + text: Christmas Island [GAZ:00005915] + description: An island in the Indian Ocean, 500 km south of Indonesia and + about 2600 km northwest of Perth. The island is the flat summit of a submarine + mountain. + meaning: GAZ:00005915 + Clipperton Island [GAZ:00005838]: + text: Clipperton Island [GAZ:00005838] + description: A nine-square km coral atoll in the North Pacific Ocean, southwest + of Mexico and west of Costa Rica. + meaning: GAZ:00005838 + Cocos Islands [GAZ:00009721]: + text: Cocos Islands [GAZ:00009721] + description: Islands that located in the Indian Ocean, about halfway between + Australia and Sri Lanka. A territory of Australia. There are two atolls + and twenty-seven coral islands in the group. + meaning: GAZ:00009721 + Colombia [GAZ:00002929]: + text: Colombia [GAZ:00002929] + description: A country located in the northwestern region of South America. + Colombia is bordered to the east by Venezuela and Brazil; to the south by + Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean + Sea; to the north-west by Panama; and to the west by the Pacific Ocean. + Besides the countries in South America, the Republic of Colombia is recognized + to share maritime borders with the Caribbean countries of Jamaica, Haiti, + the Dominican Republic and the Central American countries of Honduras, Nicaragua, + and Costa Rica. Colombia is divided into 32 departments and one capital + district which is treated as a department. There are in total 10 districts + assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, + Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia + is also subdivided into some municipalities which form departments, each + with a municipal seat capital city assigned. Colombia is also subdivided + into corregimientos which form municipalities. + meaning: GAZ:00002929 + Comoros [GAZ:00005820]: + text: Comoros [GAZ:00005820] + description: An island nation in the Indian Ocean, located off the eastern + coast of Africa on the northern end of the Mozambique Channel between northern + Madagascar and northeastern Mozambique. + meaning: GAZ:00005820 + Cook Islands [GAZ:00053798]: + text: Cook Islands [GAZ:00053798] + description: A self-governing parliamentary democracy in free association + with New Zealand. The fifteen small islands in this South Pacific Ocean + country have a total land area of 240 km2, but the Cook Islands Exclusive + Economic Zone (EEZ) covers 1.8 million km2 of ocean. + meaning: GAZ:00053798 + Coral Sea Islands [GAZ:00005917]: + text: Coral Sea Islands [GAZ:00005917] + description: A Territory of Australia which includes a group of small and + mostly uninhabited tropical islands and reefs in the Coral Sea, northeast + of Queensland, Australia. The only inhabited island is Willis Island. The + territory covers 780,000 km2, extending east and south from the outer edge + of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, + the Willis Group, and fifteen other reef/island groups. + meaning: GAZ:00005917 + Costa Rica [GAZ:00002901]: + text: Costa Rica [GAZ:00002901] + description: A republic in Central America, bordered by Nicaragua to the north, + Panama to the east-southeast, the Pacific Ocean to the west and south, and + the Caribbean Sea to the east. Costa Rica is composed of seven provinces, + which in turn are divided into 81 cantons. + meaning: GAZ:00002901 + Cote d'Ivoire [GAZ:00000906]: + text: Cote d'Ivoire [GAZ:00000906] + description: A country in West Africa. It borders Liberia and Guinea to the + west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf + of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). + The regions are further divided into 58 departments. + meaning: GAZ:00000906 + Croatia [GAZ:00002719]: + text: Croatia [GAZ:00002719] + description: A country at the crossroads of the Mediterranean, Central Europe, + and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and + Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to + the east, Montenegro to the far southeast, and the Adriatic Sea to the south. + Croatia is divided into 21 counties (zupanija) and the capital Zagreb's + city district. + meaning: GAZ:00002719 + Cuba [GAZ:00003762]: + text: Cuba [GAZ:00003762] + description: A country that consists of the island of Cuba (the largest and + second-most populous island of the Greater Antilles), Isla de la Juventud + and several adjacent small islands. Fourteen provinces and one special municipality + (the Isla de la Juventud) now compose Cuba. + meaning: GAZ:00003762 + Curacao [GAZ:00012582]: + text: Curacao [GAZ:00012582] + description: One of five island areas of the Netherlands Antilles. + meaning: GAZ:00012582 + Cyprus [GAZ:00004006]: + text: Cyprus [GAZ:00004006] + description: The third largest island in the Mediterranean Sea (after Sicily + and Sardinia), Cyprus is situated in the eastern Mediterranean, just south + of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, + it is often included in the Middle East (see also Western Asia and Near + East). Turkey is 75 km north; other neighbouring countries include Syria + and Lebanon to the east, Israel to the southeast, Egypt to the south, and + Greece to the west-north-west. + meaning: GAZ:00004006 + Czech Republic [GAZ:00002954]: + text: Czech Republic [GAZ:00002954] + description: 'A landlocked country in Central Europe. It has borders with + Poland to the north, Germany to the northwest and southwest, Austria to + the south, and Slovakia to the east. The capital and largest city is Prague. + The country is composed of the historic regions of Bohemia and Moravia, + as well as parts of Silesia. Since 2000, the Czech Republic is divided into + thirteen regions (kraje, singular kraj) and the capital city of Prague. + The older seventy-six districts (okresy, singular okres) including three + ''statutory cities'' (without Prague, which had special status) were disbanded + in 1999 in an administrative reform; they remain as territorial division + and seats of various branches of state administration. Since 2003-01-01, + the regions have been divided into around 203 Municipalities with Extended + Competence (unofficially named "Little Districts" (Czech: ''male okresy'') + which took over most of the administration of the former District Authorities. + Some of these are further divided into Municipalities with Commissioned + Local Authority. However, the old districts still exist as territorial units + and remain as seats of some of the offices.' + meaning: GAZ:00002954 + Democratic Republic of the Congo [GAZ:00001086]: + text: Democratic Republic of the Congo [GAZ:00001086] + description: A country of central Africa. It borders the Central African Republic + and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia + and Angola on the south, the Republic of the Congo on the west, and is separated + from Tanzania by Lake Tanganyika on the east. The country enjoys access + to the ocean through a 40 km stretch of Atlantic coastline at Muanda and + the roughly 9 km wide mouth of the Congo river which opens into the Gulf + of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed + into 25 Provinces from 2.2009. Each Province is divided into Zones. + meaning: GAZ:00001086 + Denmark [GAZ:00005852]: + text: Denmark [GAZ:00005852] + description: That part of the Kingdom of Denmark located in continental Europe. + The mainland is bordered to the south by Germany; Denmark is located to + the southwest of Sweden and the south of Norway. Denmark borders both the + Baltic and the North Sea. The country consists of a large peninsula, Jutland + (Jylland) and a large number of islands, most notably Zealand (Sjaelland), + Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds + of minor islands often referred to as the Danish Archipelago. + meaning: GAZ:00005852 + Djibouti [GAZ:00000582]: + text: Djibouti [GAZ:00000582] + description: A country in eastern Africa. Djibouti is bordered by Eritrea + in the north, Ethiopia in the west and south, and Somalia in the southeast. + The remainder of the border is formed by the Red Sea and the Gulf of Aden. + On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the + coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. + Djibouti is divided into 5 regions and one city. It is further subdivided + into 11 districts. + meaning: GAZ:00000582 + Dominica [GAZ:00006890]: + text: Dominica [GAZ:00006890] + description: An island nation in the Caribbean Sea. Dominica is divided into + ten parishes. + meaning: GAZ:00006890 + Dominican Republic [GAZ:00003952]: + text: Dominican Republic [GAZ:00003952] + description: A country in the West Indies that occupies the E two-thirds of + the Hispaniola island. The Dominican Republic's shores are washed by the + Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona + Passage, a channel about 130 km wide, separates the country (and the Hispaniola) + from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, + the national capital, Santo Domingo, is contained within its own Distrito + Nacional (National District). The provinces are divided into municipalities + (municipios; singular municipio). + meaning: GAZ:00003952 + Ecuador [GAZ:00002912]: + text: Ecuador [GAZ:00002912] + description: A country in South America, bordered by Colombia on the north, + by Peru on the east and south, and by the Pacific Ocean to the west. The + country also includes the Galapagos Islands (Archipelago de Colon) in the + Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, + divided into 199 cantons and subdivided into parishes (or parroquias). + meaning: GAZ:00002912 + Egypt [GAZ:00003934]: + text: Egypt [GAZ:00003934] + description: A country in North Africa that includes the Sinai Peninsula, + a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, + and the Gaza Strip and Israel to the east. The northern coast borders the + Mediterranean Sea and the island of Cyprus; the eastern coast borders the + Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, + singular muhafazah). The governorates are further divided into regions (markazes). + meaning: GAZ:00003934 + El Salvador [GAZ:00002935]: + text: El Salvador [GAZ:00002935] + description: A country in Central America, bordering the Pacific Ocean between + Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), + which, in turn, are subdivided into 267 municipalities (municipios). + meaning: GAZ:00002935 + Equatorial Guinea [GAZ:00001091]: + text: Equatorial Guinea [GAZ:00001091] + description: 'A country in Central Africa. It is one of the smallest countries + in continental Africa, and comprises two regions: Rio Muni, continental + region including several offshore islands; and Insular Region containing + Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando + Po) that contains the capital, Malabo. Equatorial Guinea is divided into + seven provinces which are divided into districts.' + meaning: GAZ:00001091 + Eritrea [GAZ:00000581]: + text: Eritrea [GAZ:00000581] + description: A country situated in northern East Africa. It is bordered by + Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. + The east and northeast of the country have an extensive coastline on the + Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago + and several of the Hanish Islands are part of Eritrea. Eritrea is divided + into six regions (zobas) and subdivided into districts ("sub-zobas"). + meaning: GAZ:00000581 + Estonia [GAZ:00002959]: + text: Estonia [GAZ:00002959] + description: A country in Northern Europe. Estonia has land borders to the + south with Latvia and to the east with Russia. It is separated from Finland + in the north by the Gulf of Finland and from Sweden in the west by the Baltic + Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). + Estonian counties are divided into rural (vallad, singular vald) and urban + (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) + municipalities. The municipalities comprise populated places (asula or asustusuksus) + - various settlements and territorial units that have no administrative + function. A group of populated places form a rural municipality with local + administration. Most towns constitute separate urban municipalities, while + some have joined with surrounding rural municipalities. + meaning: GAZ:00002959 + Eswatini [GAZ:00001099]: + text: Eswatini [GAZ:00001099] + description: A small, landlocked country in Africa embedded between South + Africa in the west, north and south and Mozambique in the east. Swaziland + is divided into four districts, each of which is divided into Tinkhundla + (singular, Inkhundla). + meaning: GAZ:00001099 + Ethiopia [GAZ:00000567]: + text: Ethiopia [GAZ:00000567] + description: 'A country situated in the Horn of Africa that has been landlocked + since the independence of its northern neighbor Eritrea in 1993. Apart from + Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to + the south, Djibouti to the northeast, and Somalia to the east. Since 1996 + Ethiopia has had a tiered government system consisting of a federal government + overseeing ethnically-based regional states, zones, districts (woredas), + and neighborhoods (kebele). It is divided into nine ethnically-based administrative + states (kililoch, singular kilil) and subdivided into sixty-eight zones + and two chartered cities (astedader akababiwoch, singular astedader akababi): + Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and + six special woredas.' + meaning: GAZ:00000567 + Europa Island [GAZ:00005811]: + text: Europa Island [GAZ:00005811] + description: A 28 km2 low-lying tropical island in the Mozambique Channel, + about a third of the way from southern Madagascar to southern Mozambique. + meaning: GAZ:00005811 + Falkland Islands (Islas Malvinas) [GAZ:00001412]: + text: Falkland Islands (Islas Malvinas) [GAZ:00001412] + description: An archipelago in the South Atlantic Ocean, located 483 km from + the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), + and 940 km north of Antarctica (Elephant Island). They consist of two main + islands, East Falkland and West Falkland, together with 776 smaller islands. + meaning: GAZ:00001412 + Faroe Islands [GAZ:00059206]: + text: Faroe Islands [GAZ:00059206] + description: An autonomous province of the Kingdom of Denmark since 1948 located + in the Faroes. Administratively, the islands are divided into 34 municipalities + (kommunur) within which 120 or so cities and villages lie. + meaning: GAZ:00059206 + Fiji [GAZ:00006891]: + text: Fiji [GAZ:00006891] + description: An island nation in the South Pacific Ocean east of Vanuatu, + west of Tonga and south of Tuvalu. The country occupies an archipelago of + about 322 islands, of which 106 are permanently inhabited, and 522 islets. + The two major islands, Viti Levu and Vanua Levu, account for 87% of the + population. + meaning: GAZ:00006891 + Finland [GAZ:00002937]: + text: Finland [GAZ:00002937] + description: A Nordic country situated in the Fennoscandian region of Northern + Europe. It has borders with Sweden to the west, Russia to the east, and + Norway to the north, while Estonia lies to its south across the Gulf of + Finland. The capital city is Helsinki. Finland is divided into six administrative + provinces (laani, plural laanit). These are divided into 20 regions (maakunt), + 77 subregions (seutukunta) and then into municipalities (kunta). + meaning: GAZ:00002937 + France [GAZ:00003940]: + text: France [GAZ:00003940] + description: A part of the country of France that extends from the Mediterranean + Sea to the English Channel and the North Sea, and from the Rhine to the + Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, + Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas + departments. + meaning: GAZ:00003940 + French Guiana [GAZ:00002516]: + text: French Guiana [GAZ:00002516] + description: An overseas department (departement d'outre-mer) of France, located + on the northern coast of South America. It is bordered by Suriname, to the + E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. + French Guiana is divided into 2 departmental arrondissements, 19 cantons + and 22 communes. + meaning: GAZ:00002516 + French Polynesia [GAZ:00002918]: + text: French Polynesia [GAZ:00002918] + description: 'A French overseas collectivity in the southern Pacific Ocean. + It is made up of several groups of Polynesian islands. French Polynesia + has five administrative subdivisions (French: subdivisions administratives).' + meaning: GAZ:00002918 + French Southern and Antarctic Lands [GAZ:00003753]: + text: French Southern and Antarctic Lands [GAZ:00003753] + description: The French Southern and Antarctic Lands have formed a territoire + d'outre-mer (an overseas territory) of France since 1955. The territory + is divided into five districts. + meaning: GAZ:00003753 + Gabon [GAZ:00001092]: + text: Gabon [GAZ:00001092] + description: A country in west central Africa sharing borders with Equatorial + Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital + and largest city is Libreville. Gabon is divided into 9 provinces and further + divided into 37 departments. + meaning: GAZ:00001092 + Gambia [GAZ:00000907]: + text: Gambia [GAZ:00000907] + description: A country in Western Africa. It is the smallest country on the + African continental mainland and is bordered to the north, east, and south + by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing + through the centre of the country and discharging to the Atlantic Ocean + is the Gambia River. The Gambia is divided into five divisions and one city + (Banjul). The divisions are further subdivided into 37 districts. + meaning: GAZ:00000907 + Gaza Strip [GAZ:00009571]: + text: Gaza Strip [GAZ:00009571] + description: A Palestinian enclave on the eastern coast of the Mediterranean + Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel + on the east and north along a 51 km (32 mi) border. Gaza and the West Bank + are claimed by the de jure sovereign State of Palestine. + meaning: GAZ:00009571 + Georgia [GAZ:00004942]: + text: Georgia [GAZ:00004942] + description: 'A Eurasian country in the Caucasus located at the east coast + of the Black Sea. In the north, Georgia has a 723 km common border with + Russia, specifically with the Northern Caucasus federal district. The following + Russian republics/subdivisions: from west to east: border Georgia: Krasnodar + Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, + Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) + to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to + the south-west. It is a transcontinental country, located at the juncture + of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 + autonomous republics (avtonomiuri respublika), and 1 city (k''alak''i). + The regions are further subdivided into 69 districts (raioni).' + meaning: GAZ:00004942 + Germany [GAZ:00002646]: + text: Germany [GAZ:00002646] + description: A country in Central Europe. It is bordered to the north by the + North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech + Republic; to the south by Austria and Switzerland; and to the west by France, + Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, + Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) + and cities (kreisfreie Stadte). + meaning: GAZ:00002646 + Ghana [GAZ:00000908]: + text: Ghana [GAZ:00000908] + description: A country in West Africa. It borders Cote d'Ivoire to the west, + Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the + south. Ghana is a divided into 10 regions, subdivided into a total of 138 + districts. + meaning: GAZ:00000908 + Gibraltar [GAZ:00003987]: + text: Gibraltar [GAZ:00003987] + description: A British overseas territory located near the southernmost tip + of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory + shares a border with Spain to the north. + meaning: GAZ:00003987 + Glorioso Islands [GAZ:00005808]: + text: Glorioso Islands [GAZ:00005808] + description: A group of islands and rocks totalling 5 km2, in the northern + Mozambique channel, about 160 km northwest of Madagascar. + meaning: GAZ:00005808 + Greece [GAZ:00002945]: + text: Greece [GAZ:00002945] + description: A country in southeastern Europe, situated on the southern end + of the Balkan Peninsula. It has borders with Albania, the former Yugoslav + Republic of Macedonia and Bulgaria to the north, and Turkey to the east. + The Aegean Sea lies to the east and south of mainland Greece, while the + Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin + feature a vast number of islands. Greece consists of thirteen peripheries + subdivided into a total of fifty-one prefectures (nomoi, singular nomos). + There is also one autonomous area, Mount Athos, which borders the periphery + of Central Macedonia. + meaning: GAZ:00002945 + Greenland [GAZ:00001507]: + text: Greenland [GAZ:00001507] + description: A self-governing Danish province located between the Arctic and + Atlantic Oceans, east of the Canadian Arctic Archipelago. + meaning: GAZ:00001507 + Grenada [GAZ:02000573]: + text: Grenada [GAZ:02000573] + description: An island country in the West Indies in the Caribbean Sea at + the southern end of the Grenadines island chain. Grenada consists of the + island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, + and several small islands which lie to the north of the main island and + are a part of the Grenadines. It is located northwest of Trinidad and Tobago, + northeast of Venezuela and southwest of Saint Vincent and the Grenadines. + Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated + population of 112,523 in July 2020. + meaning: GAZ:02000573 + Guadeloupe [GAZ:00067142]: + text: Guadeloupe [GAZ:00067142] + description: "An archipelago and overseas department and region of France\ + \ in the Caribbean. It consists of six inhabited islands\u2014Basse-Terre,\ + \ Grande-Terre, Marie-Galante, La D\xE9sirade, and the two inhabited \xCE\ + les des Saintes\u2014as well as many uninhabited islands and outcroppings.\ + \ It is south of Antigua and Barbuda and Montserrat, and north of Dominica." + meaning: GAZ:00067142 + Guam [GAZ:00003706]: + text: Guam [GAZ:00003706] + description: An organized, unincorporated territory of the United States in + the Micronesia subregion of the western Pacific Ocean. It is the westernmost + point and territory of the United States (reckoned from the geographic center + of the U.S.); in Oceania, it is the largest and southernmost of the Mariana + Islands and the largest island in Micronesia. + meaning: GAZ:00003706 + Guatemala [GAZ:00002936]: + text: Guatemala [GAZ:00002936] + description: A country in Central America bordered by Mexico to the northwest, + the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the + northeast, and Honduras and El Salvador to the southeast. Guatemala is divided + into 22 departments (departamentos) and sub-divided into about 332 municipalities + (municipios). + meaning: GAZ:00002936 + Guernsey [GAZ:00001550]: + text: Guernsey [GAZ:00001550] + description: A British Crown Dependency in the English Channel off the coast + of Normandy. + meaning: GAZ:00001550 + Guinea [GAZ:00000909]: + text: Guinea [GAZ:00000909] + description: A nation in West Africa, formerly known as French Guinea. Guinea's + territory has a curved shape, with its base at the Atlantic Ocean, inland + to the east, and turning south. The base borders Guinea-Bissau and Senegal + to the north, and Mali to the north and north-east; the inland part borders + Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone + to the west of the southern tip. + meaning: GAZ:00000909 + Guinea-Bissau [GAZ:00000910]: + text: Guinea-Bissau [GAZ:00000910] + description: A country in western Africa, and one of the smallest nations + in continental Africa. It is bordered by Senegal to the north, and Guinea + to the south and east, with the Atlantic Ocean to its west. Formerly the + Portuguese colony of Portuguese Guinea, upon independence, the name of its + capital, Bissau, was added to the country's name in order to prevent confusion + between itself and the Republic of Guinea. + meaning: GAZ:00000910 + Guyana [GAZ:00002522]: + text: Guyana [GAZ:00002522] + description: A country in the N of South America. Guyana lies north of the + equator, in the tropics, and is located on the Atlantic Ocean. Guyana is + bordered to the east by Suriname, to the south and southwest by Brazil and + to the west by Venezuela. Guyana is divided into 10 regions. The regions + of Guyana are divided into 27 neighborhood councils. + meaning: GAZ:00002522 + Haiti [GAZ:00003953]: + text: Haiti [GAZ:00003953] + description: A country located in the Greater Antilles archipelago on the + Caribbean island of Hispaniola, which it shares with the Dominican Republic. + Haiti is divided into 10 departments. The departments are further divided + into 41 arrondissements, and 133 communes which serve as second and third + level administrative divisions. + meaning: GAZ:00003953 + Heard Island and McDonald Islands [GAZ:00009718]: + text: Heard Island and McDonald Islands [GAZ:00009718] + description: An Australian external territory comprising a volcanic group + of mostly barren Antarctic islands, about two-thirds of the way from Madagascar + to Antarctica. + meaning: GAZ:00009718 + Honduras [GAZ:00002894]: + text: Honduras [GAZ:00002894] + description: A republic in Central America. The country is bordered to the + west by Guatemala, to the southwest by El Salvador, to the southeast by + Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and + to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. + Honduras is divided into 18 departments. The capital city is Tegucigalpa + Central District of the department of Francisco Morazan. + meaning: GAZ:00002894 + Hong Kong [GAZ:00003203]: + text: Hong Kong [GAZ:00003203] + description: A special administrative region of the People's Republic of China + (PRC). The territory lies on the eastern side of the Pearl River Delta, + bordering Guangdong province in the north and facing the South China Sea + in the east, west and south. Hong Kong was a crown colony of the United + Kingdom from 1842 until the transfer of its sovereignty to the People's + Republic of China in 1997. + meaning: GAZ:00003203 + Howland Island [GAZ:00007120]: + text: Howland Island [GAZ:00007120] + description: An uninhabited coral island located just north of the equator + in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. + The island is almost half way between Hawaii and Australia and is an unincorporated, + unorganized territory of the United States, and is often included as one + of the Phoenix Islands. For statistical purposes, Howland is grouped as + one of the United States Minor Outlying Islands. + meaning: GAZ:00007120 + Hungary [GAZ:00002952]: + text: Hungary [GAZ:00002952] + description: 'A landlocked country in the Carpathian Basin of Central Europe, + bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. + Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: + megye). In addition, the capital city (fovaros), Budapest, is independent + of any county government. The counties are further subdivided into 173 subregions + (kistersegek), and Budapest is comprised of its own subregion. Since 1996, + the counties and City of Budapest have been grouped into 7 regions for statistical + and development purposes. These seven regions constitute NUTS second-level + units of Hungary.' + meaning: GAZ:00002952 + Iceland [GAZ:00000843]: + text: Iceland [GAZ:00000843] + description: A country in northern Europe, comprising the island of Iceland + and its outlying islands in the North Atlantic Ocean between the rest of + Europe and Greenland. + meaning: GAZ:00000843 + India [GAZ:00002839]: + text: India [GAZ:00002839] + description: A country in South Asia. Bounded by the Indian Ocean on the south, + the Arabian Sea on the west, and the Bay of Bengal on the east, India has + a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, + and Bhutan to the north-east; and Bangladesh and Burma to the east. India + is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian + Ocean. India is a federal republic of twenty-eight states and seven Union + Territories. Each state or union territory is divided into basic units of + government and administration called districts. There are nearly 600 districts + in India. The districts in turn are further divided into tehsils and eventually + into villages. + meaning: GAZ:00002839 + Indonesia [GAZ:00003727]: + text: Indonesia [GAZ:00003727] + description: An archipelagic state in Southeast Asia. The country shares land + borders with Papua New Guinea, East Timor and Malaysia. Other neighboring + countries include Singapore, the Philippines, Australia, and the Indian + territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, + five of which have special status. The provinces are subdivided into regencies + (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), + which are further subdivided into subdistricts (kecamatan), and again into + village groupings (either desa or kelurahan). + meaning: GAZ:00003727 + Iran [GAZ:00004474]: + text: Iran [GAZ:00004474] + description: A country in Central Eurasia. Iran is bounded by the Gulf of + Oman and the Persian Gulf to the south and the Caspian Sea to its north. + It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and + Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into + 30 provinces (ostan). The provinces are divided into counties (shahrestan), + and subdivided into districts (bakhsh) and sub-districts (dehestan). + meaning: GAZ:00004474 + Iraq [GAZ:00004483]: + text: Iraq [GAZ:00004483] + description: 'A country in the Middle East spanning most of the northwestern + end of the Zagros mountain range, the eastern part of the Syrian Desert + and the northern part of the Arabian Desert. It shares borders with Kuwait + and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, + Turkey to the north, and Iran to the east. It has a very narrow section + of coastline at Umm Qasr on the Persian Gulf. There are two major flowing + rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates + (or provinces) (muhafazah). The governorates are divided into qadhas (or + districts).' + meaning: GAZ:00004483 + Ireland [GAZ:00002943]: + text: Ireland [GAZ:00002943] + description: A country in north-western Europe. The modern sovereign state + occupies five-sixths of the island of Ireland, which was partitioned in + 1921. It is bordered by Northern Ireland (part of the United Kingdom) to + the north, by the Atlantic Ocean to the west and by the Irish Sea to the + east. Administration follows the 34 "county-level" counties and cities of + Ireland. Of these twenty-nine are counties, governed by county councils + while the five cities of Dublin, Cork, Limerick, Galway and Waterford have + city councils, (previously known as corporations), and are administered + separately from the counties bearing those names. The City of Kilkenny is + the only city in the republic which does not have a "city council"; it is + still a borough but not a county borough and is administered as part of + County Kilkenny. Ireland is split into eight regions for NUTS statistical + purposes. These are not related to the four traditional provinces but are + based on the administrative counties. + meaning: GAZ:00002943 + Isle of Man [GAZ:00052477]: + text: Isle of Man [GAZ:00052477] + description: A Crown dependency of the United Kingdom in the centre of the + Irish Sea. It is not part of the United Kingdom, European Union or United + Nations. + meaning: GAZ:00052477 + Israel [GAZ:00002476]: + text: Israel [GAZ:00002476] + description: 'A country in Western Asia located on the eastern edge of the + Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, + Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, + which are partially administrated by the Palestinian National Authority, + are also adjacent. The State of Israel is divided into six main administrative + districts, known as mehozot (singular mahoz). Districts are further divided + into fifteen sub-districts known as nafot (singular: nafa), which are themselves + partitioned into fifty natural regions.' + meaning: GAZ:00002476 + Italy [GAZ:00002650]: + text: Italy [GAZ:00002650] + description: A country located on the Italian Peninsula in Southern Europe, + and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. + Italy shares its northern Alpine boundary with France, Switzerland, Austria + and Slovenia. The independent states of San Marino and the Vatican City + are enclaves within the Italian Peninsula, while Campione d'Italia is an + Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, + singular regione). Five of these regions have a special autonomous status + that enables them to enact legislation on some of their local matters. It + is further divided into 109 provinces (province) and 8,101 municipalities + (comuni). + meaning: GAZ:00002650 + Jamaica [GAZ:00003781]: + text: Jamaica [GAZ:00003781] + description: A nation of the Greater Antilles. Jamaica is divided into 14 + parishes, which are grouped into three historic counties that have no administrative + relevance. + meaning: GAZ:00003781 + Jan Mayen [GAZ:00005853]: + text: Jan Mayen [GAZ:00005853] + description: 'A volcanic island that is part of the Kingdom of Norway, It + has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus + 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and + 1,000 km west of the Norwegian mainland. The island is mountainous, the + highest summit being the Beerenberg volcano in the north. The isthmus is + the location of the two largest lakes of the island, Sorlaguna (South Lagoon), + and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng + Lagoon). Jan Mayen was formed by the Jan Mayen hotspot.' + meaning: GAZ:00005853 + Japan [GAZ:00002747]: + text: Japan [GAZ:00002747] + description: An island country in East Asia. Located in the Pacific Ocean, + it lies to the east of China, Korea and Russia, stretching from the Sea + of Okhotsk in the north to the East China Sea in the south. + meaning: GAZ:00002747 + Jarvis Island [GAZ:00007118]: + text: Jarvis Island [GAZ:00007118] + description: An uninhabited 4.5 km2 coral atoll located in the South Pacific + Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated + territory of the United States administered from Washington, DC by the United + States Fish and Wildlife Service of the United States Department of the + Interior as part of the National Wildlife Refuge system. Jarvis is one of + the southern Line Islands and for statistical purposes is also grouped as + one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount. + meaning: GAZ:00007118 + Jersey [GAZ:00001551]: + text: Jersey [GAZ:00001551] + description: A British Crown Dependency[6] off the coast of Normandy, France. + As well as the island of Jersey itself, the bailiwick includes two groups + of small islands that are no longer permanently inhabited, the Minquiers + and Ecrehous, and the Pierres de Lecq. + meaning: GAZ:00001551 + Johnston Atoll [GAZ:00007114]: + text: Johnston Atoll [GAZ:00007114] + description: A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 + nm) west of Hawaii. There are four islands located on the coral reef platform, + two natural islands, Johnston Island and Sand Island, which have been expanded + by coral dredging, as well as North Island (Akau) and East Island (Hikina), + artificial islands formed from coral dredging. Johnston is an unincorporated + territory of the United States, administered by the US Fish and Wildlife + Service of the Department of the Interior as part of the United States Pacific + Island Wildlife Refuges. Sits atop Johnston Seamount. + meaning: GAZ:00007114 + Jordan [GAZ:00002473]: + text: Jordan [GAZ:00002473] + description: A country in Southwest Asia, bordered by Syria to the north, + Iraq to the north-east, Israel and the West Bank to the west, and Saudi + Arabia to the east and south. It shares the coastlines of the Dead Sea, + and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided + into 12 provinces called governorates. The Governorates are subdivided into + approximately fifty-two nahias. + meaning: GAZ:00002473 + Juan de Nova Island [GAZ:00005809]: + text: Juan de Nova Island [GAZ:00005809] + description: A 4.4 km2 low, flat, tropical island in the narrowest part of + the Mozambique Channel, about one-third of the way between Madagascar and + Mozambique. + meaning: GAZ:00005809 + Kazakhstan [GAZ:00004999]: + text: Kazakhstan [GAZ:00004999] + description: A country in Central Asia and Europe. It is bordered by Russia, + Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders + on a significant part of the Caspian Sea. Kazakhstan is divided into 14 + provinces and two municipal districts. The provinces of Kazakhstan are divided + into raions. + meaning: GAZ:00004999 + Kenya [GAZ:00001101]: + text: Kenya [GAZ:00001101] + description: A country in Eastern Africa. It is bordered by Ethiopia to the + north, Somalia to the east, Tanzania to the south, Uganda to the west, and + Sudan to the northwest, with the Indian Ocean running along the southeast + border. Kenya comprises eight provinces each headed by a Provincial Commissioner + (centrally appointed by the president). The provinces (mkoa singular mikoa + plural in Swahili) are subdivided into districts (wilaya). There were 69 + districts as of 1999 census. Districts are then subdivided into 497 divisions + (taarafa). The divisions are then subdivided into 2,427 locations (kata) + and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the + status of a full administrative province. + meaning: GAZ:00001101 + Kerguelen Archipelago [GAZ:00005682]: + text: Kerguelen Archipelago [GAZ:00005682] + description: A group of islands in the southern Indian Ocean. It is a territory + of France. They are composed primarily of Tertiary flood basalts and a complex + of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano + at the southern end was active during the late Pleistocene. The Rallier + du Baty Peninsula on the SW tip of the island contains two youthful subglacial + eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active + fumarole field is related to a series of Holocene trachytic lava flows and + lahars that extend beyond the icecap. + meaning: GAZ:00005682 + Kingman Reef [GAZ:00007116]: + text: Kingman Reef [GAZ:00007116] + description: A largely submerged, uninhabited tropical atoll located in the + North Pacific Ocean, roughly half way between Hawaiian Islands and American + Samoa. It is the northernmost of the Northern Line Islands and lies 65 km + NNW of Palmyra Atoll, the next closest island, and has the status of an + unincorporated territory of the United States, administered from Washington, + DC by the US Navy. Sits atop Kingman Reef Seamount. + meaning: GAZ:00007116 + Kiribati [GAZ:00006894]: + text: Kiribati [GAZ:00006894] + description: 'An island nation located in the central tropical Pacific Ocean. + It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 + km2 straddling the equator and bordering the International Date Line to + the east. It is divided into three island groups which have no administrative + function, including a group which unites the Line Islands and the Phoenix + Islands (ministry at London, Christmas). Each inhabited island has its own + council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two + councils on Tabiteuea).' + meaning: GAZ:00006894 + Kosovo [GAZ:00011337]: + text: Kosovo [GAZ:00011337] + description: A country on the Balkan Peninsula. Kosovo borders Central Serbia + to the north and east, Montenegro to the northwest, Albania to the west + and the Republic of Macedonia to the south. Kosovo is divided into 7 districts + (Rreth) and 30 municipalities. Serbia does not recognise the unilateral + secession of Kosovo[8] and considers it a United Nations-governed entity + within its sovereign territory, the Autonomous Province of Kosovo and Metohija. + meaning: GAZ:00011337 + Kuwait [GAZ:00005285]: + text: Kuwait [GAZ:00005285] + description: A sovereign emirate on the coast of the Persian Gulf, enclosed + by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided + into six governorates (muhafazat, singular muhafadhah). + meaning: GAZ:00005285 + Kyrgyzstan [GAZ:00006893]: + text: Kyrgyzstan [GAZ:00006893] + description: A country in Central Asia. Landlocked and mountainous, it is + bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan + to the southwest and China to the east. Kyrgyzstan is divided into seven + provinces (oblast. The capital, Bishkek, and the second large city Osh are + administratively the independent cities (shaar) with a status equal to a + province. Each province comprises a number of districts (raions). + meaning: GAZ:00006893 + Laos [GAZ:00006889]: + text: Laos [GAZ:00006889] + description: A landlocked country in southeast Asia, bordered by Burma (Myanmar) + and China to the northwest, Vietnam to the east, Cambodia to the south, + and Thailand to the west. Laos is divided into sixteen provinces (qwang) + and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided + into districts (muang). + meaning: GAZ:00006889 + Latvia [GAZ:00002958]: + text: Latvia [GAZ:00002958] + description: A country in Northern Europe. Latvia shares land borders with + Estonia to the north and Lithuania to the south, and both Russia and Belarus + to the east. It is separated from Sweden in the west by the Baltic Sea. + The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). + There are also seven cities (lielpilsetas) that have a separate status. + Latvia is also historically, culturally and constitutionally divided in + four or more distinct regions. + meaning: GAZ:00002958 + Lebanon [GAZ:00002478]: + text: Lebanon [GAZ:00002478] + description: 'A small, mostly mountainous country in Western Asia, on the + eastern shore of the Mediterranean Sea. It is bordered by Syria to the north + and east, and Israel to the south. Lebanon is divided into six governorates + (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, + singular: qadaa).' + meaning: GAZ:00002478 + Lesotho [GAZ:00001098]: + text: Lesotho [GAZ:00001098] + description: A land-locked country, entirely surrounded by the Republic of + South Africa. Lesotho is divided into ten districts; these are further subdivided + into 80 constituencies, which consists of 129 local community councils. + meaning: GAZ:00001098 + Liberia [GAZ:00000911]: + text: Liberia [GAZ:00000911] + description: A country on the west coast of Africa, bordered by Sierra Leone, + Guinea, Cote d'Ivoire, and the Atlantic Ocean. + meaning: GAZ:00000911 + Libya [GAZ:00000566]: + text: Libya [GAZ:00000566] + description: A country in North Africa. Bordering the Mediterranean Sea to + the north, Libya lies between Egypt to the east, Sudan to the southeast, + Chad and Niger to the south, and Algeria and Tunisia to the west. There + are thirty-four municipalities of Libya, known by the Arabic term sha'biyat + (singular sha'biyah). These came recently (in the 1990s to replaced old + Baladiyat systam. The Baladiyat system in turn was introduced to replace + the system of muhafazah (governorates or provinces) that existed from the + 1960s to the 1970s. + meaning: GAZ:00000566 + Liechtenstein [GAZ:00003858]: + text: Liechtenstein [GAZ:00003858] + description: A tiny, doubly landlocked alpine country in Western Europe, bordered + by Switzerland to its west and by Austria to its east. The principality + of Liechtenstein is divided into 11 municipalities called Gemeinden (singular + Gemeinde). The Gemeinden mostly consist only of a single town. Five of them + fall within the electoral district Unterland (the lower county), and the + remainder within Oberland (the upper county). + meaning: GAZ:00003858 + Line Islands [GAZ:00007144]: + text: Line Islands [GAZ:00007144] + description: A group of eleven atolls and low coral islands in the central + Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, + while three are United States territories that are grouped with the United + States Minor Outlying Islands. + meaning: GAZ:00007144 + Lithuania [GAZ:00002960]: + text: Lithuania [GAZ:00002960] + description: 'A country located along the south-eastern shore of the Baltic + Sea, sharing borders with Latvia to the north, Belarus to the southeast, + Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. + Lithuania has a three-tier administrative division: the country is divided + into 10 counties (singular apskritis, plural, apskritys) that are further + subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) + which consist of over 500 elderates (singular seniunija, plural seniunijos).' + meaning: GAZ:00002960 + Luxembourg [GAZ:00002947]: + text: Luxembourg [GAZ:00002947] + description: A small landlocked country in western Europe, bordered by Belgium, + France, and Germany. Luxembourg is divided into 3 districts, which are further + divided into 12 cantons and then 116 communes. Twelve of the communes have + city status, of which the city of Luxembourg is the largest. + meaning: GAZ:00002947 + Macau [GAZ:00003202]: + text: Macau [GAZ:00003202] + description: One of the two special administrative regions of the People's + Republic of China, the other being Hong Kong. Macau lies on the western + side of the Pearl River Delta, bordering Guangdong province in the north + and facing the South China Sea in the east and south. Macau is situated + 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the + Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula + is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang + (West River) on the west. It borders the Zhuhai Special Economic Zone in + mainland China. + meaning: GAZ:00003202 + Madagascar [GAZ:00001108]: + text: Madagascar [GAZ:00001108] + description: An island nation in the Indian Ocean off the southeastern coast + of Africa. The main island, also called Madagascar, is the fourth largest + island in the world, and is home to 5% of the world's plant and animal species, + of which more than 80% are endemic to Madagascar. Most notable are the lemur + infraorder of primates, the carnivorous fossa, three endemic bird families + and six endemic baobab species. Madagascar is divided into six autonomous + provinces (faritany mizakatena), and 22 regions. The regions are further + subdivided into 116 districts, 1,548 communes, and 16,969 fokontany. + meaning: GAZ:00001108 + Malawi [GAZ:00001105]: + text: Malawi [GAZ:00001105] + description: A country in southeastern Africa. It is bordered by Zambia to + the north-west, Tanzania to the north and Mozambique, which surrounds it + on the east, south and west. Malawi is divided into three regions (the Northern, + Central and Southern regions), which are further divided into twenty-seven + districts, which in turn are further divided into 137 traditional authorities + and 68 sub-chiefdoms. + meaning: GAZ:00001105 + Malaysia [GAZ:00003902]: + text: Malaysia [GAZ:00003902] + description: A country in southeastern Africa. It is bordered by Zambia to + the north-west, Tanzania to the north and Mozambique, which surrounds it + on the east, south and west. Malawi is divided into three regions (the Northern, + Central and Southern regions), which are further divided into twenty-seven + districts, which in turn are further divided into 137 traditional authorities + and 68 sub-chiefdoms. + meaning: GAZ:00003902 + Maldives [GAZ:00006924]: + text: Maldives [GAZ:00006924] + description: An archipelago which consists of approximately 1,196 coral islands + grouped in a double chain of 27 atolls, spread over roughly 90,000 km2. + meaning: GAZ:00006924 + Mali [GAZ:00000584]: + text: Mali [GAZ:00000584] + description: A landlocked country in northern Africa. It borders Algeria on + the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the + south, Guinea on the south-west, and Senegal and Mauritania on the west. + Mali is divided into 8 regions (regions) and 1 district, and subdivided + into 49 cercles, totalling 288 arrondissements. + meaning: GAZ:00000584 + Malta [GAZ:00004017]: + text: Malta [GAZ:00004017] + description: A Southern European country and consists of an archipelago situated + centrally in the Mediterranean. + meaning: GAZ:00004017 + Marshall Islands [GAZ:00007161]: + text: Marshall Islands [GAZ:00007161] + description: 'An archipelago that consists of twenty-nine atolls and five + isolated islands. The most important atolls and islands form two groups: + the Ratak Chain and the Ralik Chain (meaning "sunrise" and "sunset" chains). + Two-thirds of the nation''s population lives on Majuro (which is also the + capital) and Ebeye. The outer islands are sparsely populated.' + meaning: GAZ:00007161 + Martinique [GAZ:00067143]: + text: Martinique [GAZ:00067143] + description: An island and an overseas department/region and single territorial + collectivity of France. + meaning: GAZ:00067143 + Mauritania [GAZ:00000583]: + text: Mauritania [GAZ:00000583] + description: A country in North-West Africa. It is bordered by the Atlantic + Ocean on the west, by Senegal on the southwest, by Mali on the east and + southeast, by Algeria on the northeast, and by Western Sahara on the northwest + (most of which is occupied by Morocco). The capital and largest city is + Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 + regions (regions) and one capital district, which in turn are subdivided + into 44 departments (departements). + meaning: GAZ:00000583 + Mauritius [GAZ:00003745]: + text: Mauritius [GAZ:00003745] + description: An island nation off the coast of the African continent in the + southwest Indian Ocean, about 900 km east of Madagascar. In addition to + the island of Mauritius, the republic includes the islands of St. Brandon, + Rodrigues and the Agalega Islands. + meaning: GAZ:00003745 + Mayotte [GAZ:00003943]: + text: Mayotte [GAZ:00003943] + description: An overseas collectivity of France consisting of a main island, + Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and + several islets around these two. + meaning: GAZ:00003943 + Mexico [GAZ:00002852]: + text: Mexico [GAZ:00002852] + description: A federal constitutional republic in North America. It is bounded + on the north by the United States; on the south and west by the North Pacific + Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and + on the east by the Gulf of Mexico. The United Mexican States comprise a + federation of thirty-one states and a federal district, the capital Mexico + City. + meaning: GAZ:00002852 + Micronesia [GAZ:00005862]: + text: Micronesia [GAZ:00005862] + description: A subregion of Oceania, comprising hundreds of small islands + in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua + New Guinea and Melanesia to the west and southwest, and Polynesia to the + east. + meaning: GAZ:00005862 + Midway Islands [GAZ:00007112]: + text: Midway Islands [GAZ:00007112] + description: A 6.2 km2 atoll located in the North Pacific Ocean (near the + northwestern end of the Hawaiian archipelago). It is an unincorporated territory + of the United States, designated an insular area under the authority of + the US Department of the Interior. + meaning: GAZ:00007112 + Moldova [GAZ:00003897]: + text: Moldova [GAZ:00003897] + description: A landlocked country in Eastern Europe, located between Romania + to the west and Ukraine to the north, east and south. Moldova is divided + into thirty-two districts (raioane, singular raion); three municipalities + (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). + The cities of Comrat and Tiraspol also have municipality status, however + not as first-tier subdivisions of Moldova, but as parts of the regions of + Gagauzia and Transnistria, respectively. The status of Transnistria is however + under dispute. Although it is de jure part of Moldova and is recognized + as such by the international community, Transnistria is not de facto under + the control of the central government of Moldova. It is administered by + an unrecognized breakaway authority under the name Pridnestrovian Moldovan + Republic. + meaning: GAZ:00003897 + Monaco [GAZ:00003857]: + text: Monaco [GAZ:00003857] + description: A small country that is completely bordered by France to the + north, west, and south; to the east it is bordered by the Mediterranean + Sea. It consists of a single municipality (commune) currently divided into + 4 quartiers and 10 wards. + meaning: GAZ:00003857 + Mongolia [GAZ:00008744]: + text: Mongolia [GAZ:00008744] + description: A country in East-Central Asia. The landlocked country borders + Russia to the north and China to the south. The capital and largest city + is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are + in turn divided into 315 sums (districts). The capital Ulan Bator is administrated + separately as a khot (municipality) with provincial status. + meaning: GAZ:00008744 + Montenegro [GAZ:00006898]: + text: Montenegro [GAZ:00006898] + description: A country located in Southeastern Europe. It has a coast on the + Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina + to the northwest, Serbia and its partially recognized breakaway southern + province of Kosovo to the northeast and Albania to the southeast. Its capital + and largest city is Podgorica. Montenegro is divided into twenty-one municipalities + (opstina), and two urban municipalities, subdivisions of Podgorica municipality. + meaning: GAZ:00006898 + Montserrat [GAZ:00003988]: + text: Montserrat [GAZ:00003988] + description: A British overseas territory located in the Leeward Islands. + Montserrat is divided into three parishes. + meaning: GAZ:00003988 + Morocco [GAZ:00000565]: + text: Morocco [GAZ:00000565] + description: A country in North Africa. It has a coast on the Atlantic Ocean + that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco + has international borders with Algeria to the east, Spain to the north (a + water border through the Strait and land borders with two small Spanish + autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco + is divided into 16 regions, and subdivided into 62 prefectures and provinces. + Because of the conflict over Western Sahara, the status of both regions + of "Saguia el-Hamra" and "Rio de Oro" is disputed. + meaning: GAZ:00000565 + Mozambique [GAZ:00001100]: + text: Mozambique [GAZ:00001100] + description: A country in southeastern Africa bordered by the Indian Ocean + to the east, Tanzania to the north, Malawi and Zambia to the northwest, + Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique + is divided into ten provinces (provincias) and one capital city (cidade + capital) with provincial status. The provinces are subdivided into 129 districts + (distritos). Districts are further divided in "Postos Administrativos" (Administrative + Posts) and these in Localidades (Localities) the lowest geographical level + of central state administration. + meaning: GAZ:00001100 + Myanmar [GAZ:00006899]: + text: Myanmar [GAZ:00006899] + description: A country in SE Asia that is bordered by China on the north, + Laos on the east, Thailand on the southeast, Bangladesh on the west, and + India on the northwest, with the Bay of Bengal to the southwest. Myanmar + is divided into seven states and seven divisions. The administrative divisions + are further subdivided into districts, which are further subdivided into + townships, wards, and villages. + meaning: GAZ:00006899 + Namibia [GAZ:00001096]: + text: Namibia [GAZ:00001096] + description: A country in southern Africa on the Atlantic coast. It shares + borders with Angola and Zambia to the north, Botswana to the east, and South + Africa to the south. Namibia is divided into 13 regions and subdivided into + 102 constituencies. + meaning: GAZ:00001096 + Nauru [GAZ:00006900]: + text: Nauru [GAZ:00006900] + description: An island nation in the Micronesian South Pacific. The nearest + neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. + Nauru is divided into fourteen administrative districts which are grouped + into eight electoral constituencies. + meaning: GAZ:00006900 + Navassa Island [GAZ:00007119]: + text: Navassa Island [GAZ:00007119] + description: A small, uninhabited island in the Caribbean Sea, and is an unorganized + unincorporated territory of the United States, which administers it through + the US Fish and Wildlife Service. The island is also claimed by Haiti. + meaning: GAZ:00007119 + Nepal [GAZ:00004399]: + text: Nepal [GAZ:00004399] + description: A landlocked nation in South Asia. It is bordered by the Tibet + Autonomous Region of the People's Republic of China to the northeast and + India to the south and west; it is separated from Bhutan by the Indian State + of Sikkim and from Bangladesh by a small strip of the Indian State of West + Bengal, known as the "Chicken's Neck". The Himalaya mountain range runs + across Nepal's north and western parts, and eight of the world's ten highest + mountains, including the highest, Mount Everest are situated within its + territory. Nepal is divided into 14 zones and 75 districts, grouped into + 5 development regions. + meaning: GAZ:00004399 + Netherlands [GAZ:00002946]: + text: Netherlands [GAZ:00002946] + description: The European part of the Kingdom of the Netherlands. It is bordered + by the North Sea to the north and west, Belgium to the south, and Germany + to the east. The Netherlands is divided into twelve administrative regions, + called provinces. All provinces of the Netherlands are divided into municipalities + (gemeenten), together 443 (2007). + meaning: GAZ:00002946 + New Caledonia [GAZ:00005206]: + text: New Caledonia [GAZ:00005206] + description: A "sui generis collectivity" (in practice an overseas territory) + of France, made up of a main island (Grande Terre), the Loyalty Islands, + and several smaller islands. It is located in the region of Melanesia in + the southwest Pacific. Administratively, the archipelago is divided into + three provinces, and then into 33 communes. + meaning: GAZ:00005206 + New Zealand [GAZ:00000469]: + text: New Zealand [GAZ:00000469] + description: A nation in the south-western Pacific Ocean comprising two large + islands (the North Island and the South Island) and numerous smaller islands, + most notably Stewart Island/Rakiura and the Chatham Islands. + meaning: GAZ:00000469 + Nicaragua [GAZ:00002978]: + text: Nicaragua [GAZ:00002978] + description: A republic in Central America. It is also the least densely populated + with a demographic similar in size to its smaller neighbors. The country + is bordered by Honduras to the north and by Costa Rica to the south. The + Pacific Ocean lies to the west of the country, while the Caribbean Sea lies + to the east. For administrative purposes it is divided into 15 departments + (departamentos) and two self-governing regions (autonomous communities) + based on the Spanish model. The departments are then subdivided into 153 + municipios (municipalities). The two autonomous regions are Region Autonoma + del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred + to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 + they formed the single department of Zelaya. + meaning: GAZ:00002978 + Niger [GAZ:00000585]: + text: Niger [GAZ:00000585] + description: A landlocked country in Western Africa, named after the Niger + River. It borders Nigeria and Benin to the south, Burkina Faso and Mali + to the west, Algeria and Libya to the north and Chad to the east. The capital + city is Niamey. Niger is divided into 7 departments and one capital district. + The departments are subdivided into 36 arrondissements and further subdivided + into 129 communes. + meaning: GAZ:00000585 + Nigeria [GAZ:00000912]: + text: Nigeria [GAZ:00000912] + description: A federal constitutional republic comprising thirty-six states + and one Federal Capital Territory. The country is located in West Africa + and shares land borders with the Republic of Benin in the west, Chad and + Cameroon in the east, and Niger in the north. Its coast lies on the Gulf + of Guinea, part of the Atlantic Ocean, in the south. The capital city is + Abuja. Nigeria is divided into thirty-six states and one Federal Capital + Territory, which are further sub-divided into 774 Local Government Areas + (LGAs). + meaning: GAZ:00000912 + Niue [GAZ:00006902]: + text: Niue [GAZ:00006902] + description: An island nation located in the South Pacific Ocean. Although + self-governing, Niue is in free association with New Zealand, meaning that + the Sovereign in Right of New Zealand is also Niue's head of state. + meaning: GAZ:00006902 + Norfolk Island [GAZ:00005908]: + text: Norfolk Island [GAZ:00005908] + description: A Territory of Australia that includes Norfolk Island and neighboring + islands. + meaning: GAZ:00005908 + North Korea [GAZ:00002801]: + text: North Korea [GAZ:00002801] + description: A state in East Asia in the northern half of the Korean Peninsula, + with its capital in the city of Pyongyang. To the south and separated by + the Korean Demilitarized Zone is South Korea, with which it formed one nation + until division following World War II. At its northern Amnok River border + are China and, separated by the Tumen River in the extreme north-east, Russia. + meaning: GAZ:00002801 + North Macedonia [GAZ:00006895]: + text: North Macedonia [GAZ:00006895] + description: A landlocked country on the Balkan peninsula in southeastern + Europe. It is bordered by Serbia and Kosovo to the north, Albania to the + west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic + of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), + 10 of which comprise Greater Skopje. This is reduced from the previous 123 + municipalities established in 1996-09. Prior to this, local government was + organised into 34 administrative districts. + meaning: GAZ:00006895 + North Sea [GAZ:00002284]: + text: North Sea [GAZ:00002284] + description: A sea situated between the eastern coasts of the British Isles + and the western coast of Europe. + meaning: GAZ:00002284 + Northern Mariana Islands [GAZ:00003958]: + text: Northern Mariana Islands [GAZ:00003958] + description: A group of 15 islands about three-quarters of the way from Hawaii + to the Philippines. + meaning: GAZ:00003958 + Norway [GAZ:00002699]: + text: Norway [GAZ:00002699] + description: A country and constitutional monarchy in Northern Europe that + occupies the western portion of the Scandinavian Peninsula. It is bordered + by Sweden, Finland, and Russia. The Kingdom of Norway also includes the + Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty + over Svalbard is based upon the Svalbard Treaty, but that treaty does not + apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter + I Island and Queen Maud Land in Antarctica are external dependencies, but + those three entities do not form part of the kingdom. + meaning: GAZ:00002699 + Oman [GAZ:00005283]: + text: Oman [GAZ:00005283] + description: A country in southwest Asia, on the southeast coast of the Arabian + Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia + on the west, and Yemen on the southwest. The coast is formed by the Arabian + Sea on the south and east, and the Gulf of Oman on the northeast. The country + also contains Madha, an exclave enclosed by the United Arab Emirates, and + Musandam, an exclave also separated by Emirati territory. Oman is divided + into four governorates (muhafazah) and five regions (mintaqat). The regions + are subdivided into provinces (wilayat). + meaning: GAZ:00005283 + Pakistan [GAZ:00005246]: + text: Pakistan [GAZ:00005246] + description: A country in Middle East which lies on the Iranian Plateau and + some parts of South Asia. It is located in the region where South Asia converges + with Central Asia and the Middle East. It has a 1,046 km coastline along + the Arabian Sea in the south, and is bordered by Afghanistan and Iran in + the west, India in the east and China in the far northeast. Pakistan is + subdivided into four provinces and two territories. In addition, the portion + of Kashmir that is administered by the Pakistani government is divided into + two separate administrative units. The provinces are divided into a total + of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly + equivalent to counties). Tehsils may contain villages or municipalities. + There are over five thousand local governments in Pakistan. + meaning: GAZ:00005246 + Palau [GAZ:00006905]: + text: Palau [GAZ:00006905] + description: A nation that consists of eight principal islands and more than + 250 smaller ones lying roughly 500 miles southeast of the Philippines. + meaning: GAZ:00006905 + Panama [GAZ:00002892]: + text: Panama [GAZ:00002892] + description: The southernmost country of Central America. Situated on an isthmus, + some categorize it as a transcontinental nation connecting the north and + south part of America. It borders Costa Rica to the north-west, Colombia + to the south-east, the Caribbean Sea to the north and the Pacific Ocean + to the south. Panama's major divisions are nine provinces and five indigenous + territories (comarcas indigenas). The provincial borders have not changed + since they were determined at independence in 1903. The provinces are divided + into districts, which in turn are subdivided into sections called corregimientos. + Configurations of the corregimientos are changed periodically to accommodate + population changes as revealed in the census reports. + meaning: GAZ:00002892 + Papua New Guinea [GAZ:00003922]: + text: Papua New Guinea [GAZ:00003922] + description: A country in Oceania that comprises the eastern half of the island + of New Guinea and its offshore islands in Melanesia (a region of the southwestern + Pacific Ocean north of Australia). + meaning: GAZ:00003922 + Paracel Islands [GAZ:00010832]: + text: Paracel Islands [GAZ:00010832] + description: A group of small islands and reefs in the South China Sea, about + one-third of the way from Vietnam to the Philippines. + meaning: GAZ:00010832 + Paraguay [GAZ:00002933]: + text: Paraguay [GAZ:00002933] + description: A landlocked country in South America. It lies on both banks + of the Paraguay River, bordering Argentina to the south and southwest, Brazil + to the east and northeast, and Bolivia to the northwest, and is located + in the very heart of South America. Paraguay consists of seventeen departments + and one capital district (distrito capital). Each department is divided + into districts. + meaning: GAZ:00002933 + Peru [GAZ:00002932]: + text: Peru [GAZ:00002932] + description: A country in western South America. It is bordered on the north + by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, + on the south by Chile, and on the west by the Pacific Ocean. Peru is divided + into 25 regions and the province of Lima. These regions are subdivided into + provinces, which are composed of districts (provincias and distritos). There + are 195 provinces and 1833 districts in Peru. The Lima Province, located + in the central coast of the country, is unique in that it doesn't belong + to any of the twenty-five regions. The city of Lima, which is the nation's + capital, is located in this province. Callao is its own region, even though + it only contains one province, the Constitutional Province of Callao. + meaning: GAZ:00002932 + Philippines [GAZ:00004525]: + text: Philippines [GAZ:00004525] + description: 'An archipelagic nation located in Southeast Asia. The Philippine + archipelago comprises 7,107 islands in the western Pacific Ocean, bordering + countries such as Indonesia, Malaysia, Palau and the Republic of China, + although it is the only Southeast Asian country to share no land borders + with its neighbors. The Philippines is divided into three island groups: + Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, + 136 cities, 1,494 municipalities and 41,995 barangays.' + meaning: GAZ:00004525 + Pitcairn Islands [GAZ:00005867]: + text: Pitcairn Islands [GAZ:00005867] + description: A group of four islands in the southern Pacific Ocean. The Pitcairn + Islands form the southeasternmost extension of the geological archipelago + of the Tuamotus of French Polynesia. + meaning: GAZ:00005867 + Poland [GAZ:00002939]: + text: Poland [GAZ:00002939] + description: A country in Central Europe. Poland is bordered by Germany to + the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus + and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a + Russian exclave, to the north. The administrative division of Poland since + 1999 has been based on three levels of subdivision. The territory of Poland + is divided into voivodeships (provinces); these are further divided into + powiats (counties), and these in turn are divided into gminas (communes + or municipalities). Major cities normally have the status of both gmina + and powiat. Poland currently has 16 voivodeships, 379 powiats (including + 65 cities with powiat status), and 2,478 gminas. + meaning: GAZ:00002939 + Portugal [GAZ:00004126]: + text: Portugal [GAZ:00004126] + description: That part of the Portugese Republic that occupies the W part + of the Iberian Peninsula, and immediately adjacent islands. + meaning: GAZ:00004126 + Puerto Rico [GAZ:00006935]: + text: Puerto Rico [GAZ:00006935] + description: A semi-autonomous territory composed of an archipelago in the + northeastern Caribbean, east of the Dominican Republic and west of the Virgin + Islands, approximately 2,000 km off the coast of Florida (the nearest of + the mainland United States). + meaning: GAZ:00006935 + Qatar [GAZ:00005286]: + text: Qatar [GAZ:00005286] + description: 'An Arab emirate in Southwest Asia, occupying the small Qatar + Peninsula on the northeasterly coast of the larger Arabian Peninsula. It + is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds + the state. Qatar is divided into ten municipalities (Arabic: baladiyah), + which are further divided into zones (districts).' + meaning: GAZ:00005286 + Republic of the Congo [GAZ:00001088]: + text: Republic of the Congo [GAZ:00001088] + description: A country in Central Africa. It is bordered by Gabon, Cameroon, + the Central African Republic, the Democratic Republic of the Congo, the + Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic + of the Congo is divided into 10 regions (regions) and one commune, the capital + Brazzaville. The regions are subdivided into forty-six districts. + meaning: GAZ:00001088 + Reunion [GAZ:00003945]: + text: Reunion [GAZ:00003945] + description: An island, located in the Indian Ocean east of Madagascar, about + 200 km south west of Mauritius, the nearest island. + meaning: GAZ:00003945 + Romania [GAZ:00002951]: + text: Romania [GAZ:00002951] + description: A country in Southeastern Europe. It shares a border with Hungary + and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, + and Bulgaria to the south. Romania has a stretch of sea coast along the + Black Sea. It is located roughly in the lower basin of the Danube and almost + all of the Danube Delta is located within its territory. Romania is divided + into forty-one counties (judete), as well as the municipality of Bucharest + (Bucuresti) - which is its own administrative unit. The country is further + subdivided into 319 cities and 2686 communes (rural localities). + meaning: GAZ:00002951 + Ross Sea [GAZ:00023304]: + text: Ross Sea [GAZ:00023304] + description: A large embayment of the Southern Ocean, extending deeply into + Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck + on the east, at 158degW. + meaning: GAZ:00023304 + Russia [GAZ:00002721]: + text: Russia [GAZ:00002721] + description: 'A transcontinental country extending over much of northern Eurasia. + Russia shares land borders with the following countries (counter-clockwise + from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania + (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, + Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation + comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais + (territories), 4 autonomous okrugs (autonomous districts), one autonomous + oblast, and two federal cities. The federal subjects are grouped into seven + federal districts. These subjects are divided into districts (raions), cities/towns + and urban-type settlements, and, at level 4, selsovets (rural councils), + towns and urban-type settlements under the jurisdiction of the district + and city districts.' + meaning: GAZ:00002721 + Rwanda [GAZ:00001087]: + text: Rwanda [GAZ:00001087] + description: A small landlocked country in the Great Lakes region of east-central + Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo + and Tanzania. Rwanda is divided into five provinces (intara) and subdivided + into thirty districts (akarere). The districts are divided into sectors + (imirenge). + meaning: GAZ:00001087 + Saint Helena [GAZ:00000849]: + text: Saint Helena [GAZ:00000849] + description: An island of volcanic origin and a British overseas territory + in the South Atlantic Ocean. + meaning: GAZ:00000849 + Saint Kitts and Nevis [GAZ:00006906]: + text: Saint Kitts and Nevis [GAZ:00006906] + description: 'A federal two-island nation in the West Indies. Located in the + Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward + Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, + Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast + are Antigua and Barbuda, and to the southeast is the small uninhabited island + of Redonda, and the island of Montserrat. The federation of Saint Kitts + and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts + and five on Nevis.' + meaning: GAZ:00006906 + Saint Lucia [GAZ:00006909]: + text: Saint Lucia [GAZ:00006909] + description: An island nation in the eastern Caribbean Sea on the boundary + with the Atlantic Ocean. + meaning: GAZ:00006909 + Saint Pierre and Miquelon [GAZ:00003942]: + text: Saint Pierre and Miquelon [GAZ:00003942] + description: An Overseas Collectivity of France located in a group of small + islands in the North Atlantic Ocean, the main ones being Saint Pierre and + Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and + Miquelon became an overseas department in 1976, but its status changed to + that of an Overseas collectivity in 1985. + meaning: GAZ:00003942 + Saint Martin [GAZ:00005841]: + text: Saint Martin [GAZ:00005841] + description: An overseas collectivity of France that came into being on 2007-02-22, + encompassing the northern parts of the island of Saint Martin and neighboring + islets. The southern part of the island, Sint Maarten, is part of the Netherlands + Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe. + meaning: GAZ:00005841 + Saint Vincent and the Grenadines [GAZ:02000565]: + text: Saint Vincent and the Grenadines [GAZ:02000565] + description: An island nation in the Lesser Antilles chain of the Caribbean + Sea. + meaning: GAZ:02000565 + Samoa [GAZ:00006910]: + text: Samoa [GAZ:00006910] + description: A country governing the western part of the Samoan Islands archipelago + in the South Pacific Ocean. Samoa is made up of eleven itumalo (political + districts). + meaning: GAZ:00006910 + San Marino [GAZ:00003102]: + text: San Marino [GAZ:00003102] + description: A country in the Apennine Mountains. It is a landlocked enclave, + completely surrounded by Italy. San Marino is an enclave in Italy, on the + border between the regioni of Emilia Romagna and Marche. Its topography + is dominated by the Apennines mountain range. San Marino is divided into + nine municipalities, known locally as Castelli (singular castello). + meaning: GAZ:00003102 + Sao Tome and Principe [GAZ:00006927]: + text: Sao Tome and Principe [GAZ:00006927] + description: 'An island nation in the Gulf of Guinea, off the western equatorial + coast of Africa. It consists of two islands: Sao Tome and Principe, located + about 140 km apart and about 250 and 225 km respectively, off of the northwestern + coast of Gabon. Both islands are part of an extinct volcanic mountain range. + Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The + provinces are further divided into seven districts, six on Sao Tome and + one on Principe (with Principe having self-government since 1995-04-29).' + meaning: GAZ:00006927 + Saudi Arabia [GAZ:00005279]: + text: Saudi Arabia [GAZ:00005279] + description: A country on the Arabian Peninsula. It is bordered by Jordan + on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, + and the United Arab Emirates on the east, Oman on the southeast, and Yemen + on the south. The Persian Gulf lies to the northeast and the Red Sea to + its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; + singular mintaqah). Each is then divided into Governorates. + meaning: GAZ:00005279 + Senegal [GAZ:00000913]: + text: Senegal [GAZ:00000913] + description: A country south of the Senegal River in western Africa. Senegal + is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali + to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies + almost entirely within Senegal, surrounded on the north, east and south; + from its western coast Gambia's territory follows the Gambia River more + than 300 km inland. Dakar is the capital city of Senegal, located on the + Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided + into 11 regions and further subdivided into 34 Departements, 103 Arrondissements + (neither of which have administrative function) and by Collectivites Locales. + meaning: GAZ:00000913 + Serbia [GAZ:00002957]: + text: Serbia [GAZ:00002957] + description: 'A landlocked country in Central and Southeastern Europe, covering + the southern part of the Pannonian Plain and the central part of the Balkan + Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria + to the east; Republic of Macedonia, Montenegro to the south; Croatia and + Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided + into 29 districts plus the City of Belgrade. The districts and the city + of Belgrade are further divided into municipalities. Serbia has two autonomous + provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), + and Vojvodina in the north (7 districts, 46 municipalities).' + meaning: GAZ:00002957 + Seychelles [GAZ:00006922]: + text: Seychelles [GAZ:00006922] + description: An archipelagic island country in the Indian Ocean at the eastern + edge of the Somali Sea. It consists of 115 islands. + meaning: GAZ:00006922 + Sierra Leone [GAZ:00000914]: + text: Sierra Leone [GAZ:00000914] + description: A country in West Africa. It is bordered by Guinea in the north + and east, Liberia in the southeast, and the Atlantic Ocean in the southwest + and west. The Republic of Sierra Leone is composed of 3 provinces and one + area called the Western Area; the provinces are further divided into 12 + districts. The Western Area is also divided into 2 districts. + meaning: GAZ:00000914 + Singapore [GAZ:00003923]: + text: Singapore [GAZ:00003923] + description: An island nation located at the southern tip of the Malay Peninsula. + It lies 137 km north of the Equator, south of the Malaysian State of Johor + and north of Indonesia's Riau Islands. Singapore consists of 63 islands, + including mainland Singapore. There are two man-made connections to Johor, + Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in + the west. Since 2001-11-24, Singapore has had an administrative subdivision + into 5 districts. It is also divided into five Regions, urban planning subdivisions + with no administrative role. + meaning: GAZ:00003923 + Sint Maarten [GAZ:00012579]: + text: Sint Maarten [GAZ:00012579] + description: One of five island areas (Eilandgebieden) of the Netherlands + Antilles, encompassing the southern half of the island of Saint Martin/Sint + Maarten. + meaning: GAZ:00012579 + Slovakia [GAZ:00002956]: + text: Slovakia [GAZ:00002956] + description: A landlocked country in Central Europe. The Slovak Republic borders + the Czech Republic and Austria to the west, Poland to the north, Ukraine + to the east and Hungary to the south. The largest city is its capital, Bratislava. + Slovakia is subdivided into 8 kraje (singular - kraj, usually translated + as regions. The kraje are subdivided into many okresy (singular okres, usually + translated as districts). Slovakia currently has 79 districts. + meaning: GAZ:00002956 + Slovenia [GAZ:00002955]: + text: Slovenia [GAZ:00002955] + description: A country in southern Central Europe bordering Italy to the west, + the Adriatic Sea to the southwest, Croatia to the south and east, Hungary + to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. + As of 2005-05 Slovenia is divided into 12 statistical regions for legal + and statistical purposes. Slovenia is divided into 210 local municipalities, + eleven of which have urban status. + meaning: GAZ:00002955 + Solomon Islands [GAZ:00005275]: + text: Solomon Islands [GAZ:00005275] + description: A nation in Melanesia, east of Papua New Guinea, consisting of + nearly one thousand islands. Together they cover a land mass of 28,400 km2. + The capital is Honiara, located on the island of Guadalcanal. + meaning: GAZ:00005275 + Somalia [GAZ:00001104]: + text: Somalia [GAZ:00001104] + description: A country located in the Horn of Africa. It is bordered by Djibouti + to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on + its north, the Indian Ocean at its east, and Ethiopia to the west. Prior + to the civil war, Somalia was divided into eighteen regions (gobollada, + singular gobol), which were in turn subdivided into districts. On a de facto + basis, northern Somalia is now divided up among the quasi-independent states + of Puntland, Somaliland, Galmudug and Maakhir. + meaning: GAZ:00001104 + South Africa [GAZ:00001094]: + text: South Africa [GAZ:00001094] + description: 'A country located at the southern tip of Africa. It borders + the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, + Swaziland, and Lesotho, an independent enclave surrounded by South African + territory. It is divided into nine provinces which are further subdivided + into 52 districts: 6 metropolitan and 46 district municipalities. The 46 + district municipalities are further subdivided into 231 local municipalities. + The district municipalities also contain 20 district management areas (mostly + game parks) that are directly governed by the district municipalities. The + six metropolitan municipalities perform the functions of both district and + local municipalities.' + meaning: GAZ:00001094 + South Georgia and the South Sandwich Islands [GAZ:00003990]: + text: South Georgia and the South Sandwich Islands [GAZ:00003990] + description: A British overseas territory in the southern Atlantic Ocean. + It iconsists of South Georgia and the Sandwich Islands, some 640 km to the + SE. + meaning: GAZ:00003990 + South Korea [GAZ:00002802]: + text: South Korea [GAZ:00002802] + description: A republic in East Asia, occupying the southern half of the Korean + Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous + province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 + special city (teukbyeolsi). These are further subdivided into a variety + of smaller entities, including cities (si), counties (gun), districts (gu), + towns (eup), townships (myeon), neighborhoods (dong) and villages (ri). + meaning: GAZ:00002802 + South Sudan [GAZ:00233439]: + text: South Sudan [GAZ:00233439] + description: A state located in Africa with Juba as its capital city. It's + bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic + of the Congo to the south, and the Central African Republic to the west + and Sudan to the North. Southern Sudan includes the vast swamp region of + the Sudd formed by the White Nile, locally called the Bahr el Jebel. + meaning: GAZ:00233439 + Spain [GAZ:00003936]: + text: Spain [GAZ:00003936] + description: That part of the Kingdom of Spain that occupies the Iberian Peninsula + plus the Balaeric Islands. The Spanish mainland is bordered to the south + and east almost entirely by the Mediterranean Sea (except for a small land + boundary with Gibraltar); to the north by France, Andorra, and the Bay of + Biscay; and to the west by the Atlantic Ocean and Portugal. + meaning: GAZ:00003936 + Spratly Islands [GAZ:00010831]: + text: Spratly Islands [GAZ:00010831] + description: A group of >100 islands located in the Southeastern Asian group + of reefs and islands in the South China Sea, about two-thirds of the way + from southern Vietnam to the southern Philippines. + meaning: GAZ:00010831 + Sri Lanka [GAZ:00003924]: + text: Sri Lanka [GAZ:00003924] + description: An island nation in South Asia, located about 31 km off the southern + coast of India. Sri Lanka is divided into 9 provinces and 25 districts. + Districts are divided into Divisional Secretariats. + meaning: GAZ:00003924 + State of Palestine [GAZ:00002475]: + text: State of Palestine [GAZ:00002475] + description: The territory under the administration of the Palestine National + Authority, as established by the Oslo Accords. The PNA divides the Palestinian + territories into 16 governorates. + meaning: GAZ:00002475 + Sudan [GAZ:00000560]: + text: Sudan [GAZ:00000560] + description: A country in North Africa. It is bordered by Egypt to the north, + the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and + Uganda to the southeast, Democratic Republic of the Congo and the Central + African Republic to the southwest, Chad to the west and Libya to the northwest. + Sudan is divided into twenty-six states (wilayat, singular wilayah) which + in turn are subdivided into 133 districts. + meaning: GAZ:00000560 + Suriname [GAZ:00002525]: + text: Suriname [GAZ:00002525] + description: A country in northern South America. It is situated between French + Guiana to the east and Guyana to the west. The southern border is shared + with Brazil and the northern border is the Atlantic coast. The southernmost + border with French Guiana is disputed along the Marowijne river. Suriname + is divided into 10 districts, each of which is divided into Ressorten. + meaning: GAZ:00002525 + Svalbard [GAZ:00005396]: + text: Svalbard [GAZ:00005396] + description: An archipelago of continental islands lying in the Arctic Ocean + north of mainland Europe, about midway between Norway and the North Pole. + meaning: GAZ:00005396 + Swaziland [GAZ:00001099]: + text: Swaziland [GAZ:00001099] + description: A small, landlocked country in Africa embedded between South + Africa in the west, north and south and Mozambique in the east. Swaziland + is divided into four districts, each of which is divided into Tinkhundla + (singular, Inkhundla). + meaning: GAZ:00001099 + Sweden [GAZ:00002729]: + text: Sweden [GAZ:00002729] + description: A Nordic country on the Scandinavian Peninsula in Northern Europe. + It has borders with Norway (west and north) and Finland (northeast). Sweden + is a unitary state, currently divided into twenty-one counties (lan). Each + county further divides into a number of municipalities or kommuner, with + a total of 290 municipalities in 2004. + meaning: GAZ:00002729 + Switzerland [GAZ:00002941]: + text: Switzerland [GAZ:00002941] + description: 'A federal republic in Europe. Switzerland is bordered by Germany, + France, Italy, Austria and Liechtenstein. The Swiss Confederation consists + of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within + Switzerland there are two enclaves: Busingen belongs to Germany, Campione + d''Italia belongs to Italy.' + meaning: GAZ:00002941 + Syria [GAZ:00002474]: + text: Syria [GAZ:00002474] + description: 'A country in Southwest Asia, bordering Lebanon, the Mediterranean + Sea and the island of Cyprus to the west, Israel to the southwest, Jordan + to the south, Iraq to the east, and Turkey to the north. Syria has fourteen + governorates, or muhafazat (singular: muhafazah). The governorates are divided + into sixty districts, or manatiq (singular: mintaqah), which are further + divided into sub-districts, or nawahi (singular: nahia).' + meaning: GAZ:00002474 + Taiwan [GAZ:00005341]: + text: Taiwan [GAZ:00005341] + description: A state in East Asia with de facto rule of the island of Tawain + and adjacent territory. The Republic of China currently administers two + historical provinces of China (one completely and a small part of another + one) and centrally administers two direct-controlled municipalities. + meaning: GAZ:00005341 + Tajikistan [GAZ:00006912]: + text: Tajikistan [GAZ:00006912] + description: A mountainous landlocked country in Central Asia. Afghanistan + borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and + People's Republic of China to the east. Tajikistan consists of 4 administrative + divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous + province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican + Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly + known as Karotegin Province). Each region is divided into several districts + (nohiya or raion). + meaning: GAZ:00006912 + Tanzania [GAZ:00001103]: + text: Tanzania [GAZ:00001103] + description: A country in East Africa bordered by Kenya and Uganda on the + north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, + and Zambia, Malawi and Mozambique on the south. To the east it borders the + Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on + the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight + districts (wilaya), each with at least one council, have been created to + further increase local authority; the councils are also known as local government + authorities. Currently there are 114 councils operating in 99 districts; + 22 are urban and 92 are rural. The 22 urban units are further classified + as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, + Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) + or town councils (the remaining eleven communities). + meaning: GAZ:00001103 + Thailand [GAZ:00003744]: + text: Thailand [GAZ:00003744] + description: 'A country in Southeast Asia. To its east lie Laos and Cambodia; + to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman + Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided + into 75 provinces (changwat), which are gathered into 5 groups of provinces + by location. There are also 2 special governed districts: the capital Bangkok + (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial + level and thus often counted as a 76th province.' + meaning: GAZ:00003744 + Timor-Leste [GAZ:00006913]: + text: Timor-Leste [GAZ:00006913] + description: A country in Southeast Asia. It comprises the eastern half of + the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, + an exclave on the northwestern side of the island, within Indonesian West + Timor. The small country of 15,410 km2 is located about 640 km northwest + of Darwin, Australia. East Timor is divided into thirteen administrative + districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, + villages and hamlets. + meaning: GAZ:00006913 + Togo [GAZ:00000915]: + text: Togo [GAZ:00000915] + description: A country in West Africa bordering Ghana in the west, Benin in + the east and Burkina Faso in the north. In the south, it has a short Gulf + of Guinea coast, on which the capital Lome is located. + meaning: GAZ:00000915 + Tokelau [GAZ:00260188]: + text: Tokelau [GAZ:00260188] + description: 'A dependent territory of New Zealand in the southern Pacific + Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and + Fakaofo. They have a combined land area of 10 km2 (4 sq mi).' + meaning: GAZ:00260188 + Tonga [GAZ:00006916]: + text: Tonga [GAZ:00006916] + description: A Polynesian country, and also an archipelago comprising 169 + islands, of which 36 are inhabited. The archipelago's total surface area + is about 750 square kilometres (290 sq mi) scattered over 700,000 square + kilometres (270,000 sq mi) of the southern Pacific Ocean. + meaning: GAZ:00006916 + Trinidad and Tobago [GAZ:00003767]: + text: Trinidad and Tobago [GAZ:00003767] + description: An archipelagic state in the southern Caribbean, lying northeast + of the South American nation of Venezuela and south of Grenada in the Lesser + Antilles. It also shares maritime boundaries with Barbados to the northeast + and Guyana to the southeast. The country covers an area of 5,128 km2and + consists of two main islands, Trinidad and Tobago, and 21 smaller islands. + meaning: GAZ:00003767 + Tromelin Island [GAZ:00005812]: + text: Tromelin Island [GAZ:00005812] + description: A low, flat 0.8 km2 island in the Indian Ocean, about 350 km + east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 + m long and 700 m wide, surrounded by coral reefs. The island is 7 m high + at its highest point. + meaning: GAZ:00005812 + Tunisia [GAZ:00000562]: + text: Tunisia [GAZ:00000562] + description: A country situated on the Mediterranean coast of North Africa. + It is bordered by Algeria to the west and Libya to the southeast. Tunisia + is subdivided into 24 governorates, divided into 262 "delegations" or "districts" + (mutamadiyat), and further subdivided into municipalities (shaykhats). + meaning: GAZ:00000562 + Turkey [GAZ:00000558]: + text: Turkey [GAZ:00000558] + description: 'A Eurasian country that stretches across the Anatolian peninsula + in western Asia and Thrace (Rumelia) in the Balkan region of southeastern + Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece + to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave + of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. + The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago + are to the west; and the Black Sea is to the north. Separating Anatolia + and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus + and the Dardanelles), which are commonly reckoned to delineate the border + between Asia and Europe, thereby making Turkey transcontinental. The territory + of Turkey is subdivided into 81 provinces for administrative purposes. The + provinces are organized into 7 regions for census purposes; however, they + do not represent an administrative structure. Each province is divided into + districts, for a total of 923 districts.' + meaning: GAZ:00000558 + Turkmenistan [GAZ:00005018]: + text: Turkmenistan [GAZ:00005018] + description: A country in Central Asia. It is bordered by Afghanistan to the + southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan + to the northwest, and the Caspian Sea to the west. It was a constituent + republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan + is divided into five provinces or welayatlar (singular - welayat) and one + independent city. + meaning: GAZ:00005018 + Turks and Caicos Islands [GAZ:00003955]: + text: Turks and Caicos Islands [GAZ:00003955] + description: A British Overseas Territory consisting of two groups of tropical + islands in the West Indies. The Turks and Caicos Islands are divided into + six administrative districts (two in the Turks Islands and four in the Caicos + Islands. + meaning: GAZ:00003955 + Tuvalu [GAZ:00009715]: + text: Tuvalu [GAZ:00009715] + description: A Polynesian island nation located in the Pacific Ocean midway + between Hawaii and Australia. + meaning: GAZ:00009715 + United States of America [GAZ:00002459]: + text: United States of America [GAZ:00002459] + description: A federal constitutional republic comprising fifty states and + a federal district. The country is situated mostly in central North America, + where its forty-eight contiguous states and Washington, DC, the capital + district, lie between the Pacific and Atlantic Oceans, bordered by Canada + to the north and Mexico to the south. The State of Alaska is in the northwest + of the continent, with Canada to its east and Russia to the west across + the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United + States also possesses several territories, or insular areas, that are scattered + around the Caribbean and Pacific. The states are divided into smaller administrative + regions, called counties in most states, exceptions being Alaska (parts + of the state are organized into subdivisions called boroughs; the rest of + the state's territory that is not included in any borough is divided into + "census areas"), and Louisiana (which is divided into county-equivalents + that are called parishes). There are also independent cities which are within + particular states but not part of any particular county or consolidated + city-counties. Another type of organization is where the city and county + are unified and function as an independent city. There are thirty-nine independent + cities in Virginia and other independent cities or city-counties are San + Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, + Colorado and Carson City, Nevada. Counties can include a number of cities, + towns, villages, or hamlets, or sometimes just a part of a city. Counties + have varying degrees of political and legal significance, but they are always + administrative divisions of the state. Counties in many states are further + subdivided into townships, which, by definition, are administrative divisions + of a county. In some states, such as Michigan, a township can file a charter + with the state government, making itself into a "charter township", which + is a type of mixed municipal and township status (giving the township some + of the rights of a city without all of the responsibilities), much in the + way a metropolitan municipality is a mixed municipality and county. + meaning: GAZ:00002459 + Uganda [GAZ:00001102]: + text: Uganda [GAZ:00001102] + description: 'A landlocked country in East Africa, bordered on the east by + Kenya, the north by Sudan, on the west by the Democratic Republic of the + Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern + part of the country includes a substantial portion of Lake Victoria, within + which it shares borders with Kenya and Tanzania. Uganda is divided into + 80 districts, spread across four administrative regions: Northern, Eastern, + Central and Western. The districts are subdivided into counties.' + meaning: GAZ:00001102 + Ukraine [GAZ:00002724]: + text: Ukraine [GAZ:00002724] + description: A country in Eastern Europe. It borders Russia to the east, Belarus + to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova + to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine + is subdivided into twenty-four oblasts (provinces) and one autonomous republic + (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, + and Sevastopol, both have a special legal status. The 24 oblasts and Crimea + are subdivided into 490 raions (districts), or second-level administrative + units. + meaning: GAZ:00002724 + United Arab Emirates [GAZ:00005282]: + text: United Arab Emirates [GAZ:00005282] + description: A Middle Eastern federation of seven states situated in the southeast + of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering + Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, + Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain. + meaning: GAZ:00005282 + United Kingdom [GAZ:00002637]: + text: United Kingdom [GAZ:00002637] + description: A sovereign island country located off the northwestern coast + of mainland Europe comprising of the four constituent countries; England, + Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, + the northeast part of the island of Ireland and many small islands. Apart + from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North + Sea, the English Channel and the Irish Sea. The largest island, Great Britain, + is linked to France by the Channel Tunnel. + meaning: GAZ:00002637 + Uruguay [GAZ:00002930]: + text: Uruguay [GAZ:00002930] + description: A country located in the southeastern part of South America. + It is bordered by Brazil to the north, by Argentina across the bank of both + the Uruguay River to the west and the estuary of Rio de la Plata to the + southwest, and the South Atlantic Ocean to the southeast. Uraguay consists + of 19 departments (departamentos, singular - departamento). + meaning: GAZ:00002930 + Uzbekistan [GAZ:00004979]: + text: Uzbekistan [GAZ:00004979] + description: A doubly landlocked country in Central Asia, formerly part of + the Soviet Union. It shares borders with Kazakhstan to the west and to the + north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan + to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one + autonomous republic (respublika and one independent city (shahar). + meaning: GAZ:00004979 + Vanuatu [GAZ:00006918]: + text: Vanuatu [GAZ:00006918] + description: An island country located in the South Pacific Ocean. The archipelago, + which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern + Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New + Guinea, southeast of the Solomon Islands, and west of Fiji. + meaning: GAZ:00006918 + Venezuela [GAZ:00002931]: + text: Venezuela [GAZ:00002931] + description: A country on the northern coast of South America. The country + comprises a continental mainland and numerous islands located off the Venezuelan + coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses + borders with Guyana to the east, Brazil to the south, and Colombia to the + west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, + Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just + north, off the Venezuelan coast. Venezuela is divided into twenty-three + states (Estados), a capital district (distrito capital) corresponding to + the city of Caracas, the Federal Dependencies (Dependencias Federales, a + special territory), and Guayana Esequiba (claimed in a border dispute with + Guyana). Venezuela is further subdivided into 335 municipalities (municipios); + these are subdivided into over one thousand parishes (parroquias). + meaning: GAZ:00002931 + Viet Nam [GAZ:00003756]: + text: Viet Nam [GAZ:00003756] + description: The easternmost country on the Indochina Peninsula in Southeast + Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, + alongside China, Laos, and Cambodia. + meaning: GAZ:00003756 + Virgin Islands [GAZ:00003959]: + text: Virgin Islands [GAZ:00003959] + description: A group of islands in the Caribbean that are an insular area + of the United States. The islands are geographically part of the Virgin + Islands archipelago and are located in the Leeward Islands of the Lesser + Antilles. The US Virgin Islands are an organized, unincorporated United + States territory. The US Virgin Islands are administratively divided into + two districts and subdivided into 20 sub-districts. + meaning: GAZ:00003959 + Wake Island [GAZ:00007111]: + text: Wake Island [GAZ:00007111] + description: A coral atoll (despite its name) having a coastline of 19 km + in the North Pacific Ocean, located about two-thirds of the way from Honolulu + (3,700 km west) to Guam (2,430 km east). + meaning: GAZ:00007111 + Wallis and Futuna [GAZ:00007191]: + text: Wallis and Futuna [GAZ:00007191] + description: A Polynesian French island territory (but not part of, or even + contiguous with, French Polynesia) in the South Pacific between Fiji and + Samoa. It is made up of three main volcanic tropical islands and a number + of tiny islets. + meaning: GAZ:00007191 + West Bank [GAZ:00009572]: + text: West Bank [GAZ:00009572] + description: A landlocked territory near the Mediterranean coast of Western + Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the + south, west and north.[2] Under Israeli occupation since 1967, the area + is split into 167 Palestinian "islands" under partial Palestinian National + Authority civil rule, and 230 Israeli settlements into which Israeli law + is "pipelined". + meaning: GAZ:00009572 + Western Sahara [GAZ:00000564]: + text: Western Sahara [GAZ:00000564] + description: A territory of northwestern Africa, bordered by Morocco to the + north, Algeria in the northeast, Mauritania to the east and south, and the + Atlantic Ocean on the west. Western Sahara is administratively divided into + four regions. + meaning: GAZ:00000564 + Yemen [GAZ:00005284]: + text: Yemen [GAZ:00005284] + description: A country located on the Arabian Peninsula in Southwest Asia. + Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, + the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's + territory includes over 200 islands, the largest of which is Socotra, about + 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen + is divided into twenty governorates (muhafazah) and one municipality. The + population of each governorate is listed in the table below. The governorates + of Yemen are divided into 333 districts (muderiah). The districts are subdivided + into 2,210 sub-districts, and then into 38,284 villages (as of 2001). + meaning: GAZ:00005284 + Zambia [GAZ:00001107]: + text: Zambia [GAZ:00001107] + description: A landlocked country in Southern Africa. The neighbouring countries + are the Democratic Republic of the Congo to the north, Tanzania to the north-east, + Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, + and Angola to the west. The capital city is Lusaka. Zambia is divided into + nine provinces. Each province is subdivided into several districts with + a total of 73 districts. + meaning: GAZ:00001107 + Zimbabwe [GAZ:00001106]: + text: Zimbabwe [GAZ:00001106] + description: A landlocked country in the southern part of the continent of + Africa, between the Zambezi and Limpopo rivers. It is bordered by South + Africa to the south, Botswana to the southwest, Zambia to the northwest, + and Mozambique to the east. Zimbabwe is divided into eight provinces and + two cities with provincial status. The provinces are subdivided into 59 + districts and 1,200 municipalities. + meaning: GAZ:00001106 +types: + WhitespaceMinimizedString: + name: WhitespaceMinimizedString + typeof: string + description: 'A string that has all whitespace trimmed off of beginning and end, + and all internal whitespace segments reduced to single spaces. Whitespace includes + #x9 (tab), #xA (linefeed), and #xD (carriage return).' + base: str + uri: xsd:token + Provenance: + name: Provenance + typeof: string + description: A field containing a DataHarmonizer versioning marker. It is issued + by DataHarmonizer when validation is applied to a given row of data. + base: str + uri: xsd:token +settings: + Title_Case: (((?<=\b)[^a-z\W]\w*?|[\W])+) + UPPER_CASE: '[A-Z\W\d_]*' + lower_case: '[a-z\W\d_]*' diff --git a/web/templates/hpai/schema_core.yaml b/web/templates/hpai/schema_core.yaml new file mode 100644 index 00000000..d960a6e8 --- /dev/null +++ b/web/templates/hpai/schema_core.yaml @@ -0,0 +1,73 @@ +id: https://example.com/hpai +name: Mpox +version: 4.3.3 +description: "The HPAI specification was developed by the Public Health Alliance for Genomic Epidemiology (PHA4GE) to better enable harmonization of highly pathogenic avian influenza genomic surveillance contextual data. The specification is intended to support H5N1 monitoring, and provides standardized, ontology-based fields and terms for samples, sequences, and bioinformatics analysis." +imports: + - 'linkml:types' +prefixes: + linkml: 'https://w3id.org/linkml/' + GENEPIO: 'http://purl.obolibrary.org/obo/GENEPIO_' +classes: + dh_interface: + name: dh_interface + description: 'A DataHarmonizer interface' + from_schema: https://example.com/hpai + 'HPAI': + name: 'HPAI' + title: 'HPAI' + description: + is_a: dh_interface + see_also: + annotations: + version: 1.0.0 + 'HPAIFood': + name: 'HPAIFood' + title: 'HPAI Food' + description: + is_a: dh_interface + see_also: + annotations: + version: 1.0.0 + 'HPAIWW': + name: 'HPAIWW' + title: 'HPAI Wastewater' + description: + is_a: dh_interface + see_also: + annotations: + version: 1.0.0 + 'HPAIEnviro': + name: 'HPAIEnviro' + title: 'HPAI Environmental' + description: + is_a: dh_interface + see_also: + annotations: + version: 1.0.0 + 'HPAIHost': + name: 'HPAIHost' + title: 'HPAI Host' + description: + is_a: dh_interface + see_also: + annotations: + version: 1.0.0 +slots: {} +enums: {} +types: + WhitespaceMinimizedString: + name: 'WhitespaceMinimizedString' + typeof: string + description: 'A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).' + base: str + uri: xsd:token + Provenance: + name: 'Provenance' + typeof: string + description: 'A field containing a DataHarmonizer versioning marker. It is issued by DataHarmonizer when validation is applied to a given row of data.' + base: str + uri: xsd:token +settings: + Title_Case: "(((?<=\\b)[^a-z\\W]\\w*?|[\\W])+)" + UPPER_CASE: "[A-Z\\W\\d_]*" + lower_case: "[a-z\\W\\d_]*" diff --git a/web/templates/hpai/schema_enums.tsv b/web/templates/hpai/schema_enums.tsv new file mode 100644 index 00000000..913d4fde --- /dev/null +++ b/web/templates/hpai/schema_enums.tsv @@ -0,0 +1,1429 @@ +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description + +null value NullValue GENEPIO:0001619 Not Applicable [GENEPIO:0001619] A categorical choice recorded when a datum does not apply to a given context. + GENEPIO:0001618 Missing [GENEPIO:0001618] A categorical choice recorded when a datum is not included for an unknown reason. + GENEPIO:0001620 Not Collected [GENEPIO:0001620] A categorical choice recorded when a datum was not measured or collected. + GENEPIO:0001668 Not Provided [GENEPIO:0001668] A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage. + GENEPIO:0001810 Restricted Access [GENEPIO:0001810] A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns. + +organism menu OrganismMenu NCBITaxon:11320 Influenza A virus [NCBITaxon:11320] + +influenza_subtype menu InfluenzaSubtypeMenu NCBITaxon:102793 H5N1 subtype (Influenza A virus) [NCBITaxon:102793] + +influenza_subtyping_scheme_name menu InfluenzaSubtypingSchemeNameMenu GENEPIO:0101121 Tripartite Influenza A scheme [GENEPIO:0101121] Tripartite Influenza A scheme (A/goose/Guangdong/1/96-like viruses) [GENEPIO:0101121] + GENEPIO:0101122 USDA GenoFLU scheme [GENEPIO:0101122] USDA GenoFLU scheme (8 segment eurasian/american genotypes) [GENEPIO:0101122] + +taxonomic_identification_process menu TaxonomicIdentificationProcessMenu OBI:0002117 Whole genome sequencing assay [OBI:0002117] A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. + OBI:0002623 Whole metagenome sequencing assay [OBI:0002623] A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. + OBI:0002763 16S ribosomal gene sequencing assay [OBI:0002763] An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. + OBI:0002740 PCR assay [OBI:0002740] An organism identification assay that is based on PCR. + OBI:0001546 Comparative phenotypic assessment [OBI:0001546] Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference + +sample_collection_time_of_day menu SampleCollectionTimeOfDayMenu NCIT:C64934 Morning [NCIT:C64934] The time period between dawn and noon. + NCIT:C64935 Afternoon [NCIT:C64935] The time period between noon and sunset. + NCIT:C64936 Evening [NCIT:C64936] The time period between late afternoon and bedtime. + NCIT:C65001 Night [NCIT:C65001] The time in every 24 hour period when it is dark. + +sample_collection_duration_unit menu SampleCollectionDurationUnitMenu UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + UO:0000031 Minute [UO:0000031] A time unit which is equal to 60 seconds. + UO:0000032 Hour [UO:0000032] A time unit which is equal to 60 minutes. + UO:0000033 Day [UO:0000033] A time unit which is equal to 24 hours. + UO:0000034 Week [UO:0000034] A time unit which is equal to 7 days. + UO:0000035 Month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. + UO:0000036 Year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. + + +food_product menu FoodProductMenu ENVO:02000047 Animal feed [ENVO:02000047] Food material which can be used to meet nutritional requirements of animals, particularly livestock such as cattle, goats, sheep, horses, chickens and pigs. + FOODON:00001564 Blood meal [FOODON:00001564] Blood meal is a dry, inert powder made from blood used as a high-nitrogen organic fertilizer and a high protein animal feed. + ENVO:02000054 Bone meal [ENVO:02000054] A mixture of crushed and coarsely ground bones that is used as an organic fertilizer for plants and formerly in animal feed. + FOODON:00004310 Brassica carinata meal [FOODON:00004310] A meal that is a co-product produced after the extraction of oil from the seed of the Ethiopian mustard plant (Brassica carinata). + FOODON:00002694 Canola meal [FOODON:00002694] Canola meal is an oilseed meal made from canola grain. Canola meal is a by-product of the oil crushing process. + FOODON:00004323 Compound feed premix [FOODON:00004323] A formula mixture of micronutrients that is used as a component in compound feed. + FOODON:00004324 Compound feed premix (medicated) [FOODON:00004324] A compound feed premix in which medicinal substance has been added. + FOODON:00003927 Feather meal [FOODON:00003927] A by product of processing poultry which is made from poultry feathers by partially grinding them under elevated heat and pressure, and then grinding and drying. + FOODON:03301620 Fish meal [FOODON:03301620] Fish meal is primarily used as a protein supplement in compound feed. As of 2010, about 56% of fish meal was used to feed farmed fish, about 20% was used in pig feed, about 12% in poultry feed, and about 12% in other uses, which included fertilizer. + FOODON:00004286 Lay ration [FOODON:00004286] Food formulated for the laying hens to increase egg production and egg shell quality. + FOODON:00002738 Meat and bone meal [FOODON:00002738] Meat and bone meal (MBM) is a product of the rendering industry. It is typically about 48–52% protein, 33–35% ash, 8–12% fat, and 4–7% water. It is primarily used in the formulation of animal feed to improve the amino acid profile of the feed. + FOODON:00004282 Meat meal [FOODON:00004282] A meal that is obtained by cooking, defatting, sterilizing, grinding, and sifting by-products of an animal. + FOODON:00002682 Pet food [FOODON:00002682] Pet food is plant or animal material intended for consumption by pets. + FOODON:03302757 Soybean meal [FOODON:03302757] A type of ground protein-rich residue from the production of soybean oil used chiefly in animal feeds, in adhesives and plastics, in making synthetic protein fibers, and in fermentation media (as for the production of antibiotics). + FOODON:00004322 Animal feed ingredient [FOODON:00004322] An ingredient that is used in the preparation of animal feed. + FOODON:00001256 Dairy food product [FOODON:00001256] A dairy food product has mammilian milk or a milk component as an ingredient. + FOODON:03000287 Cheese block (whole or parts) [FOODON:03000287] A whole cheese block or some substance made from a block of processed cheese. + FOODON:03310016 Cow skim milk (powdered) [FOODON:03310016] Milk powder that is obtained by removing all of the water from pasteurized skim milk. + UBERON:0001913 Milk [UBERON:0001913] An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. + Meat, poultry and fish (organizational term) + FOODON:00001282 Beef (ground or minced) [FOODON:00001282] A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese. + FOODON:03000412 Beef (ground or minced, boneless) [FOODON:03000412] + FOODON:03000398 Beef (ground or minced, extra lean) [FOODON:03000398] + FOODON:03000394 Beef (ground or minced, lean) [FOODON:03000394] + FOODON:03000402 Beef (ground or minced, medium) [FOODON:03000402] + FOODON:03000406 Beef (ground or minced, regular) [FOODON:03000406] + FOODON:03000408 Beef (ground or minced, sirloin) [FOODON:03000408] + FOODON:00002737 Beef hamburger (dish) [FOODON:00002737] A hamburger (short: burger) is a sandwich consisting of one or more cooked patties of ground meat, usually beef, placed inside a sliced bread roll or bun. The patty may be pan fried, grilled, or flame broiled. + FOODON:03000377 Beef shoulder [FOODON:03000377] + FOODON:03000387 Beef shoulder chop [FOODON:03000387] Meat chop from the shoulder region of beef. + FOODON:03000389 Beef sirloin chop [FOODON:03000389] Meat chop from the sirloin region of beef + FOODON:00004288 Beef stew chunk [FOODON:00004288] A chunk of beef used as an ingredient in making stew. + FOODON:00003302 Beef tenderloin [FOODON:00003302] A cut of beef corresponding to the psoas major muscle, which is very tender. + FOODON:03000333 Beef (whole cut or parts) [FOODON:03000333] + FOODON:03530020 Brisket [FOODON:03530020] A cut of meat from the breast or lower chest of beef or veal. + FOODON:00002703 Chicken breast [FOODON:00002703] Chicken breast consists mainly of the breast meat portion of a chicken, and may or may not include connected bone (boneless versus "with bone") and skin. + FOODON:03000385 Chicken breast (back off) [FOODON:03000385] A chicken breast with its backbone removed. + FOODON:00003332 Chicken breast (skinless) [FOODON:00003332] + FOODON:03000374 Chicken breast (with skin) [FOODON:03000374] + FOODON:00003364 Chicken breast (skinless, boneless) [FOODON:00003364] + FOODON:00004308 Chicken breast cutlet [FOODON:00004308] A cutlet made from chicken breast. + FOODON:00002716 Chicken drumstick [FOODON:00002716] The segment of a chicken's leg between the thigh and tarsus (ankle). + FOODON:03000366 Chicken drumstick (skinless) [FOODON:03000366] + FOODON:03000368 Chicken drumstick (with skin) [FOODON:03000368] + FOODON:00001040 Chicken meat [FOODON:00001040] + FOODON:03311826 Chicken meat (ground or minced) [FOODON:03311826] A food product made of ground or minced chicken meat. + FOODON:03000392 Chicken meat (ground or minced, lean) [FOODON:03000392] A food product made of lean, ground or minced chicken meat. + FOODON:03000396 Chicken meat (ground or minced, extra lean) [FOODON:03000396] A food product made of extra lean, ground or minced chicken meat. + FOODON:03000400 Chicken meat (ground or minced, medium) [FOODON:03000400] A food product made of medium, ground or minced chicken meat. + FOODON:03000404 Chicken meat (ground or minced, regular) [FOODON:03000404] A food product made of regular, ground or minced chicken meat. + FOODON:03000410 Chicken meat (ground or minced, boneless) [FOODON:03000410] + FOODON:00002672 Chicken nugget [FOODON:00002672] A chicken nugget is a chicken product made from chicken meat that is breaded or battered, then deep-fried or baked. + FOODON:02020219 Chicken thigh [FOODON:02020219] A whole thigh that derives from a chicken. + FOODON:00003331 Chicken thigh (skinless) [FOODON:00003331] A chicken thigh after the skin has been removed. + FOODON:02020227 Chicken thigh (skinless, with bone) [FOODON:02020227] A chicken thigh that is skinless and contains bone element. + FOODON:03000417 Chicken thigh (skinless, boneless) [FOODON:03000417] + FOODON:03000381 Chicken upper thigh [FOODON:03000381] Meat from the upper thigh of a chicken. + FOODON:00003330 Chicken thigh (with skin) [FOODON:00003330] + FOODON:00003363 Chicken thigh (with skin, with bone) [FOODON_00003363] A chicken thigh that contains skin and bone material. + FOODON:00002674 Chicken wing [FOODON:00002674] A whole wing that derives from a chicken. + FOODON:00001248 Fish food product [FOODON:00001248] A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins). + FOODON:00002986 Fish steak [FOODON:00002986] A fish steak, alternatively known as a fish cutlet, is a cut of fish which is cut perpendicular to the spine and can either include the bones or be boneless. + FOODON:00002502 Ham food product [FOODON:00002502] Ham is pork from a leg cut that has been preserved by wet or dry curing, with or without smoking. As a processed meat, the term "ham" includes both whole cuts of meat and ones that have been mechanically formed. + FOODON:03315658 Head cheese [FOODON:03315658] Head cheese is a cold cut that originated in Europe. Head cheese is not a dairy cheese, but a terrine or meat jelly made with flesh from the head of a calf or pig, or less commonly a sheep or cow, and often set in aspic. A version pickled with vinegar is known as souse. + FOODON:03411669 Lamb [FOODON:03411669] A whole lamb or some material processed from a lamb. + FOODON:00004285 Meat strip [FOODON:00004285] A cut of meat which is long, narrow and boneless. + FOODON:00002912 Mutton [FOODON:00002912] The meat of an adult sheep is mutton, a term only used for the meat, not the living animals. + FOODON:00001049 Pork chop [FOODON:00001049] A cut of meat (a meat chop) cut perpendicularly to the spine of the pig and usually containing a rib or part of a vertebra, served as an individual portion. + FOODON:03309969 Pork meat (ground or minced) [FOODON:03309969] Meat from a pig that has been ground or minced. + FOODON:03000413 Pork meat (ground or minced, boneless) [FOODON:03000413] + FOODON:03000399 Pork meat (ground or minced, extra lean) [FOODON:03000399] A food product made of extra-lean, ground or minced pork meat. + FOODON:03000395 Pork meat (ground or minced, lean) [FOODON:03000395] A food product made of lean, ground or minced pork meat. + FOODON:03000403 Pork meat (ground or minced, medium) [FOODON:03000403] A food product made of medium, ground or minced pork meat. + FOODON:03000407 Pork meat (ground or minced, regular) [FOODON:03000407] A food product made of regular, ground or minced pork meat. + FOODON:03000409 Pork meat (ground or minced, Sirloin) [FOODON:03000409] Ground or minced pork meat that comes from the sirloin region. + FOODON:03000376 Pork shoulder [FOODON:03000376] + FOODON:03000388 Pork shoulder chop [FOODON:03000388] Meat chop from the blade roast of pork. + FOODON:03000390 Pork sirloin chop [FOODON:03000390] + FOODON:00003148 Pork steak [FOODON:00003148] + FOODON:03000416 Pork tenderloin [FOODON:03000416] + FOODON:03315883 Poultry meat [FOODON:03315883] Any meat from one or more poultry birds. + FOODON:03530159 Leg (poultry meat cut) [FOODON:03530159] The leg cut of a poultry bird. + FOODON:00003469 Poultry drumstick [FOODON:00003469] The calf part of a poultry hindleg (hindlimb zeugopod) + FOODON:03530294 Neck (poultry meat cut) [FOODON:03530294] The neck cut of a poultry bird. + FOODON:03530160 Thigh (poultry meat cut) [FOODON:03530160] The thigh cut of a poultry bird. + FOODON:03530157 Wing (poultry meat cut) [FOODON:03530157] The wing cut of a poultry bird. + FOODON:03315904 Sausage (whole) [FOODON:03315904] A food product that is highly seasoned minced meat and is encased in a skin in the shape of a cylinder. + FOODON:03311003 Pepperoni [FOODON:03311003] A highly seasoned and spicy beef or pork sausage. + FOODON:03312067 Salami [FOODON:03312067] A cured sausage which consists of fermented and air-dried meat, typically pork. + FOODON:03411433 Shellfish [FOODON:03411433] The term shellfish is used both broadly and specifically. For regulatory purposes it is often narrowly defined as filter-feeding molluscs such as clams, mussels, and oyster to the exclusion of crustaceans and all else. Although their shells may differ, all shellfish are invertebrates. + FOODON:03301673 Shrimp [FOODON:03301673] A whole shrimp or some material processed from a shrimp. + FOODON:03411489 Scallop [FOODON:03411489] + FOODON:00002690 Turkey breast [FOODON:00002690] Turkey breast consists mainly of the breast meat portion of a turkey, and may or may not include connected bone ("deboned or boneless versus bone-in") and skin. + FOODON:03000386 Turkey breast (back off) [FOODON:03000386] A turkey breast with its backbone removed. + FOODON:03000372 Turkey breast (skinless) [FOODON:03000372] + FOODON:03000373 Turkey breast (skinless, boneless) [FOODON:03000373] + FOODON:03000375 Turkey breast (with skin) [FOODON:03000375] + FOODON:03000365 Turkey drumstick [FOODON:03000365] + FOODON:03000367 Turkey drumstick (skinless) [FOODON:03000367] + FOODON:03000369 Turkey drumstick (with skin) [FOODON:03000369] + FOODON:00001286 Turkey meat [FOODON:00001286] A turkey meat food product is any food product made predominantly of turkey parts. + FOODON:00002714 Turkey meat (ground or minced) [FOODON:00002714] A food product made of ground or minced turkey meat. + FOODON:03000393 Turkey meat (ground or minced, lean) [FOODON:03000393] A food product made of lean, ground or minced turkey meat. + FOODON:03000397 Turkey meat (ground or minced, extra lean) [FOODON:03000397] A food product made of extra-lean, ground or minced turkey meat. + FOODON:03000401 Turkey meat (ground or minced, medium) [FOODON:03000401] A food product made of medium, ground or minced turkey meat. + FOODON:03000405 Turkey meat (ground or minced, regular) [FOODON:03000405] A food product made of regular, ground or minced turkey meat. + FOODON:03000411 Turkey meat (ground or minced, boneless) [FOODON:03000411] + FOODON:00003325 Turkey thigh [FOODON:00003325] A thigh poultry cut of turkey. + FOODON:00003329 Turkey thigh (skinless) [FOODON:00003329] A turkey thigh after the skin has been removed. + FOODON:03000370 Turkey thigh (skinless, boneless) [FOODON:03000370] + FOODON:00003328 Turkey thigh (with skin) [FOODON:00003328] A turkey thigh that still contains the skin. + FOODON:03000382 Turkey upper thigh [FOODON:03000382] Meat from the upper thigh of a turkey. + FOODON:03000384 Turkey upper thigh (with skin) [FOODON:03000384] Turkey's upper thigh that contains the skin. + FOODON:03000371 Turkey wing [FOODON:03000371] + FOODON:00003083 Veal [FOODON:00003083] Veal is the meat of calves, in contrast to the beef from older cattle. Veal can be produced from a calf of either sex and any breed; however, most veal comes from young males of dairy breeds which are not used for breeding. + OODON:000039111 Formula fed veal [FOODON:000039111] + FOODON:00004280 Grain-fed veal [FOODON:00004280] Meat from a calf that is raised on grain, hay, or other solid food, in addition to milk + + +food_product_properties menu FoodProductPropertiesMenu FOODON:03510128 Organic food claim or use [FOODON:03510128] USA: The 1990 Farm Act specifies that a food labeled 'organic' must meet four requirements: 1) the food must be raised by specified methods to replenish and maintain the fertility of the soil; 2) the food must be certified as having been produced with a nationally approved list of materials and practices; 3) to be eligible for certification at least three years must have elapsed between the first organic harvest and first use of nationally approved materials on land and crops;and 4) organic foods must meet all local, state and federal regulations governing the quality and safety of the food supply. Europe: Foods produced in accordance with Council Regulation (EC) No 834/2007 of 28 June 2007 on organic production and labelling of organic products and repealing Regulation (EEC) No 2092/91. [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2007:189:0001:0023:EN:PDF] + FOODON:03311126 Food (raw) [FOODON:03311126] A food material that has not been cooked. + FOODON:03316043 Food (heat treated) [FOODON:03316043] + FOODON:00002654 Food (pasteurized) [FOODON:00002654] + Dairy product (no fat removed, whole) + Dairy product (skimmed, non-fat) + Dairy product (semi-skimmed, reduced fat, 1%) + Dairy product (semi-skimmed, reduced fat, 2%) + +food_packaging menu FoodPackagingMenu FOODON:03490214 Bottle [FOODON:03490214 A rigid or semirigid container typically of glass or plastic having a comparatively narrow neck or mouth and usually no handle. + FOODON:03490197 Bag [FOODON:03490197] According to FSTA Thesaurus Packaging 3.1 package types, includes boil-in bag, carrier bag, flat bag, inner bag, retort pouch, shipping bag, valve bag, and valve sack + FOODON:03490213 Carton [FOODON:03490213] + +environmental_site menu EnvironmentalSiteMenu ENVO:01000925 Abattoir [ENVO:01000925] A facility in which non-human animals are slaughtered and processed for human consumption. + ENVO:00000114 Agricultural Field [ENVO:00000114] A field which is located on land and used for agricultural purposes, such as the grazing of livestock or the cultivation of crops. + ENVO:01000922 Animal cage [ENVO:01000922] A manufactured cage which may be used to confine, contain, or protect an animal. + ENVO:03501406 Artificial wetland [ENVO:03501406] A wetland ecosystem which is constructed to treat municipal or industrial wastewater, greywater or stormwater runoff. + ENVO:03501441 Breeding ground [ENVO:03501441] A place where animals breed. + ENVO:00000073 Building [ENVO:00000073] A permanent walled and roofed construction. + ENVO:03501257 Barn [ENVO:03501257] A farm building used for housing livestock, storing machinery or crops etc + ENVO:03501383 Breeder barn [ENVO:03501383] A barn where animals are kept for breeding purposes. + ENVO:03501386 Broiler barn [ENVO:03501386] A barn where broiler chickens are reared. + ENVO:03501385 Sheep barn [ENVO:03501385] A barn where sheep are kept. + ENVO:00003862 Dairy [ENVO:00003862] A dairy is a building in which animal milk is harvested and, optionally, processed for human consumption. + ENVO:00000078 Farm [ENVO:00000078] An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein. + ENVO:03501443 Beef farm [ENVO:03501443] A farm where cows are kept for the purpose of meat production. + ENVO:03501384 Breeder farm [ENVO:03501384] A farm where animals are kept for breeding purposes. + ENVO:03501416 Dairy farm [ENVO:03501416] A farm where cows are kept for the purpose of producing milk and other dairy products. + ENVO:01000627 Feedlot [ENVO:01000627] A feedlot is a plot of land on which livestock are fattened for market [URL:http://www.merriam-webster.com/dictionary/feedlot ]. + ENVO:03501444 Beef cattle feedlot [ENVO:03501444] A feedlot where beef cattle are kept with a focus on efficient growth and weight gain of the animals. + ENVO:00000294 Fish farm [ENVO:00000294] A facility in which fish are raised commercially in tanks or enclosures, usually for food. + ENVO:03501417 Research farm [ENVO:03501417] A farm which is used for conducting agricultural research. + GAZ:00004603 Central Experimental Farm [GAZ:00004603] An agricultural facility, working farm, and research centre of the Research Branch of Agriculture and Agri-Food Canada. This farm is centrally located in and completely surrounded by the City of Ottawa, Ontario, Canada. The CEF is bordered by the Rideau Canal (a National Historic Site as well) to the east, by Baseline Road to the south, by Merivale and Fisher Roads to the west, and Carling Avenue to the north. + ENVO:01000306 Freshwater environment [ENVO:01000306] An aquatic environment which is determined by freshwater. + ENVO:01001873 Hatchery [ENVO:01001873] A construction in which eggs are hatched under artificial conditions. + ENVO:01001874 Poultry hatchery [ENVO:01001874] A hatchery in which the eggs of poultry are hatched under artificial conditions + ENVO:00002173 Hospital [ENVO:00002173] A building in which health care services are provided by specialized staff and equipment. + ENVO:00000020 Lake [ENVO:00000020] A body of water or other liquid of considerable size contained in a depression on a landmass. + ENVO:00000033 Pond [ENVO:00000033] A body of water, usually of smaller size than a lake. + ENVO:00000025 Reservoir [ENVO:00000025] An artificial body of water, often contained by a dam, constructed for the purpose of water storage. + ENVO:00000450 Irrigation reservoir [ENVO:00000450] A reservoir constructed for the purpose of providing water for irrigation. + ENVO:01001448 Retail environment [ENVO:01001448] A planned environmental usage process during which an environment supports the sale of goods to ultimate consumers, usually in small quantities. + ENVO:00002221 Shop [ENVO:00002221] A building in which a business presents a selection of goods and offers to trade or sell them to customers for money or other goods. + ENVO:01000984 Supermarket [ENVO:01000984] A food shop in which food products are the primary offer for sale or trade. + ENVO:00000022 River [ENVO:00000022] A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply. + ENVO:03501439 Roost (bird) [ENVO:03501439] A perch on which birds rest. + ENVO:00002272 Wastewater treatment plant [ENVO:00002272] A plant in which wastewater is treated. + ENVO:00000043 Wetland [ENVO:00000043] An area that is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances do support, a prevalence of vegetation typically adapted for life in saturated soil conditions. + +environmental_material menu EnvironmentalMaterialMenu ENVO:00002005 Air [ENVO:00002005] The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth. + AGRO:00000079 Animal manure [AGRO:00000079] Organic matter mostly derived from animal feces which can be used as organic fertilizer in agriculture. + AGRO:00000675 Animal feeding equipment [AGRO:00000675] An equipment used to feed and water livestock animals. + AGRO:00000679 Animal feeder [AGRO:00000679] An animal feeding equipment that has a food storage unit and which enables livestock to obtain their own food. + AGRO:00000680 Animal drinker [AGRO:00000680] An animal feeding equipment that has a water storage unit which enables livestock to obtain their own water. + AGRO:00000676 Feed pan [AGRO:00000676] A bowl or pan which is used to feed livestock. + AGRO:00000677 Watering bowl [AGRO:00000677] A bowl from which animals can drink. + AGRO:00000671 Animal transportation equipment [AGRO:00000671] An equipment used in the transportation of an animal + GENEPIO:0100896 Dead haul trailer [GENEPIO:0100896] A trailer used by a dead haul truck to transport dead animal from an abattoir. + AGRO:00000673 Dead haul truck [AGRO:00000673] A truck used to haul dead animals from an abattoir. + GENEPIO:0100897 Live haul trailer [GENEPIO:0100897] A trailer used by a live haul truck to transport live animals. + AGRO:00000674 Live haul truck [AGRO:00000674] A truck used to haul live animals. + NCIT:C49844 Belt [NCIT:C49844] A device consisting of a narrow loop of material moving over shafts or pulleys. + AGRO:00000670 Egg belt [AGRO:00000670] A conveyor belt used to collect eggs in an industrial egg production environment. + AGRO:00000669 Plucking belt [AGRO:00000669] A part of the plucking machine that moves the birds through the stages of plucking within the plucking apparatus. + ENVO:00002059 Biosolids [ENVO:00002059] A treated form of sludge, sometimes used as a fertilizer in agriculture. + GSSO:012935 Boot [GSSO:012935] A footwear which covers the foot, the ankle, and sometimes the leg below the knee. + OBI:0002806 Boot cover [OBI:0002806] A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants. + ENVO:03501431 Broom [ENVO:03501431] A cleaning equipment piece which is a bundle of fibres attached to a long handle, and is used for sweeping. + ENVO:03501379 Bulk tank [ENVO:03501379] A manufactured product which used to safely store and/or transport solids, liquids, gases and a variety of compounds and mixtures. + AGRO:00000678 Chick box [AGRO:00000678] The box which is used to transport chick (juvenile chicken). + AGRO:00000672 Chick pad [AGRO:00000672] The lining of a box or crate used to transport chicks (juvenile chickens). + ENVO:03501430 Cleaning equipment [ENVO:03501430] An equipment piece used for cleaning a built environment or a manufactured product. + ENVO:00002170 Compost [ENVO:00002170] The aerobically decomposed remnants of organic materials. + ENVO:03501372 Crate [ENVO:03501372] A manufactured product which is a container, traditionally made of wooden slates, designed to protect transported goods from damage. + ENVO:03501400 Dumpster [ENVO:03501400] A manufactured product which is a reusable container that accumulates waste until it is periodically emptied or replaced. + ENVO:00002008 Dust [ENVO:00002008] Minute solid particles with diameters less than 500 micrometers. Occurs in and may be deposited from, the atmosphere. + NCIT:C49947 Fan [NCIT:C49947] A device designed to create an air current through the rotation of a planar surface. + ENVO:03501415 Freezer [ENVO:03501415] A manufactured product which is a device used to keep things frozen by maintaining a temperature below the freezing point of water. + ENVO:03501414 Freezer handle [ENVO:03501414] A manufactured product which is the handle of a freezer door. + ENVO:03501424 Manure digester equipment [ENVO:03501424] An equipment piece which is used in the aerobic or anaerobic microbial digestion of manure. + ENVO:03501432 Nest [ENVO:03501432] A structure that is built for certain animals to hold eggs or young. + ENVO:00005805 Bird's nest [ENVO:00005805] A bird nest is the spot in which a bird lays and incubates its eggs and raises its young. [ https://en.wikipedia.org/wiki/Bird_nest ] + ENVO:00000134 Permafrost [ENVO:00000134] Soil or rock and included ice or organic material at or below the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) for two or more years. + UBERON:0008291 Poultry fluff [UBERON:0008291] A feather lacking a vane and having a rudimentary rachis and a tuft of non-interlocked barbs with elongated barbules extending from the calamus. + AGRO:00000080 Poultry litter [AGRO:00000080] Manure which is primarily composed of pig feces. + ENVO:00002007 Sediment [ENVO:00002007] Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid. + ENVO:00001998 Soil [ENVO:00001998] Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. + ENVO:00002259 Agricultural soil [ENVO:00002259] A type of soil used for agriculture that supports the physical, chemical, and biological needs of the desired crop during production. + ENVO:00002261 Forest soil [ENVO:00002261] A portion of soil which is found in a forested area. + ENVO:00003869 Straw [ENVO:00003869] An agricultural byproduct, the dry stalk of a cereal plant, after the nutrient grain or seed has been removed. + CHEBI:15377 Water [CHEBI:15377] An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. + ENVO:00003064 Drinking water [ENVO:00003064] Water which is suitable for consumption by humans + ENVO:03501436 Fecal slurry [ENVO:03501436] A mixture of fecal material mixed, buffer, and other materials, that is homogenized and strained and used in fecal microbiota translpantation. + GENEPIO:0004323 Fluid from meat rinse [GENEPIO:0004323] + ENVO:01001004 Groundwater [ENVO:01001004] Underground water which is located in pore spaces found in rock or unconsolidated deposits such as soil, clay, or gravel. + AGRO:00000693 Poultry plucking water [AGRO_00000693] A type of water obtained from rinsing poultry carcasses during the feather plucking process. + ENVO:03501408 Surface runoff [ENVO:03501408] Surface water which is 1) from some rainwater, stormwater, meltwater, or other local source and 2) which can no longer sufficiently rapidly infiltrate into soil, and instead flows along a drainage slope. + ENVO:00002042 Surface water [ENVO:00002042] Water that is found on the surface of an astronomical object. + ENVO:00002001 Wastewater [ENVO:00002001] Water that has been adversely affected in quality by anthropogenic influence + ENVO:00002044 Sludge [ENVO:00002044] The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes. + ENVO:00002057 Primary sludge [ENVO:00002057] Sludge generated from the initial processes (i.e., precipitation, sedimentation) of wastewater treatment. + ENVO:00002058 Secondary sludge [ENVO:00002058] Activated waste biomass generated during wastewater treatment. + GENEPIO:0100891 Wastewater effluent [GENEPIO:0100891] + GENEPIO:0100892 Primary wastewater effluent [GENEPIO:0100892] A wastewater effluent which has been discharged from a primary clarifier after the first stage of sedimentation. + GENEPIO:0100893 Secondary wastewater effluent [GENEPIO:0100893] A wastewater effluent which has been discharged from a secondary clarifier after the second stage of sedimentation. + GENEPIO:0100890 Wastewater sediment [GENEPIO:0100890] + AGRO:00000692 Weep fluid [AGRO:00000692] A fluid that leaks from a bag containing an animal carcass, and can include water, chemicals and anatomical fluids. + +anatomical_material menu AnatomicalMaterialMenu UBERON:0000178 Blood [UBERON:0000178] A fluid that is composed of blood plasma and erythrocytes. + UBERON:0006314 Fluid [UBERON:0006314] Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. + UBERON:0001359 Fluid (cerebrospinal (CSF)) [UBERON:0001359] A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. + UBERON:0000173 Fluid (amniotic) [UBERON:0000173] Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. + UBERON:0001836 Saliva [UBERON:0001836] A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. + UBERON:0000479 Tissue [UBERON:0000479] Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. + +body_product menu BodyProductMenu GENEPIO:0100898 Digestive tract substance [GENEPIO:0100898] Undigested food material, microbiota, and other materials found in the digestive tract. + GENEPIO:0100899 Caecal content [GENEPIO:0100899] Undigested food material, microbiota, and other materials found in the cecum + GENEPIO:0100900 Intestinal content [GENEPIO:0100900] Undigested food material, microbiota, and other materials found in the intestine + GENEPIO:0100901 Stomach content [GENEPIO:0100901] Undigested food material, microbiota, and other materials found in the stomach + UBERON:0001988 Feces [UBERON:0001988] Portion of semisolid bodily waste discharged through the anus. + GENEPIO:0004512 Fecal composite [GENEPIO:0004512] A mixture of feces obtained from multiple individuals. + GENEPIO:0004513 Feces (fresh) [GENEPIO:0004513] Feces that was recently excreted. + GENEPIO:0004514 Feces (environmental) [GENEPIO:0004514] Feces which is deposited in the environment. + UBERON:0007109 Meconium [UBERON:0007109] A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth. + UBERON:0001913 Milk [UBERON:0001913] An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. + UBERON:0001914 Colostrum [UBERON:0001914] The thin, yellow, serous fluid secreted by the mammary glands during pregnancy and immediately postpartum before lactation begins. It consists of immunologically active substances, white blood cells, water, protein, fat, and carbohydrates. [ MESH : A12.200.194 http://en.wikipedia.org/wiki/Colostrum ] + UBERON:0000912 Mucus [UBERON:0000912] Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. + UBERON:0001088 Urine [UBERON:0001088] Excretion that is the output of a kidney. + +anatomical_part menu AnatomicalPartMenu UBERON:0008979 Carcass [UBERON:0008979] A body of a multi-cellular organism that is no longer living. + UBERON:0001007 Digestive system [UBERON:0001007] Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. + UBERON:0001153 Caecum [UBERON:0001153] pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. + UBERON:0001155 Colon [UBERON:0001155] A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. + UBERON:0006925 Digestive gland [UBERON:0006925] Any gland that is part of the digestive system. + UBERON:0001041 Foregut [UBERON:0001041] Anterior subdivision of a digestive tract. + UBERON:0002110 Gall bladder [UBERON:0002110] An organ that aids digestion and stores bile produced by the liver. + UBERON:0004786 Gastrointestinal system mucosa [UBERON:0004786] A mucosa that is part of a gastrointestinal system. + UBERON:0005052 Gizzard [UBERON:0005052] The muscular enlargement of the alimentary canal that has usually thick muscular walls and a tough horny lining for grinding the food and when the crop is present follows it and the proventriculus. + UBERON:0001046 Hindgut [UBERON:0001046] The caudalmost subdivision of a digestive tract. + UBERON:0000160 Intestine [UBERON:0000160] Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. + UBERON:0002108 Small intestine [UBERON:0002108] Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum. + UBERON:0002114 Duodenum [UBERON:0002114] The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). + UBERON:0002116 Ileum [UBERON:0002116] The portion of the small intestine that extends from the jejunum to the colon. + UBERON:0002115 Jejunum [UBERON:0002115] The portion of the small intestine that extends from the duodenum to the ileum. + UBERON:0000945 Stomach [UBERON:0000945] An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. + UBERON:0007358 Abomasum [UBERON:0007358] The fourth stomach of ruminating animals, which is an elongated pear-shaped sac lying on the floor of the abdomen, on the right-hand side, and roughly between the seventh and twelfth ribs. It leads to the beginning of the small intestine. + UBERON:0007365 Rumen [UBERON:0007365] The first compartment of the ruminant stomach. It lies on the left side of the body, occupying the whole of the left side of the abdomen and even stretching across the median plane of the body to the right side. It is capacious, divided into an upper and a lower sac, each of which has a blind sac at its posterior extremity. + Excretory system (organizational term) + UBERON:0001245 Anus [UBERON:0001245] Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. + UBERON:0011253 Anal gland [UBERON:0011253] A type of gland occurring as solitary or in pairs or groups, near the anus and sometimes opening into the rectum. + UBERON:0000162 Cloaca [UBERON:0000162] Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures. + UBERON:0002107 Liver [UBERON:0002107] An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes + UBERON:0002113 Kidney [UBERON:0002113] A paired organ of the urinary tract which has the production of urine as its primary function. + UBERON:0001052 Rectum [UBERON:0001052] The terminal portion of the intestinal tube, terminating with the anus. + UBERON:0002106 Spleen [UBERON:0002106] The organ that functions to filter blood and to store red corpuscles and platelets. + UBERON:0001255 Urinary bladder [UBERON:0001255] Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion. + UBERON:0002387 Foot [UBERON:0002387] The terminal part of the vertebrate leg upon which an individual stands. 2: An invertebrate organ of locomotion or attachment; especially: a ventral muscular surface or process of a mollusk. + UBERON:0000033 Head [UBERON:0000033] The head is the anterior-most division of the body. + UBERON:0000955 Brain [UBERON:0000955] The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell. + UBERON:0001690 Ear [UBERON:0001690] Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. + UBERON:0000970 Eye [UBERON:0000970] An organ that detects light. + UBERON:0000165 Mouth [UBERON:0000165] The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). + UBERON:0000004 Nose [UBERON:0000004] The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. + UBERON:0035612 Nasal turbinal [UBERON:0035612] A skeletal element of the ethmoid region with complex morphology that are lined with mucuous membranes involved in either olfaction or air conditioning. + UBERON:0001728 Nasopharynx (NP) [UBERON:0001728] The section of the pharynx that lies above the soft palate. + UBERON:0002109 Pair of nares [UBERON:0002109] Pair of nostrils. + UBERON:0001825 Paranasal sinus [UBERON:0001825] The paired air-filled cavities surrounded by the bones of the face that are lined by mucous membranes and are continuous with the nasal cavity. + UBERON:0006333 Snout [UBERON:0006333] The projecting nose and mouth of an animal, especially a mammal. + UBERON:0006558 Lymphatic system [UBERON:0006558] An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system. + UBERON:0000029 Lymph node [UBERON:0000029] Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. + UBERON:0002509 Mesenteric lymph node [UBERON:0002509] The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group. + GENEPIO:0100927 Mantle (bird) [GENEPIO:0100927] The forward area of a bird's upper side that is sandwiched between the nape and the start of the back. + UBERON:0000974 Neck [UBERON:0000974] An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. + UBERON:0001043 Esophagus [UBERON:0001043] Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation. + UBERON:0003126 Trachea [UBERON:0003126] The trachea is the portion of the airway that attaches to the bronchi as it branches. + UBERON:0001021 Nerve [UBERON:0001021] An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. + UBERON:0002240 Spinal cord [UBERON:0002240] Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. + GENEPIO:0001117 Organs or organ parts [GENEPIO:0001117] An object aggregate which has as members whole organs or parts of organs, possibly from different organisms. + UBERON:0000062 Organ [UBERON:0000062] Anatomical structure that performs a specific function or group of functions + UBERON:0001630 Muscle organ [UBERON:0001630] Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work. + UBERON:0002097 Skin of body [UBERON:0002097] The organ covering the body that consists of the dermis and epidermis. + UBERON:0000990 Reproductive system [UBERON:0000990] Anatomical system that has as its parts the organs concerned with reproduction. + UBERON:0000922 Embryo [UBERON:0000922] Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. + UBERON:0000323 Fetus [UBERON:0000323] An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching + UBERON:0000992 Ovary [UBERON:0000992] The gonad of a female organism which contains germ cells. + UBERON:0000993 Oviduct [UBERON:0000993] A tube or collection of tubes in an animal from the ovaries to the outside of the body. + UBERON:0001987 Placenta [UBERON:0001987] Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. + UBERON:0000473 Testis [UBERON:0000473] A gonad of a male animal. A gonad produces and releases sperm. + UBERON:0013216 Udder [UBERON:0013216] A large pendulous organ consisting of two or more mammary glands enclosed in a common envelope and each provided with a single nipple. + UBERON:0000995 Uterus [UBERON:0000995] The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth. + UBERON:0000996 Vagina [UBERON:0000996] A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles + UBERON:0001040 Yolk sac [UBERON:0001040] A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes. + UBERON:0001004 Respiratory system [UBERON:0001004] Functional system which consists of structures involved in respiration. + UBERON:0009060 Air sac [UBERON:0009060] Any of the membranous air-filled extensions of the lungs of birds, which increase the efficiency of gaseous exchange in the lungs. + UBERON:0002048 Lung [UBERON:0002048] Respiration organ that develops as an outpocketing of the esophagus + UBERON:0000977 Pleura [UBERON:0000977] The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). + UBERON:0004785 Respiratory system mucosa [UBERON:0004785] The mucous membrane lining the respiratory tract. + UBERON:0001434 Skeletal system [UBERON:0001434] Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. + UBERON:0000982 Skeletal joint [UBERON:0000982] Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue. + UBERON:0001474 Bone element [UBERON:0001474] Skeletal element that is composed of bone tissue. + UBERON:0000915 Thoracic segment of trunk [UBERON:0000915] Subdivision of trunk that lies between the head and the abdomen. + UBERON:0000916 Abdomen [UBERON:0000916] The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. + UBERON:0002378 Muscle of abdomen [UBERON:0002378] Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. + UBERON:0002358 Peritoneum [UBERON:0002358] Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. + UBERON:0007798 Vascular system [UBERON:0007798] Anatomical system that consists of all blood and lymph vessels. + UBERON:0001981 Blood vessel [UBERON:0001981] A vessel through which blood circulates in the body. + UBERON:0003903 Bursa of Fabricius [UBERON:0003903] An epithelial and lymphoid organ that develops as a dorsal diverticulum of the proctodeal region of the cloaca in birds. The luminal (interior) surface of the bursa is plicated with as many as 15 primary and 7 secondary plicae or folds. These plicae have hundreds of bursal follicles containing follicle-associated epithelial cells, lymphocytes, macrophages, and plasma cells. Lymphoid stem cells migrate from the fetal liver to the bursa during ontogeny. In the bursa, these stem cells acquire the characteristics of mature, immunocompetent B cells. The bursa is an organ found in birds involved in B cell differentiation. + UBERON:0002535 Gill [UBERON:0002535] Anatomical surface structure found in many aquatic organisms. It is a respiration organ whose function is the extraction of oxygen from water and the excretion of carbon dioxide. The microscopic structure of a gill is such that it presents a very large surface area to the external environment. Gills usually consist of thin filaments of tissue, branches, or slender tufted processes which have a highly folded surface to increase surface area. A high surface area is crucial to the gas exchange of aquatic organisms as water contains only 1/20 parts dissolved Oxygen compared to air. With the exception of some aquatic insects, the filaments and lamellae (folds) contain blood or coelomic fluid, from which gases are exchanged through the thin walls. Oxygen is carried by the blood to other parts of the body. Carbon dioxide passes from the blood through the thin gill tissue into the water. Gills or gill-like organs, located in different parts of the body, are found in various groups of aquatic animals, including mollusks, crustaceans, insects, fish, and amphibians. [ http://en.wikipedia.org/wiki/Gill ] + UBERON:0000948 Heart [UBERON:0000948] A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. + UBERON:0002048 Lung [UBERON:0002048] Respiration organ that develops as an outpocketing of the esophagus + UBERON:0002407 Pericardium [UBERON:0002407] The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. + UBERON:2000298 Vent (anatomical) [UBERON:2000298] The external opening of the rectum or cloaca. + UBERON:0012464 Bird vent [UBERON:0012464] The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. [ http://orcid.org/0000-0002-6601-2165 ] + GENEPIO:0100902 Fish vent [GENEPIO:0100902] The external opening which opens to the reproductive and digestive tracts of the fish. During spawning, the vent serves as an outlet for eggs and sperm. In most fishes, the vent is in front of the anal fin. + +collection_device menu CollectionDeviceMenu ENVO:00003968 Air filter [ENVO:00003968] + AGRO:00000405 Auger (earth auger) [AGRO:00000405] Manually operated hand tool that consists of cutter head having semicircular blades connected to pipe with the help of clamp and flange. The connecting pipe is further connected to a handle. + GSSO:008558 Bag [GSSO:008558] A sac or pouch. + GENEPIO:0002122 Whirlpak sampling bag [GENEPIO:0002122] A sterilized sampling bag that is puncture proof tabs for protection from damage due to wire-end protrusion and leak-proof closures. + FOODON:03490214 Bottle [FOODON:03490214] A rigid or semirigid container typically of glass or plastic having a comparatively narrow neck or mouth and usually no handle. + GENEPIO:0100928 Box corer [GENEPIO:0100928] A specimen collection device that is used to collect soft sediments in lakes or oceans. + OBI:0002826 Bronchoscope [OBI:0002826] A device which is a thin, tube-like instrument which includes a light and a lens used to examine a lung. + OBI:0002088 Collection Container [OBI:0002088] A container with the function of containing a specimen. + GENEPIO:0100026 Collection Cup [GENEPIO:0100026] A device which is used to collect liquid samples. + GENEPIO:0004318 Culture plate [GENEPIO:0004318] A low flat-bottomed laboratory container for growing a layer of organisms such as bacteria, molds, and cells on a thin layer of nutrient medium. + NCIT:C96141 Petri dish [NCIT:C96141] A shallow dish with a lid used to culture cells. + OBI:0002825 Fibrobronchoscope Brush [OBI:0002825] + GENEPIO:0100103 Filter [GENEPIO:0100103] A manufactured product which separates solids from fluids by adding a medium through which only a fluid can pass. + OBI:0002827 Fine Needle [OBI:0002827] + OBI:0001128 Micropipette [OBI:0001128] + OBI:0000436 Needle [OBI:0000436] A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. + GENEPIO:0100929 PONAR grab sampler [GENEPIO:0100929] A specimen collection device that is designed to collect sediment samples from the hard bottoms of a body of water i.e. sand, gravel, consolidated marl or clay." + GENEPIO:0002125 Scoop [GENEPIO:0002125] A shovel-like utensil that has a deep curved dish and a short handle and is used for digging into a soft substance for lifting out a portion. + GENEPIO:0100930 Soil sample probe [GENEPIO:0100930] A specimen collection device designed to penetrate soil with a hollow tube to collect soil sample cores. + CIT:C149941 Spatula [NCIT:C149941] + OBI:0002819 Sponge [OBI:0002819] A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter. + OBI:0002831 Suction Catheter [OBI:0002831] A catheter which is used to remove mucus and other secretions from the body. + GENEPIO:0100027 Swab [GENEPIO:0100027] A device which is a soft, absorbent material mounted on one or both ends of a stick. + OBI:0002822 Drag swab [OBI:0002822] A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string + OBI:0002824 Surface wipe [OBI:0002824] A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces. + GENEPIO:0101196 Tube [GENEPIO:0101196] A sample collection device which is cylindrical shape that is open at one end, used to collect material. + OBI:0002859 Blood Collection Tube [OBI:0002859] A specimen collection tube which is designed for the collection of whole blood. See also: https://en.wikipedia.org/wiki/Blood_culture#Collection + OBI:0002858 Microcapillary tube [OBI:0002858] + OBI:0002860 Serum Collection Tube [OBI:0002860] A specimen collection tube which is designed for collecting whole blood and enabling the separation of serum. + OBI:0002861 Sputum Collection Tube [OBI:0002861] A specimen collection tube which is designed for collecting sputum. + OBI:0002862 Urine Collection Tube [OBI:0002862] A specimen container which is designed for holding urine. + GENEPIO:0002127 Vacuum device [GENEPIO:0002127] A device which generates a vacuum to provide suction of material. + OBIB:0000032 Vacutainer [OBIB:0000032] A test tube which is either a sterile glass or plastic tube with a closure that is evacuated to create a vacuum inside the tube facilitating the draw of a predetermined volume of liquid. Most commonly used to draw a blood sample directly from the vein, these also are used to collect urine samples. Vacutainer tube may contain additives designed to stabilize and preserve the specimen prior to analytical testing. + +collection_method menu CollectionMethodMenu HP:0002835 Aspiration [HP:0002835] Inspiration of a foreign object into the airway. + OBI:0002650 Biopsy [OBI:0002650] A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. + GENEPIO:0004326 Fecal grab [GENEPIO:0004326] A fecal specimen collection method in which feces is obtained by inserting the collection device into the anus of the host, or the feces is captured as it is excreted. + OBI:0302885 Filtration [OBI:0302885] A process which separates components suspended in a fluid based on granularity properties relying on a filter device. + GENEPIO:0100031 Air filtration [GENEPIO:0100031] A filtration process which removes solid particulates from the air via an air filtration device. + GENEPIO:0100931 Water filtration [GENEPIO:0100931] A filtration process which removes or reduces the concentration of particulate matter, including suspended particles, parasites, bacteria, algae, viruses, and fungi, as well as other undesirable chemical and biological contaminants from contaminated water using water filters to produce safe and clean water. + OBI:0600044 Lavage [OBI:0600044] A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid + GENEPIO:0100032 Bronchoalveolar lavage [GENEPIO:0100032] The collection of bronchoalveolar lavage fluid (BAL) from the lungs. + GENEPIO:0100033 Gastric lavage [GENEPIO:0100033] The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach. + MMO:0000344 Necropsy [MMO:0000344] A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. + NCIT:C28221 Phlebotomy [NCIT:C28221] The collection of blood from a vein, most commonly via needle venipuncture. + GENEPIO:0002116 Rinsing for specimen collection [GENEPIO_0002116] The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids. + GENEPIO:0100932 Scooping [GENEPIO:0100932] A specimen collection process that is used to dig out an amount of sample using a scoop. + GENEPIO:0100933 Sediment collection [GENEPIO:0100933] A specimen collection process that is used to collect a sediment sample. + GENEPIO:0100934 Soil coring [GENEPIO:0100934] A specimen collection process that is used to collect soil sample cores. + GENEPIO:0101003 Weep fluid collection (pouring) [GENEPIO:0101003] A specimen collection process that is used to collect weep fluid via pouring from the source container into the sample collection device. (e.g. bag or tube) + +sample_volume_measurement_unit menu SampleVolumeMeasurementUnitMenu UO:0000101 microliter (uL) [UO:0000101] A metric unit of volume equivalent to one thousandth of a cubic centimeter or one millionth of a liter. + UO:0000098 milliliter (mL) [UO:0000098] A metric unit of volume equivalent to one cubic centimeter or one thousandth of a liter. + UO:0000099 liter (L) [UO:0000099] A metric unit of volume equivalent to 1000 cubic centimeters + +residual_sample_status menu ResidualSampleStatusMenu GENEPIO:0101087 Residual sample remaining (some sample left) [GENEPIO:0101087] + GENEPIO:0101088 No residual sample (sample all used) [GENEPIO:0101088] + GENEPIO:0101089 Residual sample status unkown [GENEPIO:0101089] + + +purpose of sampling PurposeOfSampling GENEPIO:0100001 Cluster/Outbreak investigation [GENEPIO:0100001] A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. + GENEPIO:0100002 Diagnostic testing [GENEPIO:0100002] A sampling strategy in which individuals are sampled in the context of diagnostic testing. + GENEPIO:0100548 Environmental testing [GENEPIO:0100548] A sampling strategy in which environments are sampled in the context of testing for the presence of, or change in the levels of, chemicals, pathogens or other phenomena. + GENEPIO:0100003 Research [GENEPIO:0100003] A sampling strategy in which samples are collected in order to perform research. + GENEPIO:0100549 Clinical trial [GENEPIO:0100549] A sampling strategy in which individuals are sampled in the context of experiments or observations performed as part of clinical research. + GENEPIO:0100550 Field experiment [GENEPIO:0100550] A sampling strategy in which samples are taken during real-life experiments which test directly whether proposed interventions actually work. + GENEPIO:0100582 Survey study [GENEPIO:0100582] A sampling strategy in which individuals and/or materials are sampled for surveillance performed for research purposes. + GENEPIO:0100004 Surveillance [GENEPIO:0100004] A sampling strategy in which individuals are sampled for surveillance investigations. + +presampling activity PresamplingActivity GENEPIO:0100536 Addition of substances to food/water [GENEPIO:0100536] The addition of substances to food or water administered to an individual or group of individuals. + GENEPIO:0100537 Antimicrobial pre-treatment [GENEPIO:0100537] The administration of an antimicrobial agent to an individual or its addition to a substance prior to some other event or activity. + GENEPIO:0100538 Certified animal husbandry practices [GENEPIO:0100538] The implementation of animal husbandy practices that have been certified by an authorized organization. + GENEPIO:0100894 Certified humane animal husbandry practices [GENEPIO:0100894] A certification organization in Washington DC that is dedicated to improving the lives of farm animals in food production from birth through slaughter. + GENEPIO:0100539 Certified organic farming practices [GENEPIO:0100539] The implementation of organic farming practices that have been certified by an authorized organization. + GENEPIO:0100895 Conventional farming practices [GENEPIO:0100895] The implementation of farming practices that include man-made inputs such as chemical fertilizers and genetically-modified seeds. + GENEPIO:0100540 Change in storage conditions [GENEPIO:0100540] A change in the storage conditions of a material or a substance. + GENEPIO:0100541 Cleaning/disinfection [GENEPIO:0100541] A process of removing unwanted substances, such as dirt, infectious agents, and other impurities, from an object or environment. + GENEPIO:0100542 Extended downtime between activities [GENEPIO:0100542] A prolonged period of inactivity between processes or events. + GENEPIO:0100546 Microbial pre-treatment [GENEPIO:0100546] The deliberate addition of microbes or a mixture of microbes to an individual or substance prior to some other event or activity. + GENEPIO:0100547 Probiotic pre-treatment [GENEPIO:0100547] The addition of a probiotic substance to an individual or material prior to some other event or activity. + NCIT:C15346 Vaccination [NCIT:C15346] Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis or treatment. + +sample storage duration unit SampleStorageDurationUnit UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + UO:0000031 Minute [UO:0000031] A time unit which is equal to 60 seconds. + UO:0000032 Hour [UO:0000032] A time unit which is equal to 60 minutes. + UO:0000033 Day [UO:0000033] A time unit which is equal to 24 hours. + UO:0000034 Week [UO:0000034] A time unit which is equal to 7 days. + UO:0000035 Month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. + UO:0000036 Year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. + +specimen processing SpecimenProcessing OBI:0600041 Concentration [OBI:0600041] A process used to increase the density of a material of interest by removing other materials in the entity containing the material of interest. + OBI:0302886 Centrifugation [OBI:0302886] A process separating molecules by size or density using centrifugal forces generated by a spinning rotor. + OBI:0302885 Filtration [OBI:0302885] A process which separates components suspended in a fluid based on granularity properties relying on a filter device. + OBI:0600016 Pooling specimens [OBI:0600016] Physical combination of several instances of like material. + +experimental specimen role type ExperimentalSpecimenRoleType GENEPIO:0101018 Positive experimental control [GENEPIO:0101018] A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment. + GENEPIO:0101123 Validation strain [GENEPIO:0101123] + GENEPIO:0101124 Proficiency test isolate [GENEPIO:0101124] + GENEPIO:0101019 Negative experimental control [GENEPIO:0101019] A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment + EFO:0002090 Technical replicate [EFO:0002090] A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment. + EFO:0002091 Biological replicate [EFO:0002091] A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples. + GENEPIO:0101039 Synthetic lab construct [GENEPIO:0101039] + GENEPIO:0101120 Negative sample [GENEPIO:0101120] + +available_data_types menu AvailableDataTypesMenu GENEPIO:0100702 Documentation [GENEPIO:0100702] A dataset attribute bundle which indicates the presence of documentation data. + GENEPIO:0100703 Experimental parameters documentation [GENEPIO:0100703] A documentation data tag which indicates the presence of data that describes experimental parameters. + GENEPIO:0100704 Feed history [GENEPIO:0100704] A documentation data tag which indicates the presence of data that describes feed history. + GENEPIO:0100705 Land use information [GENEPIO:0100705] A documentation data tag which indicates the presence of data that describes land use information. + GENEPIO:0100706 Therapeutic administration history [GENEPIO:0100706] A documentation data tag which indicates the presence of data that describes a history of therapeutic administration. + GENEPIO:0100707 Chemical characterization [GENEPIO:0100707] A dataset attribute bundle which indicates the presence of chemical characterization data. + GENEPIO:0100714 Microbiological characterization [GENEPIO:0100714] A dataset attribute bundle which indicates the presence of microbiological characterization data. + GENEPIO:0100715 Microbiological identification [GENEPIO:0100715] A microbiological characterization data tag which indicates the presence of microbiological identification data. + GENEPIO:0100716 Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Beckson Dickson BBL Crystal identification system. + GENEPIO:0100717 Microbiological identification (bioMérieux API) [GENEPIO:0100717] A microbiological characterization data tag which indicates the presence of microbiological identification data dervied using the bioMérieux API identification system. + GENEPIO:0100718 Microbiological identification (Biolog) [GENEPIO:0100718] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Biolog identification system. + GENEPIO:0100719 Microbiological identification (FAME) [GENEPIO:0100719] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Fatty acid methyl esters (FAME) identification system. + GENEPIO:0100720 Microbiological identification (Sensititre) [GENEPIO:0100720] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Sensititre identification system. + GENEPIO:0100721 Microbiological identification (ViTek) [GENEPIO:0100721] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the ViTek identification system. + GENEPIO:0100722 Phage type [GENEPIO:0100722] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using phage type identification. + GENEPIO:0100723 Serotype [GENEPIO:0100723] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using serotype identification. + GENEPIO:0100724 Phenotypic microbiological characterization [GENEPIO:0100724] A microbiological characterization data tag which indicates the presence of phenotypic microbiological characterization data. + GENEPIO:0100725 AMR phenotypic testing [GENEPIO:0100725] A phenotypic microbiological characterization data tag which indicates the presence of antimicrobial resistance (AMR) phenotypic testing characterization data. + GENEPIO:0100726 Biolog phenotype microarray [GENEPIO:0100726] A phenotypic microbiological characterization data tag which indicates the presence of biolog phenotype microarray characterization data. + GENEPIO:0100727 Microbiological quantification [GENEPIO:0100727] A dataset attribute bundle which indicates the presence of microbiological quantification data. + GENEPIO:0100728 Colony count [GENEPIO:0100728] A microbiological quantification data tag which indicates the presence of colony count data. + GENEPIO:0100729 Total coliform count [GENEPIO:0100729] A colony count microbiological quantification data tag which indicates the presence of data that describes total colony count of coliforms. + GENEPIO:0100730 Total fecal coliform count [GENEPIO:0100730] A colony count microbiological quantification data tag that indicates the presence of data which describes total colony count of fecal coliforms. + GENEPIO:0100731 Infectivity assay [GENEPIO:0100731] A microbiological quantification data tag which indicates the presence of infectivity assay data. + GENEPIO:0100732 ELISA toxin binding [GENEPIO:0100732] A microbiological quantification data tag which indicates the presence of data which describes enzyme-linked immunosorbent assay (ELISA) toxin binding. + GENEPIO:0100733 Molecular characterization [GENEPIO:0100733] A dataset attribute bundle which indicates the presence of molecular characterization data. + GENEPIO:0100734 16S rRNA Sanger sequencing [GENEPIO:0100734] A molecular characterization data tag which indicates the presence of 16S rRNA Sanger sequencing characterization data. + GENEPIO:0101024 Metagenomic sequencing [GENEPIO:0101024] A molecular characterization data tag which indicates the presence of metagenomic sequencing characterization data. + GENEPIO:0100735 PCR marker detection [GENEPIO:0100735] A molecular characterization data tag which indicates the presence of polymerase chain reaction (PCR) marker detection characterization data. + GENEPIO:0100736 BOX PCR fingerprint [GENEPIO:0100736] A PCR marker detection characterization data tag which indicates the presence of BOX-A1R-based repetitive extragenic palindromic (BOX) PCR fingerprint data. + GENEPIO:0100737 ERIC PCR fingerprint [GENEPIO:0100737] A PCR marker detection characterization data tag which indicates the presence of enterobacterial repetitive intergenic consensus (ERIC) PCR fingerprint data. + GENEPIO:0100738 Plasmid type [GENEPIO:0100738] A molecular characterization data tag which indicates the presence of plasmid type characterization data. + GENEPIO:0100739 Ribotype [GENEPIO:0100739] A molecular characterization data tag which indicates the presence of ribotype characterization data. + GENEPIO:0100740 Molecular quantification [GENEPIO:0100740] A dataset attribute bundle which indicates the presence of molecular quantification data. + GENEPIO:0100741 qPCR marker organism quantification [GENEPIO:0100741] A molecular quantification data tag which indicates the presence of quantitative polymerase chain reaction (qPCR) marker organism quantification data. + GENEPIO:0100742 Physical characterization [GENEPIO:0100742] A dataset attribute bundle which indicates the presence of physical characterization data. + GENEPIO:0100743 Conductivity measurement [GENEPIO:0100743] A physical characterization data tag which indicates the presence of data that describes conductivity measurement characterization. + GENEPIO:0100744 Mollusc shell measurement [GENEPIO:0100744] A physical characterization data tag which indicates the presence of data that describes a measurement of a mollusc shell. + GENEPIO:0100746 Matter compostion [GENEPIO:0100746] A physical characterization data tag which indicates the presence of matter compostion characterization data. + GENEPIO:0100747 Dry matter composition [GENEPIO:0100747] A matter composition characterization data tag which indicates the presence of data that describes dry matter composition. + GENEPIO:0100748 Organic matter composition [GENEPIO:0100748] A matter composition characterization data tag which indicates the presence of data that describes organic matter composition. + +host (common name) menu HostCommonNameMenu NCBITaxon:8782 Bird [NCBITaxon:8782] A group of warm-blooded vertebrates in class Aves, that are characterized by feathers, wings, toothless beaked jaws and the laying of hard-shelled eggs and are usually able to fly. + NCBITaxon:9031 Chicken [NCBITaxon:9031] "A domesticated junglefowl of the species Gallus gallus. " + FOODON:00004504 Seabird [FOODON:00004504] A bird that is adapted to live within the marine environment. + NCBITaxon:9206 Cormorant [NCBITaxon:9206] A family of aquatic birds (Phalacrocoracidae). + NCBITaxon:56069 Double Crested Cormorant [NCBITaxon:56069] A species of the cormorant family of water birds (Phalacrocorax auritus). + NCBITaxon:9109 Crane [NCBITaxon:9109] A family of large, long-legged, and long-necked birds (Gruidae). + NCBITaxon:9117 Whooping Crane [NCBITaxon:9117] An endangered crane species that is native to North America and is named for its whooping sound. + NCBITaxon:8911 Gull (Seagull) [NCBITaxon:8911] A large genus of gulls within the family Laridae. + NCBITaxon:119606 Glaucous-winged Gull [NCBITaxon:119606] A species of large, white-headed gull (Larus glaucescens). + NCBITaxon:8912 Great Black-backed Gull [NCBITaxon:8912] A species of white gull that has a black back and wings (Larus marinus). + NCBITaxon:35669 Herring Gull [NCBITaxon:35669] A species of large gull, that is up to 66 cm (26 in) long (Larus argentatus). + NCBITaxon:126683 Ring-billed Gull [NCBITaxon:126683] A species of ring-billed gull that has a black ring around its bill (Larus delawarensis). + NCBITaxon:50366 Eider [NCBITaxon:50366] A genus of large seaducks (Somateria). + NCBITaxon:76058 Common Eider [NCBITaxon:76058] A species of a large sea-duck that is distributed over the northern coasts of Europe, North America and eastern Siberia (Somateria mollissima). + NCBITaxon:9103 Turkey [NCBITaxon:9103] A large, mainly domesticated game bird characterized by a bald head and wattles (in the male) of the species Meleagris gallopavo. + FOODON:03411222 Fish [FOODON:03411222] Fish are the gill-bearing aquatic craniate animals that lack limbs with digits. Most fish are ectothermic ("cold-blooded"), allowing their body temperatures to vary as ambient temperatures change, though some of the large active swimmers like white shark and tuna can hold a higher core temperature. + FOODON:03411134 Mammal [FOODON:03411134] Mammals (from Latin mamma "breast") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones. + FOODON:03000300 Companion animal [FOODON:03000300] An animal that is kept as a companion. + NCBITaxon:9913 Cow [NCBITaxon:9913] A group of large, domesticated, cloven-hooved herbivores. + NCBITaxon:9850 Deer [NCBITaxon:9850] + NCBITaxon:9606 Human [NCBITaxon:9606] A bipedal primate mammal of the species Homo sapiens. + NCBITaxon:9823 Pig [NCBITaxon:9823] A stout-bodied, hooved and short-legged, omnivorous mammal from the species Sus scofus, with thick skin usually sparsely coated with short bristles. + NCBITaxon:9940 Sheep [NCBITaxon:9940] A domesticated, even-toed, ungluate, ruminant mammal typically kept as livestock for its wool and meat, usually of the species Ovis aries. + FOODON:03411433 Shellfish [FOODON:03411433] The term shellfish is used both broadly and specifically. For regulatory purposes it is often narrowly defined as filter-feeding molluscs such as clams, mussels, and oyster to the exclusion of crustaceans and all else. Although their shells may differ, all shellfish are invertebrates. + + +host (scientific name) menu HostScientificNameMenu NCBITaxon:229290 Anoplopoma fimbria [NCBITaxon:229290] One of two members of the fish family Anoplopomatidae and the only species in the genus Anoplopoma. + NCBITaxon:9913 Bos taurus [NCBITaxon:9913] A group of large, domesticated, cloven-hooved herbivores. + NCBITaxon:6565 Crassostrea virginica [NCBITaxon:6565] A species of true oyster (Crassostrea virginica). + NCBITaxon:9031 Gallus gallus [NCBITaxon:9031] "A domesticated junglefowl of the species Gallus gallus. " + NCBITaxon:9117 Grus americana [NCBITaxon:9117] An endangered crane species that is native to North America and is named for its whooping sound. + NCBITaxon:6706 Homarus americanus [NCBITaxon:6706] A species of lobster that is found on the Atlantic coast of North America (Homarus americanus). + NCBITaxon:9606 Homo sapiens [NCBITaxon:9606] A bipedal primate mammal of the species Homo sapiens. + NCBITaxon:35669 Larus argentatus [NCBITaxon:35669] A species of large gull, that is up to 66 cm (26 in) long (Larus argentatus). + NCBITaxon:126683 Larus delawarensis [NCBITaxon:126683] A species of ring-billed gull that has a black ring around its bill (Larus delawarensis). + NCBITaxon:119606 Larus glaucescens [NCBITaxon:119606] A species of large, white-headed gull (Larus glaucescens). + NCBITaxon:8912 Larus marinus [NCBITaxon:8912] A species of white gull that has a black back and wings (Larus marinus). + NCBITaxon:9103 Meleagris gallopavo [NCBITaxon:9103] A large, mainly domesticated game bird characterized by a bald head and wattles (in the male) of the species Meleagris gallopavo. + NCBITaxon:6550 Mytilus edulis [NCBITaxon:6550] A medium-sized edible marine bivalve mollusc in the family Mytilidae, the mussels. + NCBITaxon:8019 Oncorhynchus kisutch [NCBITaxon:8019] A species of pacific salmon in North America, that is commonly called as coho salmon. + NCBITaxon:8022 Oncorhynchus mykiss [NCBITaxon:8022] A species of trout native to cold-water tributaries of the Pacific Ocean in Asia and North America (Oncorhynchus mykiss). + NCBITaxon:74940 Oncorhynchus tshawytscha [NCBITaxon:74940] The largest species of pacific salmon in North America (Oncorhynchus tshawytscha). + NCBITaxon:9940 Ovis aries [NCBITaxon:9940] A domesticated, even-toed, ungluate, ruminant mammal typically kept as livestock for its wool and meat, usually of the species Ovis aries. + NCBITaxon:56069 Phalacrocorax auritus [NCBITaxon:56069] A species of the cormorant family of water birds (Phalacrocorax auritus). + NCBITaxon:8030 Salmo salar [NCBITaxon:8030] A species of ray-finned fish in the family Salmonidae (Salmo salar). + NCBITaxon:76058 Somateria mollissima [NCBITaxon:76058] A species of a large sea-duck that is distributed over the northern coasts of Europe, North America and eastern Siberia (Somateria mollissima). + NCBITaxon:9825 Sus scrofa domesticus [NCBITaxon:9825] A stout-bodied, hooved and short-legged, omnivorous mammal, with thick skin usually sparsely coated with short bristles raised for its meat. + + +host (food production name) menu HostFoodProductionNameMenu Cow (by age/production stage) (organizational term) + FOODON:03411349 Calf [FOODON:03411349] Calves are the young of domestic cattle. Calves are reared to become adult cattle, or are slaughtered for their meat, called veal. + FOODON:00004411 Dry cow [FOODON:00004411] A cow that is in a stage of its lactation cycle where milk production ceases prior to calving. + FOODON:00004292 Feeder cow [FOODON:00004292] A young cow mature enough either to undergo backgrounding or to be fattened in preparation for slaughter. + FOODON:00004293 Finisher cow [FOODON:00004293] + FOODON:03411201 Milker cow [FOODON:03411201] A cow that is bred specifically for milk production. + FOODON:00004294 Stocker cow [FOODON:00004294] A type of cow that has been weaned and is being fed in a way to add physical bulk to its body. + FOODON:00004295 Weanling cow [FOODON:00004295] A type of young cow that has been weaned and consumes solid food. + Cow (by sex/reproductive stage) (organizational term) + FOODON:00000015 Bull [FOODON:00000015] A cattle bull is an adult "intact" (i.e. not castrated) male of a cattle species. + NCBITaxon:9913 Cow [NCBITaxon:9913] A group of large, domesticated, cloven-hooved herbivores. + FOODON:00004296 Freemartin [FOODON:00004296] A cow that is genetically female, but has many characteristics of a male and is usually infertile. + FOODON:00002518 Heifer [FOODON:00002518] A heifer is a young female, under three years of age, of a cattle species before she has had a calf of her own. + FOODON:00002531 Steer [FOODON:00002531] A cattle steer is an adult castrated male of a cattle species. + Pig (by age/production stage) (organizational term) + FOODON:00003371 Finisher pig [FOODON:00003371] A grower pig over 70 kg (150 lb) liveweight. + FOODON:00003370 Grower pig [FOODON:00003370] A pig between weaning and sale or transfer to the breeding herd, sold for slaughter or killed for rations. + OODON:00004297 Nursing pig [FOODON:00004297 ] + NCBITaxon:9823 Pig [NCBITaxon:9823] A stout-bodied, hooved and short-legged, omnivorous mammal from the species Sus scofus, with thick skin usually sparsely coated with short bristles. + FOODON:00003952 Piglet [FOODON:00003952] An unweaned or immature pig. + FOODON:00003373 Weanling (weaner) pig [FOODON:00003373] A young pig recently separated from the sow + Pig (by sex/reproductive stage) (organizational term) + FOODON:03411280 Barrow [FOODON:03411280] A male swine castrated before sexual maturity. + FOODON:03412248 Boar [FOODON:03412248] An adult male swine. + FOODON:00003369 Gilt [FOODON:00003369] A female pig under the age of 1 year. The term is also often used to refer to a pig who has not farrowed, or given birth to a litter. + FOODON:00003333 Sow [FOODON:00003333] An adult female swine. + FOODON:03411563 Poultry or game bird [FOODON:03411563] Domesticated birds kept by humans for their eggs, their meat or their feathers. + FOODON:03411198 Broiler or fryer chicken [FOODON:03411198] A chicken younger than 10 weeks old (previously younger than 13 weeks), of either sex, that is tender-meated with soft, pliable, smooth-textured skin and flexible breastbone cartilage. + FOODON:03411711 Capon [FOODON:03411711] A surgically neutered male chicken younger than four months old (previously younger than eight months) that is tender-meated with soft, pliable, smooth-textured skin. + FOODON:00004299 Chick [FOODON:00004299] A young offspring of any bird. + NCBITaxon:9031 Chicken [NCBITaxon:9031] "A domesticated junglefowl of the species Gallus gallus. " + UBERON:0007379 Egg [UBERON:0007379] The hard-shelled reproductive body produced by a bird (especially by the common domestic chicken) or a reptile; also: its contents used as food. + FOODON:00004300 Hatchling [FOODON:00004300] A young animal that has recently emerged from its egg. + FOODON:00003282 Hen [FOODON:00003282] An adult female chicken. + FOODON:00004301 Layer chicken [FOODON:00004301] A type of chicken kept for laying eggs. + FOODON:00004302 Layer turkey [FOODON:00004302] A type of turkey kept for laying eggs. + FOODON:00002962 Poult [FOODON:00002962] A poult is a young domestic chicken, turkey, pheasant, or other fowl being raised for food. + FOODON:00004303 Pullet [FOODON:00004303] A young hen, especially one less than one year old. + FOODON:03411714 Rooster [FOODON:03411714] A mature male chicken with coarse skin, toughened and darkened meat, and hardened breastbone tip. + OODON:00004304 Tom (Gobbler) [FOODON:00004304 ] + NCBITaxon:9103 Turkey [NCBITaxon:9103] A large, mainly domesticated game bird characterized by a bald head and wattles (in the male) of the species Meleagris gallopavo. + NCBITaxon:9940 Sheep [NCBITaxon:9940] A domesticated, even-toed, ungluate, ruminant mammal typically kept as livestock for its wool and meat, usually of the species Ovis aries. + FOODON:00004305 Ram [FOODON:00004305] An adult male sheep kept for breeding and for wool production. + FOODON:00004306 Wether sheep [FOODON:00004306] A castrated male sheep. + FOODON:03412610 Ewe [FOODON:03412610] A ewe is a female sheep. + FOODON:03411669 Lamb [FOODON:03411669] A whole lamb or some material processed from a lamb. + FOODON:03411222 Fish [FOODON:03411222] Fish are the gill-bearing aquatic craniate animals that lack limbs with digits. Most fish are ectothermic ("cold-blooded"), allowing their body temperatures to vary as ambient temperatures change, though some of the large active swimmers like white shark and tuna can hold a higher core temperature. + FOODON:00004319 Fish egg [FOODON_00004319] An egg or spawn of a fish that is contained within or separated from the ovary. + FOODON:00004318 Fry (fish) [FOODON_00004318] A fish that is recently hatched and has reached the stage where its yolk-sac has almost disappeared and its swim bladder is operational to the point where the fish can actively feed for itself. + FOODON:00004317 Juvenile fish [FOODON_00004317] A fish that has not reached to sexual maturity. + +host_age_unit menu HostAgeUnitMenu UO:0000035 month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. + UO:0000036 year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. + + +host_age_bin menu HostAgeBinMenu GENEPIO:0100684 First winter [GENEPIO:0100684] An age group used to classify birds identified by their first winter nonbreeding plumage, generally indicating a juvenile bird. + GENEPIO:0100685 First summer [GENEPIO:0100685] An age group used to classify birds identified by their first summer nonbreeding plumage, generally indicating a juvenile bird. + GENEPIO:0100686 Second winter [GENEPIO:0100686] An age group used to classify birds identified by their second winter plumage (many types of birds molt several times during the same season). + GENEPIO:0100687 Second summer [GENEPIO:0100687] An age group used to classify birds identified by their second summer plumage (many types of birds molt several times during the same season). + GENEPIO:0100688 Third winter [GENEPIO:0100688] An age group used to classify birds identified by their third winter plumage (many types of birds molt several times during the same season). + GENEPIO:0100689 Third summer [GENEPIO:0100689] An age group used to classify birds identified by their third summer plumage (many types of birds molt several times during the same season). + ENEPIO:0100049 0 - 9 [GENEPIO:0100049]] + GENEPIO:0100050 10 - 19 [GENEPIO:0100050] An age group that stratifies the age of a case to be between 10 to 19 years old (inclusive). + GENEPIO:0100051 20 - 29 [GENEPIO:0100051] An age group that stratifies the age of a case to be between 20 to 29 years old (inclusive). + GENEPIO:0100052 30 - 39 [GENEPIO:0100052] An age group that stratifies the age of a case to be between 30 to 39 years old (inclusive). + GENEPIO:0100053 40 - 49 [GENEPIO:0100053] An age group that stratifies the age of a case to be between 40 to 49 years old (inclusive). + GENEPIO:0100054 50 - 59 [GENEPIO:0100054] An age group that stratifies the age of a case to be between 50 to 59 years old (inclusive). + GENEPIO:0100055 60 - 69 [GENEPIO:0100055] An age group that stratifies the age of a case to be between 60 to 69 years old (inclusive). + GENEPIO:0100056 70 - 79 [GENEPIO:0100056] An age group that stratifies the age of a case to be between 70 to 79 years old (inclusive). + GENEPIO:0100057 80 - 89 [GENEPIO:0100057] An age group that stratifies the age of a case to be between 80 to 89 years old (inclusive). + GENEPIO:0100058 90 - 99 [GENEPIO:0100058] An age group that stratifies the age of a case to be between 90 to 99 years old (inclusive). + GENEPIO:0100059 100+ [GENEPIO:0100059] An age group that stratifies the age of a case to be greater than or equal to 100 years old. + +host_gender HostGender NCIT:C46110 Female [NCIT:C46110] An individual who reports belonging to the cultural gender role distinction of female. + NCIT:C46109 Male [NCIT:C46109] An individual who reports belonging to the cultural gender role distinction of male. + GSSO:000132 Non-binary gender [GSSO:000132] Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female. + GSSO:004004 Transgender (assigned male at birth) [GSSO:004004] Having a feminine gender (identity) which is different from the sex one was assigned at birth. + GSSO:004005 Transgender (assigned female at birth) [GSSO:004005] Having a masculine gender (identity) which is different from the sex one was assigned at birth. + CIT:C110959 Undeclared [NCIT:C110959] + + + +host_disease menu HostDiseaseMenu Highly pathogenic avian influenza A (HPAI) + +host_health_state menu HostHealthStateMenu NCIT:C3833 Asymptomatic [NCIT:C3833] Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction. + NCIT:C28554 Deceased [NCIT:C28554] The cessation of life. + CIT:C115935 Healthy [NCIT:C115935] + NCIT:C49498 Recovered [NCIT:C49498] One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated. + NCIT:C25269 Symptomatic [NCIT:C25269] Exhibiting the symptoms of a particular disease. + +host_health_status_details menu HostHealthStatusDetailsMenu NCIT:C25179 Hospitalized [NCIT:C25179] The condition of being treated as a patient in a hospital. + GENEPIO:0100045 Hospitalized (Non-ICU) [GENEPIO:0100045] The condition of being treated as a patient in a hospital without admission to an intensive care unit (ICU). + GENEPIO:0100046 Hospitalized (ICU) [GENEPIO:0100046] The condition of being treated as a patient in a hospital intensive care unit (ICU). + NCIT:C70909 Mechanical Ventilation [NCIT:C70909] + GENEPIO:0100047 Medically Isolated [GENEPIO:0100047] Separation of people with a contagious disease from population to reduce the spread of the disease. + GENEPIO:0100048 Medically Isolated (Negative Pressure) [GENEPIO:0100048] Medical isolation in a negative pressure environment: 6 to 12 air exchanges per hour, and direct exhaust to the outside or through a high efficiency particulate air filter. + CIT:C173768 Self-quarantining [NCIT:C173768] + +host_health_outcome menu HostHealthOutcomeMenu NCIT:C28554 Deceased [NCIT:C28554] The cessation of life. + NCIT:C25254 Deteriorating [NCIT:C25254] Advancing in extent or severity. + NCIT:C49498 Recovered [NCIT:C49498] One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated. + NCIT:C30103 Stable [NCIT:C30103] Subject to little fluctuation; showing little if any change. + +signs_and_symptoms menu SignsAndSymptomsMenu HP:0030829 Abnormal lung auscultation [HP:0030829] + HP:0033677 Acute Respiratory Distress Syndrome [HP:0033677] + HP:0011446 Altered mental status [HP:0011446] + HP:0100543 Cognitive impairment [HP:0100543] + HP:0001259 Coma [HP:0001259] + HP:0001289 Confusion [HP:0001289] + HP:0031258 Delirium (sudden severe confusion) [HP:0031258] + HP:0011675 Arrhythmia [HP:0011675] + HP:0025406 Asthenia (generalized weakness) [HP:0025406] + GENEPIO:0101182 Bleeding gums [GENEPIO:0101182] + HP:0031352 Chest tightness or pressure [HP:0031352] + HP:0025145 Rigors (fever shakes) [HP:0025145] + HP:0025143 Chills (sudden cold sensation) [HP:0025143] A sudden sensation of feeling cold. + HP:0000509 Conjunctivitis (pink eye) [HP:0000509] Inflammation of the conjunctiva. + MP:0001867 Coryza (rhinitis) [MP:0001867] + HP:0012735 Cough [HP:0012735] A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. + HP:0031246 Nonproductive cough (dry cough) [HP:0031246] + HP:0031245 Productive cough (wet cough) [HP:0031245] + DOID:13250 Diarrhea [DOID:13250] + HP:0002094 Dyspnea (breathing difficulty) [HP:0002094] + HP:0012378 Fatigue (tiredness) [HP:0012378] A subjective feeling of tiredness characterized by a lack of energy and motivation. + HP:0001945 Fever [HP:0001945] Body temperature elevated above the normal range. + GENEPIO:0100066 Fever (>=38°C) [GENEPIO:0100066] + HP:0002315 Headache [HP:0002315] Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve. + HP:0012418 Hypoxemia (low blood oxygen) [HP:0012418] + GENEPIO:0100068 Silent hypoxemia [GENEPIO:0100068] + HP:0033834 Malaise (general discomfort/unease) [HP:0033834] + HP:0001324 Muscle weakness [HP:0001324] + HP:0001742 Nasal obstruction (stuffy nose) [HP:0001742] + HP:0002018 Nausea [HP:0002018] A sensation of unease in the stomach together with an urge to vomit. + HP:0012531 Pain [HP:0012531] + HP:0002829 Arthralgia (painful joints) [HP:0002829] + HP:0003326 Myalgia (muscle pain) [HP:0003326] Pain in muscle. + HP:0025439 Pharyngitis (sore throat) [HP:0025439] + HP:0031417 Rhinorrhea (runny nose) [HP:0031417] + HP:0025144 Shivering (involuntary muscle twitching) [HP:0025144] + HP:0025095 Sneezing [HP:0025095] + HP:0033709 Sputum Production [HP:0033709] + HP:0002716 Swollen Lymph Nodes [HP:0002716] Enlargment (swelling) of a lymph node. + HP:0002789 Tachypnea (accelerated respiratory rate) [HP:0002789] + HP:0002013 Vomiting (throwing up) [HP:0002013] Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. + +pre-existing_conditions_and_risk_factors menu PreExistingConditionsAndRiskFactorsMenu VO:0004925 Age 60+ [VO:0004925] + DOID:2355 Anemia [DOID:2355] + DOID:2860 Hemoglobinopathy [DOID:2860] + HP:0002039 Anorexia [HP:0002039] + NCIT:C92743 Birthing labor [NCIT:C92743] + NCIT:C80693 Bone marrow failure [NCIT:C80693] + MONDO:0004992 Cancer [MONDO:0004992] A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas. + MONDO:0007254 Breast cancer [MONDO:0007254] + MONDO:0005575 Colorectal cancer [MONDO:0005575] + DOID:2531 Hematologic malignancy (cancer of the blood) [DOID:2531] + MONDO:0008903 Lung cancer [MONDO:0008903] + MONDO:0024880 Metastatic disease [MONDO:0024880] + NCIT:C16212 Cancer treatment [NCIT:C16212] Any intervention for management of a malignant neoplasm. + NCIT:C157740 Cancer surgery [NCIT:C157740] + NCIT:C15632 Chemotherapy [NCIT:C15632] The use of synthetic or naturally-occurring chemicals for the treatment of diseases. + NCIT:C15360 Adjuvant chemotherapy [NCIT:C15360] + NCIT:C3079 Cardiac disorder [NCIT:C3079] + HP:0011675 Arrhythmia [HP:0011675] + MONDO:0005267 Cardiac disease [MONDO:0005267] + HP:0001638 Cardiomyopathy [HP:0001638] + GENEPIO:0100074 Cardiac injury [GENEPIO:0100074] + HP:0000822 Hypertension (high blood pressure) [HP:0000822] + HP:0002615 Hypotension (low blood pressure) [HP:0002615] + HP:0011410 Cesarean section [HP:0011410] + GENEPIO:0100075 Chronic cough [GENEPIO:0100075] + GENEPIO:0100076 Chronic gastrointestinal disease [GENEPIO:0100076] + NCIT:C211 Corticosteroids [NCIT:C211] + HP:0000819 Diabetes mellitus (diabetes) [HP:0000819] A group of abnormalities characterized by hyperglycemia and glucose intolerance. + HP:0100651 Type I diabetes mellitus (T1D) [HP:0100651] A chronic condition in which the pancreas produces little or no insulin. Type I diabetes mellitus is manifested by the sudden onset of severe hyperglycemia with rapid progression to diabetic ketoacidosis unless treated with insulin. + HP:0005978 Type II diabetes mellitus (T2D) [HP:0005978] A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia. + HP:0000964 Eczema [HP:0000964] + HP:0003111 Electrolyte disturbance [HP:0003111] + HP:0002901 Hypocalcemia [HP:0002901] + HP:0002900 Hypokalemia [HP:0002900] + HP:0002917 Hypomagnesemia [HP:0002917] + HP:0002383 Encephalitis (brain inflammation) [HP:0002383] + MONDO:0005027 Epilepsy [MONDO:0005027] + NCIT:C15248 Hemodialysis [NCIT:C15248] + MONDO:0044348 Hemoglobinopathy [MONDO:0044348] + MONDO:0005109 Human immunodeficiency virus (HIV) [MONDO:0005109] An infection caused by the human immunodeficiency virus. + MONDO:0012268 Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268] A syndrome resulting from the acquired deficiency of cellular immunity caused by the human immunodeficiency virus (HIV). It is characterized by the reduction of the Helper T-lymphocytes in the peripheral blood and the lymph nodes. + NCIT:C16118 HIV and antiretroviral therapy (ART) [NCIT:C16118] Treatment of human immunodeficiency virus (HIV) infections with medications that target the virus directly, limiting the ability of infected cells to produce new HIV particles. + NCIT:C14139 Immunocompromised [NCIT:C14139] A loss of any arm of immune functions, resulting in potential or actual increase in infections. This state may be reached secondary to specific genetic lesions, syndromes with unidentified or polygenic causes, acquired deficits from other disease states, or as result of therapy for other diseases or conditions. + MONDO:0004670 Lupus [MONDO:0004670] An autoimmune, connective tissue chronic inflammatory disorder affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood cells. It is more commonly seen in women than men. Variants include discoid and systemic lupus erythematosus. + MONDO:0005265 Inflammatory bowel disease (IBD) [MONDO:0005265] + HP:0002583 Colitis [HP:0002583] + HP:0100279 Ulcerative colitis [HP:0100279] + HP:0100280 Crohn's disease [HP:0100280] + NCIT:C3149 Renal disorder [NCIT:C3149] + MONDO:0005240 Renal disease [MONDO:0005240] + HP:0012622 Chronic renal disease [HP:0012622] + HP:0000083 Renal failure [HP:0000083] + MONDO:0005154 Liver disease [MONDO:0005154] + NCIT:C113609 Chronic liver disease [NCIT:C113609] + HP:0001397 Fatty liver disease (FLD) [HP:0001397] + HP:0003326 Myalgia (muscle pain) [HP:0003326] Pain in muscle. + MONDO:0005404 Myalgic encephalomyelitis (ME) [MONDO:0005404] + MONDO:0005071 Neurological disorder [MONDO:0005071] + MONDO:0019056 Neuromuscular disorder [MONDO:0019056] + HP:0001513 Obesity [HP:0001513] + MONDO:0005139 Severe obesity [MONDO:0005139] + MONDO:0005087 Respiratory disorder [MONDO:0005087] + HP:0002099 Asthma [HP:0002099] + HP:0004469 Chronic bronchitis [HP:0004469] + HP:0006510 Chronic obstructive pulmonary disease [HP:0006510] + HP:0002097 Emphysema [HP:0002097] + MONDO:0005275 Lung disease [MONDO:0005275] + HP:0006528 Chronic lung disease [HP:0006528] + HP:0002206 Pulmonary fibrosis [HP:0002206] + HP:0002090 Pneumonia [HP:0002090] + HP:0002878 Respiratory failure [HP:0002878] + HP:0033677 Adult respiratory distress syndrome [HP:0033677] + MONDO:0009971 Newborn respiratory distress syndrome [MONDO:0009971] + MONDO:0018076 Tuberculosis [MONDO:0018076] + GENEPIO:0100077 Postpartum (≤6 weeks) [GENEPIO:0100077] + NCIT:C25742 Pregnancy [NCIT:C25742] The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth. + DOID:14525 Reye syndrome [DOID:14525] + MONDO:0005554 Rheumatic disease [MONDO:0005554] + MONDO:0011382 Sickle cell disease [MONDO:0011382] + NBO:0001845 Substance use [NBO:0001845] + MONDO:0002046 Alcohol abuse [MONDO:0002046] + GENEPIO:0100078 Drug abuse [GENEPIO:0100078] + GENEPIO:0100079 Injection drug abuse [GENEPIO:0100079] + NBO:0015005 Smoking [NBO:0015005] + NCIT:C173621 Vaping [NCIT:C173621] + HP:0002789 Tachypnea (accelerated respiratory rate) [HP:0002789] + CIT:C159659 Transplant [NCIT:C159659] + NCIT:C131759 Cardiac transplant [NCIT:C131759] + GENEPIO:0100080 Hematopoietic stem cell transplant (bone marrow transplant) [GENEPIO:0100080] + NCIT:C157332 Kidney transplant [NCIT:C157332] + GENEPIO:0100081 Liver transplant [GENEPIO:0100081] + +complications menu ComplicationsMenu HP:0500165 Abnormal blood oxygen level [HP:0500165] + MONDO:0015796 Acute lung injury [MONDO:0015796] + GENEPIO:0100092 Ventilation induced lung injury (VILI) [GENEPIO:0100092] + MONDO:0001208 Acute respiratory failure [MONDO:0001208] + HP:0011675 Arrhythmia (complication) [HP:0011675] + HP:0001649 Tachycardia [HP:0001649] + GENEPIO:0100074 Cardiac injury [GENEPIO:0100074] + HP:0001695 Cardiac arrest [HP:0001695] + HP:0001977 Blood clot [HP:0001977] + HP:0004420 Arterial clot [HP:0004420] + HP:0002625 Deep vein thrombosis (DVT) [HP:0002625] + HP:0002204 Pulmonary embolism (PE) [HP:0002204] + HP:0001638 Cardiomyopathy [HP:0001638] + MONDO:0024619 Central nervous system invasion [MONDO:0024619] + HP:0001297 Stroke (complication) [HP:0001297] + MONDO:0003346 Central Nervous System Vasculitis [MONDO:0003346] + HP:0002140 Acute ischemic stroke [HP:0002140] + HP:0001259 Coma [HP:0001259] + HP:0011097 Convulsions [HP:0011097] + MONDO:0009061 Cystic fibrosis [MONDO:0009061] + MONDO:0600008 Cytokine release syndrome [MONDO:0600008] + MPATH:108 Disseminated intravascular coagulation (DIC) [MPATH:108] + HP:0001298 Encephalopathy [HP:0001298] + GENEPIO:0100088 Fulminant myocarditis [GENEPIO:0100088] + MONDO:0016218 Guillain-Barré syndrome [MONDO:0016218] + HP:0011029 Internal hemorrhage (complication; internal bleeding) [HP:0011029] + MONDO:0013792 Intracerebral haemorrhage [MONDO:0013792] + MONDO:0012727 Kawasaki disease [MONDO:0012727] + GENEPIO:0100089 Complete Kawasaki disease [GENEPIO:0100089] + GENEPIO:0100090 Incomplete Kawasaki disease [GENEPIO:0100090] + HP:0001410 Liver dysfunction [HP:0001410] + GENEPIO:0100091 Acute liver injury [GENEPIO:0100091] + MONDO:0100233 Long COVID-19 [MONDO:0100233] + HP:0001287 Meningitis [HP:0001287] + HP:0002076 Migraine [HP:0002076] + HP:0005268 Miscarriage [HP:0005268] + MONDO:0100163 Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163] + MONDO:0100319 Multisystem inflammatory syndrome in adults (MIS-A) [MONDO:0100319] + GENEPIO:0100093 Muscle injury [GENEPIO:0100093] + MONDO:0005404 Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404] + MONDO:0005068 Myocardial infarction (heart attack) [MONDO:0005068] + HP:0001700 Myocardial injury [HP:0001700] + CIT:C168498 Neonatal complications [NCIT:C168498] + GENEPIO:0100085 Noncardiogenic pulmonary edema [GENEPIO:0100085] + HP:0033677 Acute respiratory distress syndrome (ARDS) [HP:0033677] + GENEPIO:0100094 Organ failure [GENEPIO:0100094] + HP:0003470 Paralysis [HP:0003470] + HP:0002107 Pneumothorax (collapsed lung) [HP:0002107] + HP:0002090 Pneumonia (complication) [HP:0002090] + HP:0001197 Pregancy complications [HP:0001197] + HP:0003201 Rhabdomyolysis [HP:0003201] + IDO:0000567 Secondary infection [IDO:0000567] An infection bearing the secondary infection role. + HP:0001250 Seizure (complication) [HP:0001250] + HP:0100806 Sepsis/Septicemia [HP:0100806] Systemic inflammatory response to infection. + IDO:0000636 Sepsis (systemic inflammatory response to infection) [IDO:0000636] + NCIT:C3364 Septicemia (bloodstream infection) [NCIT:C3364] + HP:0031273 Shock [HP:0031273] + GENEPIO:0100097 Hyperinflammatory shock [GENEPIO:0100097] + NCIT:C35018 Septic shock [NCIT:C35018] + HP:0002633 Vasculitis [HP:0002633] + +exposure_event menu ExposureEventMenu GENEPIO:0100237 Mass Gathering [GENEPIO:0100237] A gathering or event attended by a sufficient number of people to strain the planning and response resources of the host community, state/province, nation, or region where it is being held. + GENEPIO:0100238 Convention [GENEPIO:0100238] A gathering of individuals who meet at an arranged place and time in order to discuss or engage in some common interest. The most common conventions are based upon industry, profession, and fandom. + GENEPIO:0100239 Convocation [GENEPIO:0100239] + GENEPIO:0100240 Agricultural Event [GENEPIO:0100240] A gathering exhibiting the equipment, animals, sports and recreation associated with agriculture and animal husbandry. + GENEPIO:0100241 Religious Gathering [GENEPIO:0100241] + GENEPIO:0100242 Mass [GENEPIO:0100242] + PCO:0000033 Social Gathering [PCO:0000033] A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. + PCO:0000039 Baby Shower [PCO:0000039] + PCO:0000034 Community Event [PCO:0000034] + GENEPIO:0100243 Family Gathering [GENEPIO:0100243] + GENEPIO:0100244 Family Reunion [GENEPIO:0100244] + GENEPIO:0100245 Funeral [GENEPIO:0100245] + PCO:0000035 Party [PCO:0000035] + PCO:0000037 Potluck [PCO:0000037] + PCO:0000038 Wedding [PCO:0000038] + GENEPIO:0101183 Animal contact event [GENEPIO:0101183] + GENEPIO:0101185 Trip to a live animal market [GENEPIO:0101185] + GENEPIO:0101186 Trip to a farm [GENEPIO:0101186] + GENEPIO:0101188 Wildlife encounter [GENEPIO:0101188] + GENEPIO:0101184 Hunting trip [GENEPIO:0101184] + GENEPIO:0101187 Animal transportation event [GENEPIO:0101187] + Other exposure event + +exposure_contact_level menu ExposureContactLevelMenu GENEPIO:0101189 Contact with infected animal [GENEPIO:0101189] + GENEPIO:0101190 Direct (host-to-animal contact) [GENEPIO:0101190] + GENEPIO:0101191 Indirect contact (host-to-animal) [GENEPIO:0101191] + GENEPIO:0101192 Close animal contact (face-to-face contact) [GENEPIO:0101192] + GENEPIO:0101193 Casual animal contact [GENEPIO:0101193] + Contact with infected individual + TRANS:0000001 Direct (human-to-human contact) [TRANS:0000001] Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission. + GENEPIO:0100246 Indirect contact [GENEPIO:0100246] A type of contact in which an individual does not come in direct contact with a source of infection e.g. through airborne transmission, contact with contaminated surfaces. + GENEPIO:0100247 Close contact (face-to-face contact) [GENEPIO:0100247] A type of indirect contact where an individual sustains unprotected exposure by being within 6 feet of an infected individual over a sustained period of time. + GENEPIO:0100248 Casual contact [GENEPIO:0100248] A type of indirect contact where an individual may at the same location at the same time as a positive case; however, they may have been there only briefly, or it may have been a location that carries a lower risk of transmission. + +host_role menu HostRoleMenu GENEPIO:0100249 Attendee [GENEPIO:0100249] A role inhering in a person that is realized when the bearer is present on a given occasion or at a given place. + OMRSE:00000058 Student [OMRSE:00000058] A human social role that, if realized, is realized by the process of formal education that the bearer undergoes. + OMRSE:00000030 Patient [OMRSE:00000030] A patient role that inheres in a human being. + NCIT:C25182 Inpatient [NCIT:C25182] A patient who is residing in the hospital where he is being treated. + NCIT:C28293 Outpatient [NCIT:C28293] A patient who comes to a healthcare facility for diagnosis or treatment but is not admitted for an overnight stay. + GENEPIO:0100250 Passenger [GENEPIO:0100250] A role inhering in a person that is realized when the bearer travels in a vehicle but bears little to no responsibility for vehicle operation nor arrival at its destination. + GENEPIO:0100251 Resident [GENEPIO:0100251] A role inhering in a person that is realized when the bearer maintains residency in a given place. + GENEPIO:0100252 Visitor [GENEPIO:0100252] A role inhering in a person that is realized when the bearer pays a visit to a specific place or event. + GENEPIO:0100253 Volunteer [GENEPIO:0100253] A role inhering in a person that is realized when the bearer enters into any service of their own free will. + GENEPIO:0100254 Work [GENEPIO:0100254] A role inhering in a person that is realized when the bearer performs labor for a living. + GENEPIO:0100255 Administrator [GENEPIO:0100255] A role inhering in a person that is realized when the bearer is engaged in administration or administrative work. + GENEPIO:0100256 First Responder [GENEPIO:0100256] A role inhering in a person that is realized when the bearer is among the first to arrive at the scene of an emergency and has specialized training to provide assistance. + GENEPIO:0100257 Firefighter [GENEPIO:0100257] + GENEPIO:0100258 Paramedic [GENEPIO:0100258] + GENEPIO:0100259 Police Officer [GENEPIO:0100259] + GENEPIO:0100260 Housekeeper [GENEPIO:0100260] A role inhering in a person that is realized when the bearer is an individual who performs cleaning duties and/or is responsible for the supervision of cleaning staff. + GENEPIO:0100261 Kitchen Worker [GENEPIO:0100261] A role inhering in a person that is realized when the bearer is an employee that performs labor in a kitchen. + GENEPIO:0100334 Healthcare Worker [GENEPIO:0100334] A role inhering in a person that is realized when the bearer is an employee that performs labor in a healthcare setting. + GENEPIO:0100420 Community Healthcare Worker [GENEPIO:0100420] A role inhering in a person that is realized when the bearer a professional caregiver that provides health care or supportive care in the individual home where the patient or client is living, as opposed to care provided in group accommodations like clinics or nursing home. + GENEPIO:0100262 Laboratory Worker [GENEPIO:0100262] A role inhering in a person that is realized when the bearer is an employee that performs labor in a laboratory. + OMRSE:00000014 Nurse [OMRSE:00000014] A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life. + GENEPIO:0100263 Personal Care Aid [GENEPIO:0100263] A role inhering in a person that is realized when the bearer works to help another person complete their daily activities. + GENEPIO:0100264 Pharmacist [GENEPIO:0100264] A role inhering in a person that is realized when the bearer is a health professional who specializes in dispensing prescription drugs at a healthcare facility. + OMRSE:00000013 Physician [OMRSE:00000013] A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments. + GENEPIO:0100354 Rotational Worker [GENEPIO:0100354] A role inhering in a person that is realized when the bearer performs labor on a regular schedule, often requiring travel to geographic locations other than where they live. + GENEPIO:0100355 Seasonal Worker [GENEPIO:0100355] A role inhering in a person that is realized when the bearer performs labor for a particular period of the year, such as harvest, or Christmas. + GENEPIO:0100265 Veterinarian [GENEPIO:0100265] A role inhering in a person that is realized when the bearer is a professional who practices veterinary medicine. + OMRSE:00000001 Social role [OMRSE:00000001] A social role inhering in a human being. + GENEPIO:0100266 Acquaintance of case [GENEPIO:0100266] A role inhering in a person that is realized when the bearer is in a state of being acquainted with a person. + GENEPIO:0100267 Relative of case [GENEPIO:0100267] A role inhering in a person that is realized when the bearer is a relative of the case. + GENEPIO:0100268 Child of case [GENEPIO:0100268] A role inhering in a person that is realized when the bearer is a person younger than the age of majority. + GENEPIO:0100269 Parent of case [GENEPIO:0100269] A role inhering in a person that is realized when the bearer is a caregiver of the offspring of their own species. + GENEPIO:0100270 Father of case [GENEPIO:0100270] A role inhering in a person that is realized when the bearer is the male parent of a child. + GENEPIO:0100271 Mother of case [GENEPIO:0100271] A role inhering in a person that is realized when the bearer is the female parent of a child. + GENEPIO:0100272 Spouse of case [GENEPIO:0100272] A role inhering in a person that is realized when the bearer is a significant other in a marriage, civil union, or common-law marriage. + Other Host Role + +exposure_setting menu ExposureSettingMenu ECTO:3000005 Human Exposure [ECTO:3000005] A history of exposure to Homo sapiens. + GENEPIO:0100185 Contact with Patient [GENEPIO:0100185] A process occuring within or in the vicinity of a human patient that exposes the recipient organism to a material entity. + GENEPIO:0100187 Contact with Person with Acute Respiratory Illness [GENEPIO:0100187] + GENEPIO:0100188 Contact with Person with Fever and/or Cough [GENEPIO:0100188] + GENEPIO:0100190 Occupational, Residency or Patronage Exposure [GENEPIO:0100190] A process occuring within or in the vicinity of a human residential environment that exposes the recipient organism to a material entity. + ECTO:1000033 Abbatoir [ECTO:1000033] A exposure event involving the interaction of an exposure receptor to abattoir. + GENEPIO:0100191 Animal Rescue [GENEPIO:0100191] A process occuring within or in the vicinity of an animal rescue facility that exposes the recipient organism to a material entity. + GENEPIO:0100192 Childcare [GENEPIO:0100192] A process occuring within or in the vicinity of a human childcare environment that exposes the recipient organism to a material entity. + GENEPIO:0100193 Daycare [GENEPIO:0100193] A process occuring within or in the vicinity of a human daycare environment that exposes the recipient organism to a material entity. + GENEPIO:0100194 Nursery [GENEPIO:0100194] A process occuring within or in the vicinity of a human nursery that exposes the recipient organism to a material entity. + GENEPIO:0100195 Community Service Centre [GENEPIO:0100195] A process occuring within or in the vicinity of a community service centre that exposes the recipient organism to a material entity. + GENEPIO:0100196 Correctional Facility [GENEPIO:0100196] A process occuring within or in the vicinity of a correctional facility that exposes the recipient organism to a material entity. + GENEPIO:0100197 Dormitory [GENEPIO:0100197] A process occuring within or in the vicinity of a dormitory that exposes the recipient organism to a material entity. + ECTO:1000034 Farm [ECTO:1000034] A exposure event involving the interaction of an exposure receptor to farm + GENEPIO:0100198 First Nations Reserve [GENEPIO:0100198] A process occuring within or in the vicinity of a first nations reserve that exposes the recipient organism to a material entity. + GENEPIO:0100199 Funeral Home [GENEPIO:0100199] A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity. + GENEPIO:0100200 Group Home [GENEPIO:0100200] A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity. + GENEPIO:0100201 Healthcare Setting [GENEPIO:0100201] A process occuring within or in the vicinity of a healthcare environment that exposes the recipient organism to a material entity. + GENEPIO:0100202 Ambulance [GENEPIO:0100202] A process occuring within or in the vicinity of an ambulance that exposes the recipient organism to a material entity. + GENEPIO:0100203 Acute Care Facility [GENEPIO:0100203] A process occuring within or in the vicinity of an acute care facility that exposes the recipient organism to a material entity. + GENEPIO:0100204 Clinic [GENEPIO:0100204] A process occuring within or in the vicinity of a medical clinic that exposes the recipient organism to a material entity. + GENEPIO:0100415 Community Healthcare (At-Home) Setting [GENEPIO:0100415] A process occuring within or in the vicinty of a the individual home where the patient or client is living and health care or supportive care is being being delivered, as opposed to care provided in group accommodations like clinics or nursing home. + GENEPIO:0100205 Community Health Centre [GENEPIO:0100205] A process occuring within or in the vicinity of a community health centre that exposes the recipient organism to a material entity. + ECTO:1000035 Hospital [ECTO:1000035] A exposure event involving the interaction of an exposure receptor to hospital. + GENEPIO:0100206 Emergency Department [GENEPIO:0100206] A process occuring within or in the vicinity of an emergency department that exposes the recipient organism to a material entity. + GENEPIO:0100207 ICU [GENEPIO:0100207] A process occuring within or in the vicinity of an ICU that exposes the recipient organism to a material entity. + GENEPIO:0100208 Ward [GENEPIO:0100208] A process occuring within or in the vicinity of a hospital ward that exposes the recipient organism to a material entity. + ECTO:1000036 Laboratory [ECTO:1000036] A exposure event involving the interaction of an exposure receptor to laboratory facility. + GENEPIO:0100209 Long-Term Care Facility [GENEPIO:0100209] A process occuring within or in the vicinity of a long-term care facility that exposes the recipient organism to a material entity. + GENEPIO:0100210 Pharmacy [GENEPIO:0100210] A process occuring within or in the vicinity of a pharmacy that exposes the recipient organism to a material entity. + GENEPIO:0100211 Physician's Office [GENEPIO:0100211] A process occuring within or in the vicinity of a physician's office that exposes the recipient organism to a material entity. + GENEPIO:0100212 Household [GENEPIO:0100212] A process occuring within or in the vicinity of a household that exposes the recipient organism to a material entity. + GENEPIO:0100213 Insecure Housing (Homeless) [GENEPIO:0100213] A process occuring that exposes the recipient organism to a material entity as a consequence of said organism having insecure housing. + GENEPIO:0100214 Occupational Exposure [GENEPIO:0100214] A process occuring within or in the vicinity of a human occupational environment that exposes the recipient organism to a material entity. + GENEPIO:0100215 Worksite [GENEPIO:0100215] A process occuring within or in the vicinity of an office that exposes the recipient organism to a material entity. + ECTO:1000037 Office [ECTO:1000037] A exposure event involving the interaction of an exposure receptor to office. + GENEPIO:0100216 Outdoors [GENEPIO:0100216] A process occuring outdoors that exposes the recipient organism to a material entity. + ECTO:5000009 Camp/camping [ECTO:5000009] A exposure event involving the interaction of an exposure receptor to campground. + GENEPIO:0100217 Hiking Trail [GENEPIO:0100217] A process that exposes the recipient organism to a material entity as a consequence of hiking. + ECTO:6000030 Hunting Ground [ECTO:6000030] An exposure event involving hunting behavior + ECTO:5000008 Petting zoo [ECTO:5000008] A exposure event involving the interaction of an exposure receptor to petting zoo. + GENEPIO:0100220 Place of Worship [GENEPIO:0100220] A process occuring within or in the vicinity of a place of worship that exposes the recipient organism to a material entity. + GENEPIO:0100221 Church [GENEPIO:0100221] A process occuring within or in the vicinity of a church that exposes the recipient organism to a material entity. + GENEPIO:0100222 Mosque [GENEPIO:0100222] A process occuring within or in the vicinity of a mosque that exposes the recipient organism to a material entity. + GENEPIO:0100223 Temple [GENEPIO:0100223] A process occuring within or in the vicinity of a temple that exposes the recipient organism to a material entity. + ECTO:1000040 Restaurant [ECTO:1000040] A exposure event involving the interaction of an exposure receptor to restaurant. + ECTO:1000041 Retail Store [ECTO:1000041] A exposure event involving the interaction of an exposure receptor to shop. + GENEPIO:0100224 School [GENEPIO:0100224] A process occuring within or in the vicinity of a school that exposes the recipient organism to a material entity. + GENEPIO:0100225 Temporary Residence [GENEPIO:0100225] A process occuring within or in the vicinity of a temporary residence that exposes the recipient organism to a material entity. + GENEPIO:0100226 Homeless Shelter [GENEPIO:0100226] A process occuring within or in the vicinity of a homeless shelter that exposes the recipient organism to a material entity. + GENEPIO:0100227 Hotel [GENEPIO:0100227] A process occuring within or in the vicinity of a hotel exposure that exposes the recipient organism to a material entity. + GENEPIO:0100228 Veterinary Care Clinic [GENEPIO:0100228] A process occuring within or in the vicinity of a veterinary facility that exposes the recipient organism to a material entity. + GENEPIO:0100229 Travel Exposure [GENEPIO:0100229] A process occuring as a result of travel that exposes the recipient organism to a material entity. + GENEPIO:0100230 Travelled on a Cruise Ship [GENEPIO:0100230] A process occuring within or in the vicinity of a cruise ship that exposes the recipient organism to a material entity. + GENEPIO:0100231 Travelled on a Plane [GENEPIO:0100231] A process occuring within or in the vicinity of an airplane that exposes the recipient organism to a material entity. + GENEPIO:0100232 Travelled on Ground Transport [GENEPIO:0100232] A process occuring within or in the vicinity of ground transport that exposes the recipient organism to a material entity. + GENEPIO:0001118 Travelled outside Province/Territory [GENEPIO:0001118] + GENEPIO:0001119 Travelled outside Canada [GENEPIO:0001119] + GENEPIO:0100235 Other Exposure Setting [GENEPIO:0100235] A process occuring that exposes the recipient organism to a material entity. + +host_vaccination_status menu HostVaccinationStatusMenu GENEPIO:0100100 Fully Vaccinated [GENEPIO:0100100] Completed a full series of an authorized vaccine according to the regional health institutional guidance. + GENEPIO:0100102 Not Vaccinated [GENEPIO:0100102] Have not completed or initiated a vaccine series authorized and administered according to the regional health institutional guidance. + +influenza_antiviral_treatment_administration menu InfluenzaAntiviralTreatmentAdministrationMenu GENEPIO:0101194 Influenza antiviral treatment administered [GENEPIO:0101194] + GENEPIO:0101195 No influenza antiviral treatment administered [GENEPIO:0101195] + +water_catchment_area_human_population_range menu WaterCatchmentAreaHumanPopulationRangeMenu <10 people + 10 - 100 people + 100 - 1,000 people + 1,000 - 10,000 people + 10,000 - 100,000 people + 100,000 - 1,000,000 people + 1,000,000+ people + +water_catchment_area_human_population_density_unit menu WaterCatchmentAreaHumanPopulationDensityUnitMenu GENEPIO:0100989 persons per square mile [GENEPIO:0100989] A unit of population density that describes the average number of people in a square mile of a given area. + GENEPIO:0100990 persons per square kilometer [GENEPIO:0100990] A unit of population density that describes the average number of people in a square kilometer of a given area. + GENEPIO:0100991 residents per square mile [GENEPIO:0100991] A unit of population density that describes the average number of registered residents in a square mile of a given area. + GENEPIO:0100992 residents per square kilometer [GENEPIO:0100992] A unit of population density that describes the average number of registered residents in a square kilometer of a given area. + +populated_area_type menu PopulatedAreaTypeMenu GSSO:011077 Suburban [GSSO:011077] A mixed-use or residential area, existing either as part of a city/urban area, or as a separate residential community within commuting distance of one. Suburbs might have their own political or legal jurisdiction, especially in the United States, but this is not always the case, especially in the United Kingdom where most suburbs are located within the administrative boundaries of cities. + GSSO:011078 Rural [GSSO:011078] A geographic area that is located outside towns and cities. Rural areas are primarily used for agriculture or pastoralism and may contain rural settlements. + GSSO:011080 Urban [GSSO:011080] A human settlement with a high population density and infrastructure of built environment. Urban areas are created through urbanization and are categorized by urban morphology as cities, towns, conurbations or suburbs. In urbanism, the term contrasts to rural areas such as villages and hamlets; in urban sociology or urban anthropology it contrasts with natural environment. + +sampling_weather_conditions menu SamplingWeatherConditionsMenu ENVO:03501418 Cloudy/Overcast [ENVO:03501418] Atmospheric weather in which the sky is mostly or completely obscured by clouds. + ENVO:03501419 Partially cloudy [ENVO:03501419] Atmospheric weather in which the sky is partially obscured by clouds. + ENVO:03501420 Drizzle [ENVO:03501420] An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process. + ENVO:01000844 Fog [ENVO:01000844] A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body. + ENVO:01001564 Rain [ENVO:01001564] An aggregate of raindrops falling to a planetary surface during a precipitation process. + ENVO:01000406 Snow [ENVO:01000406] Snow is an environmental material which is primarily composed of flakes of crystalline water ice. + ENVO:01000876 Storm [ENVO:01000876] A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates. + ENVO:03501421 Sunny/Clear [ENVO:03501421] Atmospheric weather in which the sun can be seen to shine brightly. + +presampling_weather_conditions menu PresamplingWeatherConditionsMenu ENVO:03501418 Cloudy/Overcast [ENVO:03501418] Atmospheric weather in which the sky is mostly or completely obscured by clouds. + ENVO:03501419 Partially cloudy [ENVO:03501419] Atmospheric weather in which the sky is partially obscured by clouds. + ENVO:03501420 Drizzle [ENVO:03501420] An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process. + ENVO:01000844 Fog [ENVO:01000844] A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body. + ENVO:01001564 Rain [ENVO:01001564] An aggregate of raindrops falling to a planetary surface during a precipitation process. + ENVO:01000406 Snow [ENVO:01000406] Snow is an environmental material which is primarily composed of flakes of crystalline water ice. + ENVO:01000876 Storm [ENVO:01000876] A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates. + ENVO:03501421 Sunny/Clear [ENVO:03501421] Atmospheric weather in which the sun can be seen to shine brightly. + +precipitation_measurement_unit menu PrecipitationMeasurementUnitMenu UO:0000016 millimeter (mm) [UO:0000016] A length unit which is defined as one thousandth of a meter. + UO:0000015 centimeter (cm) [UO:0000015] A length unit which is equal to one hundredth of a meter or 10^[-2] m + UO:0000008 meter (m) [UO:0000008] An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second. + UO:0010011 inch (in) [UO:0010011] A non-SI unit of length defined as one twelfth of a foot. + UO:0010013 foot (ft) [UO:0010013] A non-SI unit of length which is approximately 0.3048 meters. + +air_pressure_measurement_unit menu AirPressureMeasurementUnitMenu EFO:0005212 atmosphere (atm) [EFO:0005212] A non-SI unit of pressure defined as 101,325 pascals (Pa). + bar + UO:0000110 pascal [UO:0000110] An SI unit of pressure defined as one newton per square meter (N/m^2). + +ambient_temperature_measurement_unit menu AmbientTemperatureMeasurementUnitMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +total_daily_flow_rate_measurement_unit menu TotalDailyFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) + cubic meter per minute (m^3/min) + cubic meter per hour (m^3/h) + liter per second (L/s) + liter per minute (L/min) + liter per hour (L/h) + liter per day (L/day) + million gallons per day (MGD) + +instantaneous_flow_rate_measurement_unit menu InstantaneousFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) + cubic meter per minute (m^3/min) + cubic meter per hour (m^3/h) + liter per second (L/s) + liter per minute (L/min) + liter per hour (L/h) + liter per day (L/day) + million gallons per day (MGD) + +turbidity_measurement_unit menu TurbidityMeasurementUnitMenu nephelometric turbidity unit (NTU) + UO:0000318 formazin nephelometric unit (FNU) [UO:0000318] A measure of turbidity calculated by comparing how infrared light is scattered in a water sample against the amount of infrared light scattered in a reference solution containing formazin. + +dissolved_oxygen_measurement_unit menu DissolvedOxygenMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + UO:0000083 kilogram per cubic meter (kg/m^3) [UO:0000083] An SI unit of density that is one thousandth of the density of water. + UO:0000169 part per million (ppm) [UO:0000169] A unitless measure of density that represents one item out of a million. + +oxygen_reduction_potential_(ORP)_measurement_unit menu OxygenReductionPotentialOrpMeasurementUnitMenu UO:0000247 milliVolt (mV) [UO:0000247] A non-SI unit of electromotive force that is one thousandth of a volt. + +chemical_oxygen_demand_(COD)_measurement_unit menu ChemicalOxygenDemandCodMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + +carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_unit menu CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + +total_suspended_solids_(TSS)_measurement_unit menu TotalSuspendedSolidsTssMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +total_dissolved_solids_(TDS)_measurement_unit menu TotalDissolvedSolidsTdsMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +total_solids_(TS)_measurement_unit menu TotalSolidsTsMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +alkalinity_measurement_unit menu AlkalinityMeasurementUnitMenu milliequivalent per liter (meq/L) + UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + UO:0000169 parts per million [UO:0000169] A unitless measure of density that represents one item out of a million. + +conductivity_measurement_unit menu ConductivityMeasurementUnitMenu milliSiemen per centimeter (mS/cm) + microSiemen per centimeter (μS/cm) + Siemen per meter (S/m) + +salinity_measurement_unit menu SalinityMeasurementUnitMenu practical salinity unit (PSU) + weight for weight (% w/w) + UO:0000168 parts per thousand [UO:0000168] A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +total_nitrogen_(TN)_measurement_unit menu TotalNitrogenTnMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + gram per total solids (g/gTS) + +total_phosphorpus_(TP)_measurement_unit menu TotalPhosphorpusTpMeasurementUnitMenu gram per total solids (g/gTS) + GENEPIO:0100998 orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998] A substance unit which describes the weight of orthophosphate as phosphorus (gPO4-P) within a sample to the weight of total solids. + UO:0000273 milligrams per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + GENEPIO:0100999 milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999] A density unit comparing the weight of orthophosphate as phosphorus (PO4-P) in milligrams within a standard liter volume. + +fecal contamination indicator menu FecalContaminationIndicatorMenu NCBITaxon:1211417 crAssphage [NCBITaxon:1211417] CrAss-like phage, a bacteriophage discovered in 2014 in the human fecal metagenome. + NCBITaxon:12239 PMMoV / pepper mild mottle virus [NCBITaxon:12239] A plant RNA virus that is abundant in human feces. + GENEPIO:0101000 Bacteroides HF183 A fecal indicator which is the most commonly used sewage-associated marker gene, belonging to the Bacteroides genus. + GENEPIO:0101001 Lachnospiraceae Lachno3 A fecal indicator which is a human-associated genetic marker in the Lachnospiraceae family of bacteria. + GENEPIO:0101002 F+ (male specific) coliphages A fecal indicator which is a bacteriophage that infects coliform bacteria and is used in water assessment. + CHEBI:26756 Stercobilin Bile pigment found in fecal material. + +fecal_contamination_unit menu FecalContaminationUnitMenu log10 gene copies per 100 milliliter (log10 GC/100 mL) + gene copies per liter (GC/L) + UO:0010077 PCR quantification cycle [UO:0010077] A count unit of how many Polymerase Chain Reaction (PCR) cycles it took to detect a real signal from a sample. Equivalent to the PCR cycle number at which a sample's reaction curve intersects the threshold line. + log10 gene copies per nanogram total DNA + +urinary_contamination_indicator menu UrinaryContaminationIndicatorMenu CHEBI:36378 Urobilin [CHEBI:36378] A tetrapyrroledicarboxylic acid that causes the yellow color in urine. Also known as urochrome. + +urinary_contamination_unit menu UrinaryContaminationUnitMenu EFO:0004382 nanograms per liter (ng/L) [EFO:0004382] A mass unit density which is equal to mass of an object in nanograms divided by the volume in liters. + +fecal_coliform_count_unit menu FecalColiformCountUnitMenu UO:0000213 colony forming units per milliliter (CFU/mL) [UO:0000213] A unit of microbial density that describes the number of colony forming units within a milliliter of material. + colony forming units per 100 milliliter (CFU/100 mL) + colony forming units per grams total solids (CFU/gTS) + most probable number per milliliter (MPN/mL) + most probable number per 100 milliliter (MPN/100 mL) + +sample_temperature_unit_(at collection) menu SampleTemperatureUnitAtCollectionMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +sample_temperature_unit_(when received) menu SampleTemperatureUnitWhenReceivedMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +sequencing_assay_type menu SequencingAssayTypeMenu OBI:0002767 Amplicon sequencing assay [OBI:0002767] A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. + OBI:0002763 16S ribosomal gene sequencing assay [OBI:0002763] An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. + GENEPIO:0101128 CRISPR amplicon sequencing assay [GENEPIO:0101128] + GENEPIO:0101129 Primal tiling amplicon sequencing assay [GENEPIO:0101129] + OBI:0002117 Whole genome sequencing assay [OBI:0002117] A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. + OBI:0002623 Whole metagenome sequencing assay [OBI:0002623] A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. + OBI:0002768 Whole virome sequencing assay [OBI:0002768] A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. + +purpose_of_sequencing menu PurposeOfSequencingMenu GENEPIO:0100005 Baseline surveillance (random sampling) [GENEPIO:0100005] A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling. + GENEPIO:0100006 Targeted surveillance (non-random sampling) [GENEPIO:0100006] A surveillance sampling strategy in which an aspired outcome is explicitly stated. + GENEPIO:0100007 Priority surveillance project [GENEPIO:0100007] A targeted surveillance strategy which is considered important and/or urgent. + GENEPIO:0100009 Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009] A surveillance strategy in which an individual or site is selected to undergo repeat sampling over a defined period of time. + GENEPIO:0100019 Cluster/Outbreak investigation [GENEPIO:0100019] A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. + GENEPIO:0100020 Multi-jurisdictional outbreak investigation [GENEPIO:0100020] An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that has connections to two or more jurisdictions. + GENEPIO:0100021 Intra-jurisdictional outbreak investigation [GENEPIO:0100021] An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that only has connections within a single jurisdiction. + GENEPIO:0100022 Research [GENEPIO:0100022] A sampling strategy in which sites are sampled in order to perform research. + GENEPIO:0100023 Viral passage experiment [GENEPIO:0100023] A research sampling strategy in which samples are selected in order to perform a viral passage experiment. + GENEPIO:0100024 Protocol testing experiment [GENEPIO:0100024] A research sampling strategy in which samples are collected in order to test a method or protocol. + GENEPIO:0100356 Retrospective sequencing [GENEPIO:0100356] A sampling strategy in which stored samples from past events are sequenced. + +geo_loc_name_(country) menu GeoLocNameCountryMenu GAZ:00006882 Afghanistan [GAZ:00006882] A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ] + GAZ:00002953 Albania [GAZ:00002953] A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ] + GAZ:00000563 Algeria [GAZ:00000563] A country in North Africa. It is bordered by Tunisia in the northeast, Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, a few km of the Western Sahara in the west, Morocco in the northwest, and the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). [ url:http://en.wikipedia.org/wiki/Algeria ] + GAZ:00003957 American Samoa [GAZ:00003957] An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa ] + GAZ:00002948 Andorra [GAZ:00002948] A small landlocked country in western Europe, located in the eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. Andorra consists of seven communities known as parishes (Catalan: parroquies, singular - parroquia). Until relatively recently, it had only six parishes; the seventh, Escaldes-Engordany, was created in 1978. Some parishes have a further territorial subdivision. Ordino, La Massana and Sant Julia de Loria are subdivided into quarts (quarters), while Canillo is subdivided into veinats (neighborhoods). Those mostly coincide with villages, which are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ] + GAZ:00001095 Angola [GAZ:00001095] A country in south-central Africa bordering Namibia to the south, Democratic Republic of the Congo to the north, and Zambia to the east, and with a west coast along the Atlantic Ocean. The exclave province Cabinda has a border with the Republic of the Congo and the Democratic Republic of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ] + GAZ:00009159 Anguilla [GAZ:00009159] A British overseas territory in the Caribbean, one of the most northerly of the Leeward Islands in the Lesser Antilles. It consists of the main island of Anguilla itself, approximately 26 km long by 5 km wide at its widest point, together with a number of much smaller islands and cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila ] + GAZ:00000462 Antarctica [GAZ:00000462] The Earth's southernmost continent, overlying the South Pole. It is situated in the southern hemisphere, almost entirely south of the Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica ] + GAZ:00006883 Antigua and Barbuda [GAZ:00006883] An island nation located on the eastern boundary of the Caribbean Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda ] + GAZ:00002928 Argentina [GAZ:00002928] A South American country, constituted as a federation of twenty-three provinces and an autonomous city. It is bordered by Paraguay and Bolivia in the north, Brazil and Uruguay in the northeast, and Chile in the west and south. The country claims the British controlled territories of the Falkland Islands and South Georgia and the South Sandwich Islands. Argentina also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping other claims made by Chile and the United Kingdom. Argentina is subdivided into twenty-three provinces (Spanish: provincias, singular provincia) and one federal district (Capital de la Republica or Capital de la Nacion, informally the Capital Federal). The federal district and the provinces have their own constitutions, but exist under a federal system. Provinces are then divided into departments (Spanish: departamentos, singular departamento), except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina ] + GAZ:00004094 Armenia [GAZ:00004094] A landlocked mountainous country in Eurasia between the Black Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan exclave of Azerbaijan to the south. A transcontinental country at the juncture of Eastern Europe and Western Asia. A former republic of the Soviet Union. Armenia is divided into ten marzes (provinces, singular marz), with the city (kaghak) of Yerevan having special administrative status as the country's capital. [ url:http://en.wikipedia.org/wiki/Armenia ] + GAZ:00004025 Aruba [GAZ:00004025] An autonomous region within the Kingdom of the Netherlands, Aruba has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba ] + GAZ:00005901 Ashmore and Cartier Islands [GAZ:00005901] A Territory of Australia that includes two groups of small low-lying uninhabited tropical islands in the Indian Ocean situated on the edge of the continental shelf north-west of Australia and south of the Indonesian island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands ] + GAZ:00000463 Australia [GAZ:00000463] A country in the southern hemisphere comprising the mainland of the world's smallest continent, the major island of Tasmania, and a number of other islands in the Indian and Pacific Oceans. The neighbouring countries are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to the south-east. Australia has six states, two major mainland territories, and other minor territories. + GAZ:00002942 Austria [GAZ:00002942] A landlocked country in Central Europe. It borders both Germany and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia and Italy to the south, and Switzerland and Liechtenstein to the west. The capital is the city of Vienna on the Danube River. Austria is divided into nine states (Bundeslander). These states are then divided into districts (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities (Gemeinden). Cities have the competencies otherwise granted to both districts and municipalities. + GAZ:00004941 Azerbaijan [GAZ:00004941] A country in the he South Caucasus region of Eurasia, it is bounded by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan is bordered by Armenia to the north and east, Iran to the south and west, and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts in Azerbaijan's southwest, have been controlled by Armenia since the end of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons 11 city districts (saharlar), and one autonomous republic (muxtar respublika). + GAZ:00002733 Bahamas [GAZ:00002733] A country consisting of two thousand cays and seven hundred islands that form an archipelago. It is located in the Atlantic Ocean, southeast of Florida and the United States, north of Cuba, the island of Hispanola and the Caribbean, and northwest of the British overseas territory of the Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, whose affairs are handled directly by the central government. + GAZ:00005281 Bahrain [GAZ:00005281] A borderless island country in the Persian Gulf. Saudi Arabia lies to the west and is connected to Bahrain by the King Fahd Causeway, and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into five governorates. + GAZ:00007117 Baker Island [GAZ:00007117] An uninhabited atoll located just north of the equator in the central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island is an unincorporated and unorganized territory of the US. + GAZ:00003750 Bangladesh [GAZ:00003750] A country in South Asia. It is bordered by India on all sides except for a small border with Myanmar to the far southeast and by the Bay of Bengal to the south. Bangladesh is divided into six administrative divisions. Divisions are subdivided into districts (zila). There are 64 districts in Bangladesh, each further subdivided into upazila (subdistricts) or thana ("police stations"). + GAZ:00001251 Barbados [GAZ:00001251] An island country in the Lesser Antilles of the West Indies, in the Caribbean region of the Americas, and the most easterly of the Caribbean Islands. It is 34 kilometres (21 miles) in length and up to 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is in the western part of the North Atlantic, 100 km (62 mi) east of the Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards, part of the Lesser Antilles, at roughly 13°N of the equator. It is about 168 km (104 mi) east of both the countries of Saint Lucia and Saint Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside the principal Atlantic hurricane belt. Its capital and largest city is Bridgetown. + GAZ:00005810 Bassas da India [GAZ:00005810] A roughly circular atoll about 10 km in diameter, which corresponds to a total size (including lagoon) of 80 km2. It is located in the southern Mozambique Channel, about half-way between Madagascar (which is 385 km to the east) and Mozambique, and 110 km northwest of Europa Island. It rises steeply from the seabed 3000 m below. + GAZ:00006886 Belarus [GAZ:00006886] A landlocked country in Eastern Europe, that borders Russia to the north and east, Ukraine to the south, Poland to the west, and Lithuania and Latvia to the north. Its capital is Minsk. Belarus is divided into six voblasts, or provinces. Voblasts are further subdivided into raions (commonly translated as districts or regions). As of 2002, there are six voblasts, 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special status, due to the city serving as the national capital. + GAZ:00002938 Belgium [GAZ:00002938] A country in northwest Europe. Belgium shares borders with France (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each comprise five provinces; the third region, Brussels-Capital Region, is not a province, nor does it contain any Together, these comprise 589 municipalities, which in general consist of several sub-municipalities (which were independent municipalities before the municipal merger operation mainly in 1977). + GAZ:00002934 Belize [GAZ:00002934] A country in Central America. It is the only officially English speaking country in the region. Belize was a British colony for more than a century and was known as British Honduras until 1973. It became an independent nation within The Commonwealth in 1981. Belize is divided into 6 districts, which are further divided into 31 constituencies. + GAZ:00000904 Benin [GAZ:00000904] A country in Western Africa. It borders Togo to the west, Nigeria to the east and Burkina Faso and Niger to the north; its short coastline to the south leads to the Bight of Benin. Its capital is Porto Novo, but the seat of government is Cotonou. Benin is divided into 12 departments and subdivided into 77 communes. + GAZ:00001264 Bermuda [GAZ:00001264] A British overseas territory in the North Atlantic Ocean. Located off the east coast of the United States, it is situated around 1770 km NE of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately 138 islands. + GAZ:00003920 Bhutan [GAZ:00003920] A landlocked nation in South Asia. It is located amidst the eastern end of the Himalaya Mountains and is bordered to the south, east and west by India and to the north by Tibet. Bhutan is separated from Nepal by the Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative zones). Each dzongdey is further divided into dzongkhag (districts). There are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into subdistricts known as dungkhag. At the basic level, groups of villages form a constituency called gewog. + GAZ:00002511 Bolivia [GAZ:00002511] A landlocked country in central South America. It is bordered by Brazil on the north and east, Paraguay and Argentina on the south, and Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: departamentos). Each of the departments is subdivided into provinces (provincias), which are further subdivided into municipalities (municipios). + GAZ:00025355 Borneo [GAZ:00025355] An island at the grographic centre of Maritime Southeast Adia, in relation to major Indonesian islands, it is located north of Java, west of Sulawesi, and east of Sumatra. It is the third-largest island in the world and the larest in Asia. The island is politically divided among three countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] Approximately 73% of the island is Indonesian territory. In the north, the East Malaysian states of Sabah and Sarawak make up about 26% of the island. Additionally, the Malaysian federal territory of Labuan is situated on a small island just off the coast of Borneo. The sovereign state of Brunei, located on the north coast, comprises about 1% of Borneo's land area. A little more than half of the island is in the Northern Hemisphere, including Brunei and the Malaysian portion, while the Indonesian portion spans the Northern and Southern hemispheres. + GAZ:00006887 Bosnia and Herzegovina [GAZ:00006887] A country on the Balkan peninsula of Southern Europe. Bordered by Croatia to the north, west and south, Serbia to the east, and Montenegro to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided into three political regions of which one, the Brcko District is part of the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. All three have an equal constitutional status on the whole territory of Bosnia and Herzegovina. + GAZ:00001097 Botswana [GAZ:00001097] A landlocked nation in Southern Africa. It is bordered by South Africa to the south and southeast, Namibia to the west, Zambia to the north, and Zimbabwe to the northeast. Botswana is divided into nine districts, which are subdivided into a total twenty-eight subdistricts. + GAZ:00001453 Bouvet Island [GAZ:00001453] A sub-antarctic volcanic island in the South Atlantic Ocean, south-southwest of the Cape of Good Hope (South Africa). It is a dependent area of Norway and is not subject to the Antarctic Treaty, as it is north of the latitude south of which claims are suspended. + GAZ:00002828 Brazil [GAZ:00002828] A country in South America. Bordered by the Atlantic Ocean and by Venezuela, Suriname, Guyana and the department of French Guiana to the north, Colombia to the northwest, Bolivia and Peru to the west, Argentina and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six states (estados) and one federal district (Distrito Federal). The states are subdivided into municipalities. For statistical purposes, the States are grouped into five main regions: North, Northeast, Central-West, Southeast and South. + GAZ:00003961 British Virgin Islands [GAZ:00003961] A British overseas territory, located in the Caribbean to the east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, the remaining islands constituting the US Virgin Islands. The British Virgin Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately fifteen of the islands are inhabited. + GAZ:00003901 Brunei [GAZ:00003901] A country located on the north coast of the island of Borneo, in Southeast Asia. Apart from its coastline with the South China Sea it is completely surrounded by the State of Sarawak, Malaysia, and in fact it is separated into two parts by Limbang, which is part of Sarawak. Brunei is divided into four districts (daerah), the districts are subdivided into thirty-eight mukims, which are then divided into kampong (villages). + GAZ:00002950 Bulgaria [GAZ:00002950] A country in Southeastern Europe, borders five other countries; Romania to the north (mostly along the Danube), Serbia and the Republic of Macedonia to the west, and Greece and Turkey to the south. The Black Sea defines the extent of the country to the east. Since 1999, it has consisted of twenty-eight provinces. The provinces subdivide into 264 municipalities. + GAZ:00000905 Burkina Faso [GAZ:00000905] A landlocked nation in West Africa. It is surrounded by six countries: Mali to the north, Niger to the east, Benin to the south east, Togo and Ghana to the south, and Cote d'Ivoire to the south west. Burkina Faso is divided into thirteen regions, forty-five provinces, and 301 departments (communes). + GAZ:00001090 Burundi [GAZ:00001090] A small country in the Great Lakes region of Africa. It is bordered by Rwanda on the north, Tanzania on the south and east, and the Democratic Republic of the Congo on the west. Although the country is landlocked, much of its western border is adjacent to Lake Tanganyika. Burundi is divided into 17 provinces, 117 communes, and 2,638 collines. + GAZ:00006888 Cambodia [GAZ:00006888] A country in Southeast Asia. The country borders Thailand to its west and northwest, Laos to its northeast, and Vietnam to its east and southeast. In the south it faces the Gulf of Thailand. + GAZ:00001093 Cameroon [GAZ:00001093] A country of central and western Africa. It borders Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces and 58 divisions or departments. The divisions are further sub-divided into sub-divisions (arrondissements) and districts. + GAZ:00002560 Canada [GAZ:00002560] A country occupying most of northern North America, extending from the Atlantic Ocean in the east to the Pacific Ocean in the west and northward into the Arctic Ocean. Canada is a federation composed of ten provinces and three territories; in turn, these may be grouped into regions. Western Canada consists of British Columbia and the three Prairie provinces (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec and Ontario. Atlantic Canada consists of the three Maritime provinces (New Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada together. Three territories (Yukon, Northwest Territories, and Nunavut) make up Northern Canada. + GAZ:00001227 Cape Verde [GAZ:00001227] A republic located on an archipelago in the Macaronesia ecoregion of the North Atlantic Ocean, off the western coast of Africa. Cape Verde is divided into 22 municipalities (concelhos), and subdivided into 32 parishes (freguesias). + GAZ:00003986 Cayman Islands [GAZ:00003986] A British overseas territory located in the western Caribbean Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. The Cayman Islands are divided into seven districts. + GAZ:00001089 Central African Republic [GAZ:00001089] A landlocked country in Central Africa. It borders Chad in the north, Sudan in the east, the Republic of the Congo and the Democratic Republic of the Congo in the south, and Cameroon in the west. The Central African Republic is divided into 14 administrative prefectures (prefectures), along with 2 economic prefectures (prefectures economiques) and one autonomous commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures). + GAZ:00000586 Chad [GAZ:00000586] A landlocked country in central Africa. It is bordered by Libya to the north, Sudan to the east, the Central African Republic to the south, Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided into 18 regions. The departments are divided into 200 sub-prefectures, which are in turn composed of 446 cantons. This is due to change. + GAZ:00002825 Chile [GAZ:00002825] A country in South America occupying a long and narrow coastal strip wedged between the Andes mountains and the Pacific Ocean. The Pacific forms the country's entire western border, with Peru to the north, Bolivia to the northeast, Argentina to the east, and the Drake Passage at the country's southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. Chile is divided into 15 regions. Every region is further divided into provinces. Finally each province is divided into communes. Each region is designated by a name and a Roman numeral, assigned from north to south. The only exception is the region housing the nation's capital, which is designated RM, that stands for Region Metropolitana (Metropolitan Region). Two new regions were created in 2006: Arica-Parinacota in the north, and Los Rios in the south. Both became operative in 2007-10. + GAZ:00002845 China [GAZ:00002845] A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions. + GAZ:00005915 Christmas Island [GAZ:00005915] An island in the Indian Ocean, 500 km south of Indonesia and about 2600 km northwest of Perth. The island is the flat summit of a submarine mountain. + GAZ:00005838 Clipperton Island [GAZ:00005838] A nine-square km coral atoll in the North Pacific Ocean, southwest of Mexico and west of Costa Rica. + GAZ:00009721 Cocos Islands [GAZ:00009721] Islands that located in the Indian Ocean, about halfway between Australia and Sri Lanka. A territory of Australia. There are two atolls and twenty-seven coral islands in the group. + GAZ:00002929 Colombia [GAZ:00002929] A country located in the northwestern region of South America. Colombia is bordered to the east by Venezuela and Brazil; to the south by Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean Sea; to the north-west by Panama; and to the west by the Pacific Ocean. Besides the countries in South America, the Republic of Colombia is recognized to share maritime borders with the Caribbean countries of Jamaica, Haiti, the Dominican Republic and the Central American countries of Honduras, Nicaragua, and Costa Rica. Colombia is divided into 32 departments and one capital district which is treated as a department. There are in total 10 districts assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia is also subdivided into some municipalities which form departments, each with a municipal seat capital city assigned. Colombia is also subdivided into corregimientos which form municipalities. + GAZ:00005820 Comoros [GAZ:00005820] An island nation in the Indian Ocean, located off the eastern coast of Africa on the northern end of the Mozambique Channel between northern Madagascar and northeastern Mozambique. + GAZ:00053798 Cook Islands [GAZ:00053798] A self-governing parliamentary democracy in free association with New Zealand. The fifteen small islands in this South Pacific Ocean country have a total land area of 240 km2, but the Cook Islands Exclusive Economic Zone (EEZ) covers 1.8 million km2 of ocean. + GAZ:00005917 Coral Sea Islands [GAZ:00005917] A Territory of Australia which includes a group of small and mostly uninhabited tropical islands and reefs in the Coral Sea, northeast of Queensland, Australia. The only inhabited island is Willis Island. The territory covers 780,000 km2, extending east and south from the outer edge of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, the Willis Group, and fifteen other reef/island groups. + GAZ:00002901 Costa Rica [GAZ:00002901] A republic in Central America, bordered by Nicaragua to the north, Panama to the east-southeast, the Pacific Ocean to the west and south, and the Caribbean Sea to the east. Costa Rica is composed of seven provinces, which in turn are divided into 81 cantons. + GAZ:00000906 Cote d'Ivoire [GAZ:00000906] A country in West Africa. It borders Liberia and Guinea to the west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). The regions are further divided into 58 departments. + GAZ:00002719 Croatia [GAZ:00002719] A country at the crossroads of the Mediterranean, Central Europe, and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to the east, Montenegro to the far southeast, and the Adriatic Sea to the south. Croatia is divided into 21 counties (zupanija) and the capital Zagreb's city district. + GAZ:00003762 Cuba [GAZ:00003762] A country that consists of the island of Cuba (the largest and second-most populous island of the Greater Antilles), Isla de la Juventud and several adjacent small islands. Fourteen provinces and one special municipality (the Isla de la Juventud) now compose Cuba. + GAZ:00012582 Curacao [GAZ:00012582] One of five island areas of the Netherlands Antilles. + GAZ:00004006 Cyprus [GAZ:00004006] The third largest island in the Mediterranean Sea (after Sicily and Sardinia), Cyprus is situated in the eastern Mediterranean, just south of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, it is often included in the Middle East (see also Western Asia and Near East). Turkey is 75 km north; other neighbouring countries include Syria and Lebanon to the east, Israel to the southeast, Egypt to the south, and Greece to the west-north-west. + GAZ:00002954 Czech Republic [GAZ:00002954] A landlocked country in Central Europe. It has borders with Poland to the north, Germany to the northwest and southwest, Austria to the south, and Slovakia to the east. The capital and largest city is Prague. The country is composed of the historic regions of Bohemia and Moravia, as well as parts of Silesia. Since 2000, the Czech Republic is divided into thirteen regions (kraje, singular kraj) and the capital city of Prague. The older seventy-six districts (okresy, singular okres) including three 'statutory cities' (without Prague, which had special status) were disbanded in 1999 in an administrative reform; they remain as territorial division and seats of various branches of state administration. Since 2003-01-01, the regions have been divided into around 203 Municipalities with Extended Competence (unofficially named "Little Districts" (Czech: 'male okresy') which took over most of the administration of the former District Authorities. Some of these are further divided into Municipalities with Commissioned Local Authority. However, the old districts still exist as territorial units and remain as seats of some of the offices. + GAZ:00001086 Democratic Republic of the Congo [GAZ:00001086] A country of central Africa. It borders the Central African Republic and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia and Angola on the south, the Republic of the Congo on the west, and is separated from Tanzania by Lake Tanganyika on the east. The country enjoys access to the ocean through a 40 km stretch of Atlantic coastline at Muanda and the roughly 9 km wide mouth of the Congo river which opens into the Gulf of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed into 25 Provinces from 2.2009. Each Province is divided into Zones. + GAZ:00005852 Denmark [GAZ:00005852] That part of the Kingdom of Denmark located in continental Europe. The mainland is bordered to the south by Germany; Denmark is located to the southwest of Sweden and the south of Norway. Denmark borders both the Baltic and the North Sea. The country consists of a large peninsula, Jutland (Jylland) and a large number of islands, most notably Zealand (Sjaelland), Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds of minor islands often referred to as the Danish Archipelago. + GAZ:00000582 Djibouti [GAZ:00000582] A country in eastern Africa. Djibouti is bordered by Eritrea in the north, Ethiopia in the west and south, and Somalia in the southeast. The remainder of the border is formed by the Red Sea and the Gulf of Aden. On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. Djibouti is divided into 5 regions and one city. It is further subdivided into 11 districts. + GAZ:00006890 Dominica [GAZ:00006890] An island nation in the Caribbean Sea. Dominica is divided into ten parishes. + GAZ:00003952 Dominican Republic [GAZ:00003952] A country in the West Indies that occupies the E two-thirds of the Hispaniola island. The Dominican Republic's shores are washed by the Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona Passage, a channel about 130 km wide, separates the country (and the Hispaniola) from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, the national capital, Santo Domingo, is contained within its own Distrito Nacional (National District). The provinces are divided into municipalities (municipios; singular municipio). + GAZ:00002912 Ecuador [GAZ:00002912] A country in South America, bordered by Colombia on the north, by Peru on the east and south, and by the Pacific Ocean to the west. The country also includes the Galapagos Islands (Archipelago de Colon) in the Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, divided into 199 cantons and subdivided into parishes (or parroquias). + GAZ:00003934 Egypt [GAZ:00003934] A country in North Africa that includes the Sinai Peninsula, a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, and the Gaza Strip and Israel to the east. The northern coast borders the Mediterranean Sea and the island of Cyprus; the eastern coast borders the Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, singular muhafazah). The governorates are further divided into regions (markazes). + GAZ:00002935 El Salvador [GAZ:00002935] A country in Central America, bordering the Pacific Ocean between Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), which, in turn, are subdivided into 267 municipalities (municipios). + GAZ:00001091 Equatorial Guinea [GAZ:00001091] A country in Central Africa. It is one of the smallest countries in continental Africa, and comprises two regions: Rio Muni, continental region including several offshore islands; and Insular Region containing Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando Po) that contains the capital, Malabo. Equatorial Guinea is divided into seven provinces which are divided into districts. + GAZ:00000581 Eritrea [GAZ:00000581] A country situated in northern East Africa. It is bordered by Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. The east and northeast of the country have an extensive coastline on the Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago and several of the Hanish Islands are part of Eritrea. Eritrea is divided into six regions (zobas) and subdivided into districts ("sub-zobas"). + GAZ:00002959 Estonia [GAZ:00002959] A country in Northern Europe. Estonia has land borders to the south with Latvia and to the east with Russia. It is separated from Finland in the north by the Gulf of Finland and from Sweden in the west by the Baltic Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). Estonian counties are divided into rural (vallad, singular vald) and urban (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) municipalities. The municipalities comprise populated places (asula or asustusuksus) - various settlements and territorial units that have no administrative function. A group of populated places form a rural municipality with local administration. Most towns constitute separate urban municipalities, while some have joined with surrounding rural municipalities. + GAZ:00001099 Eswatini [GAZ:00001099] A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla). + GAZ:00000567 Ethiopia [GAZ:00000567] A country situated in the Horn of Africa that has been landlocked since the independence of its northern neighbor Eritrea in 1993. Apart from Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to the south, Djibouti to the northeast, and Somalia to the east. Since 1996 Ethiopia has had a tiered government system consisting of a federal government overseeing ethnically-based regional states, zones, districts (woredas), and neighborhoods (kebele). It is divided into nine ethnically-based administrative states (kililoch, singular kilil) and subdivided into sixty-eight zones and two chartered cities (astedader akababiwoch, singular astedader akababi): Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and six special woredas. + GAZ:00005811 Europa Island [GAZ:00005811] A 28 km2 low-lying tropical island in the Mozambique Channel, about a third of the way from southern Madagascar to southern Mozambique. + GAZ:00001412 Falkland Islands (Islas Malvinas) [GAZ:00001412] An archipelago in the South Atlantic Ocean, located 483 km from the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), and 940 km north of Antarctica (Elephant Island). They consist of two main islands, East Falkland and West Falkland, together with 776 smaller islands. + GAZ:00059206 Faroe Islands [GAZ:00059206] An autonomous province of the Kingdom of Denmark since 1948 located in the Faroes. Administratively, the islands are divided into 34 municipalities (kommunur) within which 120 or so cities and villages lie. + GAZ:00006891 Fiji [GAZ:00006891] An island nation in the South Pacific Ocean east of Vanuatu, west of Tonga and south of Tuvalu. The country occupies an archipelago of about 322 islands, of which 106 are permanently inhabited, and 522 islets. The two major islands, Viti Levu and Vanua Levu, account for 87% of the population. + GAZ:00002937 Finland [GAZ:00002937] A Nordic country situated in the Fennoscandian region of Northern Europe. It has borders with Sweden to the west, Russia to the east, and Norway to the north, while Estonia lies to its south across the Gulf of Finland. The capital city is Helsinki. Finland is divided into six administrative provinces (laani, plural laanit). These are divided into 20 regions (maakunt), 77 subregions (seutukunta) and then into municipalities (kunta). + GAZ:00003940 France [GAZ:00003940] A part of the country of France that extends from the Mediterranean Sea to the English Channel and the North Sea, and from the Rhine to the Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas departments. + GAZ:00002516 French Guiana [GAZ:00002516] An overseas department (departement d'outre-mer) of France, located on the northern coast of South America. It is bordered by Suriname, to the E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. French Guiana is divided into 2 departmental arrondissements, 19 cantons and 22 communes. + GAZ:00002918 French Polynesia [GAZ:00002918] A French overseas collectivity in the southern Pacific Ocean. It is made up of several groups of Polynesian islands. French Polynesia has five administrative subdivisions (French: subdivisions administratives). + GAZ:00003753 French Southern and Antarctic Lands [GAZ:00003753] The French Southern and Antarctic Lands have formed a territoire d'outre-mer (an overseas territory) of France since 1955. The territory is divided into five districts. + GAZ:00001092 Gabon [GAZ:00001092] A country in west central Africa sharing borders with Equatorial Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital and largest city is Libreville. Gabon is divided into 9 provinces and further divided into 37 departments. + GAZ:00000907 Gambia [GAZ:00000907] A country in Western Africa. It is the smallest country on the African continental mainland and is bordered to the north, east, and south by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing through the centre of the country and discharging to the Atlantic Ocean is the Gambia River. The Gambia is divided into five divisions and one city (Banjul). The divisions are further subdivided into 37 districts. + GAZ:00009571 Gaza Strip [GAZ:00009571] A Palestinian enclave on the eastern coast of the Mediterranean Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel on the east and north along a 51 km (32 mi) border. Gaza and the West Bank are claimed by the de jure sovereign State of Palestine. + GAZ:00004942 Georgia [GAZ:00004942] A Eurasian country in the Caucasus located at the east coast of the Black Sea. In the north, Georgia has a 723 km common border with Russia, specifically with the Northern Caucasus federal district. The following Russian republics/subdivisions: from west to east: border Georgia: Krasnodar Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to the south-west. It is a transcontinental country, located at the juncture of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 autonomous republics (avtonomiuri respublika), and 1 city (k'alak'i). The regions are further subdivided into 69 districts (raioni). + GAZ:00002646 Germany [GAZ:00002646] A country in Central Europe. It is bordered to the north by the North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech Republic; to the south by Austria and Switzerland; and to the west by France, Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) and cities (kreisfreie Stadte). + GAZ:00000908 Ghana [GAZ:00000908] A country in West Africa. It borders Cote d'Ivoire to the west, Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the south. Ghana is a divided into 10 regions, subdivided into a total of 138 districts. + GAZ:00003987 Gibraltar [GAZ:00003987] A British overseas territory located near the southernmost tip of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory shares a border with Spain to the north. + GAZ:00005808 Glorioso Islands [GAZ:00005808] A group of islands and rocks totalling 5 km2, in the northern Mozambique channel, about 160 km northwest of Madagascar. + GAZ:00002945 Greece [GAZ:00002945] A country in southeastern Europe, situated on the southern end of the Balkan Peninsula. It has borders with Albania, the former Yugoslav Republic of Macedonia and Bulgaria to the north, and Turkey to the east. The Aegean Sea lies to the east and south of mainland Greece, while the Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin feature a vast number of islands. Greece consists of thirteen peripheries subdivided into a total of fifty-one prefectures (nomoi, singular nomos). There is also one autonomous area, Mount Athos, which borders the periphery of Central Macedonia. + GAZ:00001507 Greenland [GAZ:00001507] A self-governing Danish province located between the Arctic and Atlantic Oceans, east of the Canadian Arctic Archipelago. + GAZ:02000573 Grenada [GAZ:02000573] An island country in the West Indies in the Caribbean Sea at the southern end of the Grenadines island chain. Grenada consists of the island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, and several small islands which lie to the north of the main island and are a part of the Grenadines. It is located northwest of Trinidad and Tobago, northeast of Venezuela and southwest of Saint Vincent and the Grenadines. Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated population of 112,523 in July 2020. + GAZ:00067142 Guadeloupe [GAZ:00067142] An archipelago and overseas department and region of France in the Caribbean. It consists of six inhabited islands—Basse-Terre, Grande-Terre, Marie-Galante, La Désirade, and the two inhabited Îles des Saintes—as well as many uninhabited islands and outcroppings. It is south of Antigua and Barbuda and Montserrat, and north of Dominica. + GAZ:00003706 Guam [GAZ:00003706] An organized, unincorporated territory of the United States in the Micronesia subregion of the western Pacific Ocean. It is the westernmost point and territory of the United States (reckoned from the geographic center of the U.S.); in Oceania, it is the largest and southernmost of the Mariana Islands and the largest island in Micronesia. + GAZ:00002936 Guatemala [GAZ:00002936] A country in Central America bordered by Mexico to the northwest, the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the northeast, and Honduras and El Salvador to the southeast. Guatemala is divided into 22 departments (departamentos) and sub-divided into about 332 municipalities (municipios). + GAZ:00001550 Guernsey [GAZ:00001550] A British Crown Dependency in the English Channel off the coast of Normandy. + GAZ:00000909 Guinea [GAZ:00000909] A nation in West Africa, formerly known as French Guinea. Guinea's territory has a curved shape, with its base at the Atlantic Ocean, inland to the east, and turning south. The base borders Guinea-Bissau and Senegal to the north, and Mali to the north and north-east; the inland part borders Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone to the west of the southern tip. + GAZ:00000910 Guinea-Bissau [GAZ:00000910] A country in western Africa, and one of the smallest nations in continental Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west. Formerly the Portuguese colony of Portuguese Guinea, upon independence, the name of its capital, Bissau, was added to the country's name in order to prevent confusion between itself and the Republic of Guinea. + GAZ:00002522 Guyana [GAZ:00002522] A country in the N of South America. Guyana lies north of the equator, in the tropics, and is located on the Atlantic Ocean. Guyana is bordered to the east by Suriname, to the south and southwest by Brazil and to the west by Venezuela. Guyana is divided into 10 regions. The regions of Guyana are divided into 27 neighborhood councils. + GAZ:00003953 Haiti [GAZ:00003953] A country located in the Greater Antilles archipelago on the Caribbean island of Hispaniola, which it shares with the Dominican Republic. Haiti is divided into 10 departments. The departments are further divided into 41 arrondissements, and 133 communes which serve as second and third level administrative divisions. + GAZ:00009718 Heard Island and McDonald Islands [GAZ:00009718] An Australian external territory comprising a volcanic group of mostly barren Antarctic islands, about two-thirds of the way from Madagascar to Antarctica. + GAZ:00002894 Honduras [GAZ:00002894] A republic in Central America. The country is bordered to the west by Guatemala, to the southwest by El Salvador, to the southeast by Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. Honduras is divided into 18 departments. The capital city is Tegucigalpa Central District of the department of Francisco Morazan. + GAZ:00003203 Hong Kong [GAZ:00003203] A special administrative region of the People's Republic of China (PRC). The territory lies on the eastern side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east, west and south. Hong Kong was a crown colony of the United Kingdom from 1842 until the transfer of its sovereignty to the People's Republic of China in 1997. + GAZ:00007120 Howland Island [GAZ:00007120] An uninhabited coral island located just north of the equator in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. The island is almost half way between Hawaii and Australia and is an unincorporated, unorganized territory of the United States, and is often included as one of the Phoenix Islands. For statistical purposes, Howland is grouped as one of the United States Minor Outlying Islands. + GAZ:00002952 Hungary [GAZ:00002952] A landlocked country in the Carpathian Basin of Central Europe, bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: megye). In addition, the capital city (fovaros), Budapest, is independent of any county government. The counties are further subdivided into 173 subregions (kistersegek), and Budapest is comprised of its own subregion. Since 1996, the counties and City of Budapest have been grouped into 7 regions for statistical and development purposes. These seven regions constitute NUTS second-level units of Hungary. + GAZ:00000843 Iceland [GAZ:00000843] A country in northern Europe, comprising the island of Iceland and its outlying islands in the North Atlantic Ocean between the rest of Europe and Greenland. + GAZ:00002839 India [GAZ:00002839] A country in South Asia. Bounded by the Indian Ocean on the south, the Arabian Sea on the west, and the Bay of Bengal on the east, India has a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, and Bhutan to the north-east; and Bangladesh and Burma to the east. India is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian Ocean. India is a federal republic of twenty-eight states and seven Union Territories. Each state or union territory is divided into basic units of government and administration called districts. There are nearly 600 districts in India. The districts in turn are further divided into tehsils and eventually into villages. + GAZ:00003727 Indonesia [GAZ:00003727] An archipelagic state in Southeast Asia. The country shares land borders with Papua New Guinea, East Timor and Malaysia. Other neighboring countries include Singapore, the Philippines, Australia, and the Indian territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, five of which have special status. The provinces are subdivided into regencies (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), which are further subdivided into subdistricts (kecamatan), and again into village groupings (either desa or kelurahan). + GAZ:00004474 Iran [GAZ:00004474] A country in Central Eurasia. Iran is bounded by the Gulf of Oman and the Persian Gulf to the south and the Caspian Sea to its north. It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into 30 provinces (ostan). The provinces are divided into counties (shahrestan), and subdivided into districts (bakhsh) and sub-districts (dehestan). + GAZ:00004483 Iraq [GAZ:00004483] A country in the Middle East spanning most of the northwestern end of the Zagros mountain range, the eastern part of the Syrian Desert and the northern part of the Arabian Desert. It shares borders with Kuwait and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, Turkey to the north, and Iran to the east. It has a very narrow section of coastline at Umm Qasr on the Persian Gulf. There are two major flowing rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates (or provinces) (muhafazah). The governorates are divided into qadhas (or districts). + GAZ:00002943 Ireland [GAZ:00002943] A country in north-western Europe. The modern sovereign state occupies five-sixths of the island of Ireland, which was partitioned in 1921. It is bordered by Northern Ireland (part of the United Kingdom) to the north, by the Atlantic Ocean to the west and by the Irish Sea to the east. Administration follows the 34 "county-level" counties and cities of Ireland. Of these twenty-nine are counties, governed by county councils while the five cities of Dublin, Cork, Limerick, Galway and Waterford have city councils, (previously known as corporations), and are administered separately from the counties bearing those names. The City of Kilkenny is the only city in the republic which does not have a "city council"; it is still a borough but not a county borough and is administered as part of County Kilkenny. Ireland is split into eight regions for NUTS statistical purposes. These are not related to the four traditional provinces but are based on the administrative counties. + GAZ:00052477 Isle of Man [GAZ:00052477] A Crown dependency of the United Kingdom in the centre of the Irish Sea. It is not part of the United Kingdom, European Union or United Nations. + GAZ:00002476 Israel [GAZ:00002476] A country in Western Asia located on the eastern edge of the Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, which are partially administrated by the Palestinian National Authority, are also adjacent. The State of Israel is divided into six main administrative districts, known as mehozot (singular mahoz). Districts are further divided into fifteen sub-districts known as nafot (singular: nafa), which are themselves partitioned into fifty natural regions. + GAZ:00002650 Italy [GAZ:00002650] A country located on the Italian Peninsula in Southern Europe, and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. Italy shares its northern Alpine boundary with France, Switzerland, Austria and Slovenia. The independent states of San Marino and the Vatican City are enclaves within the Italian Peninsula, while Campione d'Italia is an Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, singular regione). Five of these regions have a special autonomous status that enables them to enact legislation on some of their local matters. It is further divided into 109 provinces (province) and 8,101 municipalities (comuni). + GAZ:00003781 Jamaica [GAZ:00003781] A nation of the Greater Antilles. Jamaica is divided into 14 parishes, which are grouped into three historic counties that have no administrative relevance. + GAZ:00005853 Jan Mayen [GAZ:00005853] A volcanic island that is part of the Kingdom of Norway, It has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and 1,000 km west of the Norwegian mainland. The island is mountainous, the highest summit being the Beerenberg volcano in the north. The isthmus is the location of the two largest lakes of the island, Sorlaguna (South Lagoon), and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng Lagoon). Jan Mayen was formed by the Jan Mayen hotspot. + GAZ:00002747 Japan [GAZ:00002747] An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south. + GAZ:00007118 Jarvis Island [GAZ:00007118] An uninhabited 4.5 km2 coral atoll located in the South Pacific Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated territory of the United States administered from Washington, DC by the United States Fish and Wildlife Service of the United States Department of the Interior as part of the National Wildlife Refuge system. Jarvis is one of the southern Line Islands and for statistical purposes is also grouped as one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount. + GAZ:00001551 Jersey [GAZ:00001551] A British Crown Dependency[6] off the coast of Normandy, France. As well as the island of Jersey itself, the bailiwick includes two groups of small islands that are no longer permanently inhabited, the Minquiers and Ecrehous, and the Pierres de Lecq. + GAZ:00007114 Johnston Atoll [GAZ:00007114] A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 nm) west of Hawaii. There are four islands located on the coral reef platform, two natural islands, Johnston Island and Sand Island, which have been expanded by coral dredging, as well as North Island (Akau) and East Island (Hikina), artificial islands formed from coral dredging. Johnston is an unincorporated territory of the United States, administered by the US Fish and Wildlife Service of the Department of the Interior as part of the United States Pacific Island Wildlife Refuges. Sits atop Johnston Seamount. + GAZ:00002473 Jordan [GAZ:00002473] A country in Southwest Asia, bordered by Syria to the north, Iraq to the north-east, Israel and the West Bank to the west, and Saudi Arabia to the east and south. It shares the coastlines of the Dead Sea, and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided into 12 provinces called governorates. The Governorates are subdivided into approximately fifty-two nahias. + GAZ:00005809 Juan de Nova Island [GAZ:00005809] A 4.4 km2 low, flat, tropical island in the narrowest part of the Mozambique Channel, about one-third of the way between Madagascar and Mozambique. + GAZ:00004999 Kazakhstan [GAZ:00004999] A country in Central Asia and Europe. It is bordered by Russia, Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders on a significant part of the Caspian Sea. Kazakhstan is divided into 14 provinces and two municipal districts. The provinces of Kazakhstan are divided into raions. + GAZ:00001101 Kenya [GAZ:00001101] A country in Eastern Africa. It is bordered by Ethiopia to the north, Somalia to the east, Tanzania to the south, Uganda to the west, and Sudan to the northwest, with the Indian Ocean running along the southeast border. Kenya comprises eight provinces each headed by a Provincial Commissioner (centrally appointed by the president). The provinces (mkoa singular mikoa plural in Swahili) are subdivided into districts (wilaya). There were 69 districts as of 1999 census. Districts are then subdivided into 497 divisions (taarafa). The divisions are then subdivided into 2,427 locations (kata) and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the status of a full administrative province. + GAZ:00005682 Kerguelen Archipelago [GAZ:00005682] A group of islands in the southern Indian Ocean. It is a territory of France. They are composed primarily of Tertiary flood basalts and a complex of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano at the southern end was active during the late Pleistocene. The Rallier du Baty Peninsula on the SW tip of the island contains two youthful subglacial eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active fumarole field is related to a series of Holocene trachytic lava flows and lahars that extend beyond the icecap. + GAZ:00007116 Kingman Reef [GAZ:00007116] A largely submerged, uninhabited tropical atoll located in the North Pacific Ocean, roughly half way between Hawaiian Islands and American Samoa. It is the northernmost of the Northern Line Islands and lies 65 km NNW of Palmyra Atoll, the next closest island, and has the status of an unincorporated territory of the United States, administered from Washington, DC by the US Navy. Sits atop Kingman Reef Seamount. + GAZ:00006894 Kiribati [GAZ:00006894] An island nation located in the central tropical Pacific Ocean. It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 km2 straddling the equator and bordering the International Date Line to the east. It is divided into three island groups which have no administrative function, including a group which unites the Line Islands and the Phoenix Islands (ministry at London, Christmas). Each inhabited island has its own council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two councils on Tabiteuea). + GAZ:00011337 Kosovo [GAZ:00011337] A country on the Balkan Peninsula. Kosovo borders Central Serbia to the north and east, Montenegro to the northwest, Albania to the west and the Republic of Macedonia to the south. Kosovo is divided into 7 districts (Rreth) and 30 municipalities. Serbia does not recognise the unilateral secession of Kosovo[8] and considers it a United Nations-governed entity within its sovereign territory, the Autonomous Province of Kosovo and Metohija. + GAZ:00005285 Kuwait [GAZ:00005285] A sovereign emirate on the coast of the Persian Gulf, enclosed by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided into six governorates (muhafazat, singular muhafadhah). + GAZ:00006893 Kyrgyzstan [GAZ:00006893] A country in Central Asia. Landlocked and mountainous, it is bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan to the southwest and China to the east. Kyrgyzstan is divided into seven provinces (oblast. The capital, Bishkek, and the second large city Osh are administratively the independent cities (shaar) with a status equal to a province. Each province comprises a number of districts (raions). + GAZ:00006889 Laos [GAZ:00006889] A landlocked country in southeast Asia, bordered by Burma (Myanmar) and China to the northwest, Vietnam to the east, Cambodia to the south, and Thailand to the west. Laos is divided into sixteen provinces (qwang) and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided into districts (muang). + GAZ:00002958 Latvia [GAZ:00002958] A country in Northern Europe. Latvia shares land borders with Estonia to the north and Lithuania to the south, and both Russia and Belarus to the east. It is separated from Sweden in the west by the Baltic Sea. The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). There are also seven cities (lielpilsetas) that have a separate status. Latvia is also historically, culturally and constitutionally divided in four or more distinct regions. + GAZ:00002478 Lebanon [GAZ:00002478] A small, mostly mountainous country in Western Asia, on the eastern shore of the Mediterranean Sea. It is bordered by Syria to the north and east, and Israel to the south. Lebanon is divided into six governorates (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, singular: qadaa). + GAZ:00001098 Lesotho [GAZ:00001098] A land-locked country, entirely surrounded by the Republic of South Africa. Lesotho is divided into ten districts; these are further subdivided into 80 constituencies, which consists of 129 local community councils. + GAZ:00000911 Liberia [GAZ:00000911] A country on the west coast of Africa, bordered by Sierra Leone, Guinea, Cote d'Ivoire, and the Atlantic Ocean. + GAZ:00000566 Libya [GAZ:00000566] A country in North Africa. Bordering the Mediterranean Sea to the north, Libya lies between Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west. There are thirty-four municipalities of Libya, known by the Arabic term sha'biyat (singular sha'biyah). These came recently (in the 1990s to replaced old Baladiyat systam. The Baladiyat system in turn was introduced to replace the system of muhafazah (governorates or provinces) that existed from the 1960s to the 1970s. + GAZ:00003858 Liechtenstein [GAZ:00003858] A tiny, doubly landlocked alpine country in Western Europe, bordered by Switzerland to its west and by Austria to its east. The principality of Liechtenstein is divided into 11 municipalities called Gemeinden (singular Gemeinde). The Gemeinden mostly consist only of a single town. Five of them fall within the electoral district Unterland (the lower county), and the remainder within Oberland (the upper county). + GAZ:00007144 Line Islands [GAZ:00007144] A group of eleven atolls and low coral islands in the central Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, while three are United States territories that are grouped with the United States Minor Outlying Islands. + GAZ:00002960 Lithuania [GAZ:00002960] A country located along the south-eastern shore of the Baltic Sea, sharing borders with Latvia to the north, Belarus to the southeast, Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. Lithuania has a three-tier administrative division: the country is divided into 10 counties (singular apskritis, plural, apskritys) that are further subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) which consist of over 500 elderates (singular seniunija, plural seniunijos). + GAZ:00002947 Luxembourg [GAZ:00002947] A small landlocked country in western Europe, bordered by Belgium, France, and Germany. Luxembourg is divided into 3 districts, which are further divided into 12 cantons and then 116 communes. Twelve of the communes have city status, of which the city of Luxembourg is the largest. + GAZ:00003202 Macau [GAZ:00003202] One of the two special administrative regions of the People's Republic of China, the other being Hong Kong. Macau lies on the western side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east and south. Macau is situated 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang (West River) on the west. It borders the Zhuhai Special Economic Zone in mainland China. + GAZ:00001108 Madagascar [GAZ:00001108] An island nation in the Indian Ocean off the southeastern coast of Africa. The main island, also called Madagascar, is the fourth largest island in the world, and is home to 5% of the world's plant and animal species, of which more than 80% are endemic to Madagascar. Most notable are the lemur infraorder of primates, the carnivorous fossa, three endemic bird families and six endemic baobab species. Madagascar is divided into six autonomous provinces (faritany mizakatena), and 22 regions. The regions are further subdivided into 116 districts, 1,548 communes, and 16,969 fokontany. + GAZ:00001105 Malawi [GAZ:00001105] A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. + GAZ:00003902 Malaysia [GAZ:00003902] A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. + GAZ:00006924 Maldives [GAZ:00006924] An archipelago which consists of approximately 1,196 coral islands grouped in a double chain of 27 atolls, spread over roughly 90,000 km2. + GAZ:00000584 Mali [GAZ:00000584] A landlocked country in northern Africa. It borders Algeria on the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the south, Guinea on the south-west, and Senegal and Mauritania on the west. Mali is divided into 8 regions (regions) and 1 district, and subdivided into 49 cercles, totalling 288 arrondissements. + GAZ:00004017 Malta [GAZ:00004017] A Southern European country and consists of an archipelago situated centrally in the Mediterranean. + GAZ:00007161 Marshall Islands [GAZ:00007161] An archipelago that consists of twenty-nine atolls and five isolated islands. The most important atolls and islands form two groups: the Ratak Chain and the Ralik Chain (meaning "sunrise" and "sunset" chains). Two-thirds of the nation's population lives on Majuro (which is also the capital) and Ebeye. The outer islands are sparsely populated. + GAZ:00067143 Martinique [GAZ:00067143] An island and an overseas department/region and single territorial collectivity of France. + GAZ:00000583 Mauritania [GAZ:00000583] A country in North-West Africa. It is bordered by the Atlantic Ocean on the west, by Senegal on the southwest, by Mali on the east and southeast, by Algeria on the northeast, and by Western Sahara on the northwest (most of which is occupied by Morocco). The capital and largest city is Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 regions (regions) and one capital district, which in turn are subdivided into 44 departments (departements). + GAZ:00003745 Mauritius [GAZ:00003745] An island nation off the coast of the African continent in the southwest Indian Ocean, about 900 km east of Madagascar. In addition to the island of Mauritius, the republic includes the islands of St. Brandon, Rodrigues and the Agalega Islands. + GAZ:00003943 Mayotte [GAZ:00003943] An overseas collectivity of France consisting of a main island, Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and several islets around these two. + GAZ:00002852 Mexico [GAZ:00002852] A federal constitutional republic in North America. It is bounded on the north by the United States; on the south and west by the North Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of Mexico. The United Mexican States comprise a federation of thirty-one states and a federal district, the capital Mexico City. + GAZ:00005862 Micronesia [GAZ:00005862] A subregion of Oceania, comprising hundreds of small islands in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua New Guinea and Melanesia to the west and southwest, and Polynesia to the east. + GAZ:00007112 Midway Islands [GAZ:00007112] A 6.2 km2 atoll located in the North Pacific Ocean (near the northwestern end of the Hawaiian archipelago). It is an unincorporated territory of the United States, designated an insular area under the authority of the US Department of the Interior. + GAZ:00003897 Moldova [GAZ:00003897] A landlocked country in Eastern Europe, located between Romania to the west and Ukraine to the north, east and south. Moldova is divided into thirty-two districts (raioane, singular raion); three municipalities (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). The cities of Comrat and Tiraspol also have municipality status, however not as first-tier subdivisions of Moldova, but as parts of the regions of Gagauzia and Transnistria, respectively. The status of Transnistria is however under dispute. Although it is de jure part of Moldova and is recognized as such by the international community, Transnistria is not de facto under the control of the central government of Moldova. It is administered by an unrecognized breakaway authority under the name Pridnestrovian Moldovan Republic. + GAZ:00003857 Monaco [GAZ:00003857] A small country that is completely bordered by France to the north, west, and south; to the east it is bordered by the Mediterranean Sea. It consists of a single municipality (commune) currently divided into 4 quartiers and 10 wards. + GAZ:00008744 Mongolia [GAZ:00008744] A country in East-Central Asia. The landlocked country borders Russia to the north and China to the south. The capital and largest city is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are in turn divided into 315 sums (districts). The capital Ulan Bator is administrated separately as a khot (municipality) with provincial status. + GAZ:00006898 Montenegro [GAZ:00006898] A country located in Southeastern Europe. It has a coast on the Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina to the northwest, Serbia and its partially recognized breakaway southern province of Kosovo to the northeast and Albania to the southeast. Its capital and largest city is Podgorica. Montenegro is divided into twenty-one municipalities (opstina), and two urban municipalities, subdivisions of Podgorica municipality. + GAZ:00003988 Montserrat [GAZ:00003988] A British overseas territory located in the Leeward Islands. Montserrat is divided into three parishes. + GAZ:00000565 Morocco [GAZ:00000565] A country in North Africa. It has a coast on the Atlantic Ocean that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco has international borders with Algeria to the east, Spain to the north (a water border through the Strait and land borders with two small Spanish autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco is divided into 16 regions, and subdivided into 62 prefectures and provinces. Because of the conflict over Western Sahara, the status of both regions of "Saguia el-Hamra" and "Rio de Oro" is disputed. + GAZ:00001100 Mozambique [GAZ:00001100] A country in southeastern Africa bordered by the Indian Ocean to the east, Tanzania to the north, Malawi and Zambia to the northwest, Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique is divided into ten provinces (provincias) and one capital city (cidade capital) with provincial status. The provinces are subdivided into 129 districts (distritos). Districts are further divided in "Postos Administrativos" (Administrative Posts) and these in Localidades (Localities) the lowest geographical level of central state administration. + GAZ:00006899 Myanmar [GAZ:00006899] A country in SE Asia that is bordered by China on the north, Laos on the east, Thailand on the southeast, Bangladesh on the west, and India on the northwest, with the Bay of Bengal to the southwest. Myanmar is divided into seven states and seven divisions. The administrative divisions are further subdivided into districts, which are further subdivided into townships, wards, and villages. + GAZ:00001096 Namibia [GAZ:00001096] A country in southern Africa on the Atlantic coast. It shares borders with Angola and Zambia to the north, Botswana to the east, and South Africa to the south. Namibia is divided into 13 regions and subdivided into 102 constituencies. + GAZ:00006900 Nauru [GAZ:00006900] An island nation in the Micronesian South Pacific. The nearest neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. Nauru is divided into fourteen administrative districts which are grouped into eight electoral constituencies. + GAZ:00007119 Navassa Island [GAZ:00007119] A small, uninhabited island in the Caribbean Sea, and is an unorganized unincorporated territory of the United States, which administers it through the US Fish and Wildlife Service. The island is also claimed by Haiti. + GAZ:00004399 Nepal [GAZ:00004399] A landlocked nation in South Asia. It is bordered by the Tibet Autonomous Region of the People's Republic of China to the northeast and India to the south and west; it is separated from Bhutan by the Indian State of Sikkim and from Bangladesh by a small strip of the Indian State of West Bengal, known as the "Chicken's Neck". The Himalaya mountain range runs across Nepal's north and western parts, and eight of the world's ten highest mountains, including the highest, Mount Everest are situated within its territory. Nepal is divided into 14 zones and 75 districts, grouped into 5 development regions. + GAZ:00002946 Netherlands [GAZ:00002946] The European part of the Kingdom of the Netherlands. It is bordered by the North Sea to the north and west, Belgium to the south, and Germany to the east. The Netherlands is divided into twelve administrative regions, called provinces. All provinces of the Netherlands are divided into municipalities (gemeenten), together 443 (2007). + GAZ:00005206 New Caledonia [GAZ:00005206] A "sui generis collectivity" (in practice an overseas territory) of France, made up of a main island (Grande Terre), the Loyalty Islands, and several smaller islands. It is located in the region of Melanesia in the southwest Pacific. Administratively, the archipelago is divided into three provinces, and then into 33 communes. + GAZ:00000469 New Zealand [GAZ:00000469] A nation in the south-western Pacific Ocean comprising two large islands (the North Island and the South Island) and numerous smaller islands, most notably Stewart Island/Rakiura and the Chatham Islands. + GAZ:00002978 Nicaragua [GAZ:00002978] A republic in Central America. It is also the least densely populated with a demographic similar in size to its smaller neighbors. The country is bordered by Honduras to the north and by Costa Rica to the south. The Pacific Ocean lies to the west of the country, while the Caribbean Sea lies to the east. For administrative purposes it is divided into 15 departments (departamentos) and two self-governing regions (autonomous communities) based on the Spanish model. The departments are then subdivided into 153 municipios (municipalities). The two autonomous regions are Region Autonoma del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 they formed the single department of Zelaya. + GAZ:00000585 Niger [GAZ:00000585] A landlocked country in Western Africa, named after the Niger River. It borders Nigeria and Benin to the south, Burkina Faso and Mali to the west, Algeria and Libya to the north and Chad to the east. The capital city is Niamey. Niger is divided into 7 departments and one capital district. The departments are subdivided into 36 arrondissements and further subdivided into 129 communes. + GAZ:00000912 Nigeria [GAZ:00000912] A federal constitutional republic comprising thirty-six states and one Federal Capital Territory. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in the north. Its coast lies on the Gulf of Guinea, part of the Atlantic Ocean, in the south. The capital city is Abuja. Nigeria is divided into thirty-six states and one Federal Capital Territory, which are further sub-divided into 774 Local Government Areas (LGAs). + GAZ:00006902 Niue [GAZ:00006902] An island nation located in the South Pacific Ocean. Although self-governing, Niue is in free association with New Zealand, meaning that the Sovereign in Right of New Zealand is also Niue's head of state. + GAZ:00005908 Norfolk Island [GAZ:00005908] A Territory of Australia that includes Norfolk Island and neighboring islands. + GAZ:00002801 North Korea [GAZ:00002801] A state in East Asia in the northern half of the Korean Peninsula, with its capital in the city of Pyongyang. To the south and separated by the Korean Demilitarized Zone is South Korea, with which it formed one nation until division following World War II. At its northern Amnok River border are China and, separated by the Tumen River in the extreme north-east, Russia. + GAZ:00006895 North Macedonia [GAZ:00006895] A landlocked country on the Balkan peninsula in southeastern Europe. It is bordered by Serbia and Kosovo to the north, Albania to the west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), 10 of which comprise Greater Skopje. This is reduced from the previous 123 municipalities established in 1996-09. Prior to this, local government was organised into 34 administrative districts. + GAZ:00002284 North Sea [GAZ:00002284] A sea situated between the eastern coasts of the British Isles and the western coast of Europe. + GAZ:00003958 Northern Mariana Islands [GAZ:00003958] A group of 15 islands about three-quarters of the way from Hawaii to the Philippines. + GAZ:00002699 Norway [GAZ:00002699] A country and constitutional monarchy in Northern Europe that occupies the western portion of the Scandinavian Peninsula. It is bordered by Sweden, Finland, and Russia. The Kingdom of Norway also includes the Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty over Svalbard is based upon the Svalbard Treaty, but that treaty does not apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter I Island and Queen Maud Land in Antarctica are external dependencies, but those three entities do not form part of the kingdom. + GAZ:00005283 Oman [GAZ:00005283] A country in southwest Asia, on the southeast coast of the Arabian Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia on the west, and Yemen on the southwest. The coast is formed by the Arabian Sea on the south and east, and the Gulf of Oman on the northeast. The country also contains Madha, an exclave enclosed by the United Arab Emirates, and Musandam, an exclave also separated by Emirati territory. Oman is divided into four governorates (muhafazah) and five regions (mintaqat). The regions are subdivided into provinces (wilayat). + GAZ:00005246 Pakistan [GAZ:00005246] A country in Middle East which lies on the Iranian Plateau and some parts of South Asia. It is located in the region where South Asia converges with Central Asia and the Middle East. It has a 1,046 km coastline along the Arabian Sea in the south, and is bordered by Afghanistan and Iran in the west, India in the east and China in the far northeast. Pakistan is subdivided into four provinces and two territories. In addition, the portion of Kashmir that is administered by the Pakistani government is divided into two separate administrative units. The provinces are divided into a total of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly equivalent to counties). Tehsils may contain villages or municipalities. There are over five thousand local governments in Pakistan. + GAZ:00006905 Palau [GAZ:00006905] A nation that consists of eight principal islands and more than 250 smaller ones lying roughly 500 miles southeast of the Philippines. + GAZ:00002892 Panama [GAZ:00002892] The southernmost country of Central America. Situated on an isthmus, some categorize it as a transcontinental nation connecting the north and south part of America. It borders Costa Rica to the north-west, Colombia to the south-east, the Caribbean Sea to the north and the Pacific Ocean to the south. Panama's major divisions are nine provinces and five indigenous territories (comarcas indigenas). The provincial borders have not changed since they were determined at independence in 1903. The provinces are divided into districts, which in turn are subdivided into sections called corregimientos. Configurations of the corregimientos are changed periodically to accommodate population changes as revealed in the census reports. + GAZ:00003922 Papua New Guinea [GAZ:00003922] A country in Oceania that comprises the eastern half of the island of New Guinea and its offshore islands in Melanesia (a region of the southwestern Pacific Ocean north of Australia). + GAZ:00010832 Paracel Islands [GAZ:00010832] A group of small islands and reefs in the South China Sea, about one-third of the way from Vietnam to the Philippines. + GAZ:00002933 Paraguay [GAZ:00002933] A landlocked country in South America. It lies on both banks of the Paraguay River, bordering Argentina to the south and southwest, Brazil to the east and northeast, and Bolivia to the northwest, and is located in the very heart of South America. Paraguay consists of seventeen departments and one capital district (distrito capital). Each department is divided into districts. + GAZ:00002932 Peru [GAZ:00002932] A country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean. Peru is divided into 25 regions and the province of Lima. These regions are subdivided into provinces, which are composed of districts (provincias and distritos). There are 195 provinces and 1833 districts in Peru. The Lima Province, located in the central coast of the country, is unique in that it doesn't belong to any of the twenty-five regions. The city of Lima, which is the nation's capital, is located in this province. Callao is its own region, even though it only contains one province, the Constitutional Province of Callao. + GAZ:00004525 Philippines [GAZ:00004525] An archipelagic nation located in Southeast Asia. The Philippine archipelago comprises 7,107 islands in the western Pacific Ocean, bordering countries such as Indonesia, Malaysia, Palau and the Republic of China, although it is the only Southeast Asian country to share no land borders with its neighbors. The Philippines is divided into three island groups: Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, 136 cities, 1,494 municipalities and 41,995 barangays. + GAZ:00005867 Pitcairn Islands [GAZ:00005867] A group of four islands in the southern Pacific Ocean. The Pitcairn Islands form the southeasternmost extension of the geological archipelago of the Tuamotus of French Polynesia. + GAZ:00002939 Poland [GAZ:00002939] A country in Central Europe. Poland is bordered by Germany to the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a Russian exclave, to the north. The administrative division of Poland since 1999 has been based on three levels of subdivision. The territory of Poland is divided into voivodeships (provinces); these are further divided into powiats (counties), and these in turn are divided into gminas (communes or municipalities). Major cities normally have the status of both gmina and powiat. Poland currently has 16 voivodeships, 379 powiats (including 65 cities with powiat status), and 2,478 gminas. + GAZ:00004126 Portugal [GAZ:00004126] That part of the Portugese Republic that occupies the W part of the Iberian Peninsula, and immediately adjacent islands. + GAZ:00006935 Puerto Rico [GAZ:00006935] A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States). + GAZ:00005286 Qatar [GAZ:00005286] An Arab emirate in Southwest Asia, occupying the small Qatar Peninsula on the northeasterly coast of the larger Arabian Peninsula. It is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds the state. Qatar is divided into ten municipalities (Arabic: baladiyah), which are further divided into zones (districts). + GAZ:00001088 Republic of the Congo [GAZ:00001088] A country in Central Africa. It is bordered by Gabon, Cameroon, the Central African Republic, the Democratic Republic of the Congo, the Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic of the Congo is divided into 10 regions (regions) and one commune, the capital Brazzaville. The regions are subdivided into forty-six districts. + GAZ:00003945 Reunion [GAZ:00003945] An island, located in the Indian Ocean east of Madagascar, about 200 km south west of Mauritius, the nearest island. + GAZ:00002951 Romania [GAZ:00002951] A country in Southeastern Europe. It shares a border with Hungary and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, and Bulgaria to the south. Romania has a stretch of sea coast along the Black Sea. It is located roughly in the lower basin of the Danube and almost all of the Danube Delta is located within its territory. Romania is divided into forty-one counties (judete), as well as the municipality of Bucharest (Bucuresti) - which is its own administrative unit. The country is further subdivided into 319 cities and 2686 communes (rural localities). + GAZ:00023304 Ross Sea [GAZ:00023304] A large embayment of the Southern Ocean, extending deeply into Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck on the east, at 158degW. + GAZ:00002721 Russia [GAZ:00002721] A transcontinental country extending over much of northern Eurasia. Russia shares land borders with the following countries (counter-clockwise from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais (territories), 4 autonomous okrugs (autonomous districts), one autonomous oblast, and two federal cities. The federal subjects are grouped into seven federal districts. These subjects are divided into districts (raions), cities/towns and urban-type settlements, and, at level 4, selsovets (rural councils), towns and urban-type settlements under the jurisdiction of the district and city districts. + GAZ:00001087 Rwanda [GAZ:00001087] A small landlocked country in the Great Lakes region of east-central Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo and Tanzania. Rwanda is divided into five provinces (intara) and subdivided into thirty districts (akarere). The districts are divided into sectors (imirenge). + GAZ:00000849 Saint Helena [GAZ:00000849] An island of volcanic origin and a British overseas territory in the South Atlantic Ocean. + GAZ:00006906 Saint Kitts and Nevis [GAZ:00006906] A federal two-island nation in the West Indies. Located in the Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast are Antigua and Barbuda, and to the southeast is the small uninhabited island of Redonda, and the island of Montserrat. The federation of Saint Kitts and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts and five on Nevis. + GAZ:00006909 Saint Lucia [GAZ:00006909] An island nation in the eastern Caribbean Sea on the boundary with the Atlantic Ocean. + GAZ:00003942 Saint Pierre and Miquelon [GAZ:00003942] An Overseas Collectivity of France located in a group of small islands in the North Atlantic Ocean, the main ones being Saint Pierre and Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and Miquelon became an overseas department in 1976, but its status changed to that of an Overseas collectivity in 1985. + GAZ:00005841 Saint Martin [GAZ:00005841] An overseas collectivity of France that came into being on 2007-02-22, encompassing the northern parts of the island of Saint Martin and neighboring islets. The southern part of the island, Sint Maarten, is part of the Netherlands Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe. + GAZ:02000565 Saint Vincent and the Grenadines [GAZ:02000565] An island nation in the Lesser Antilles chain of the Caribbean Sea. + GAZ:00006910 Samoa [GAZ:00006910] A country governing the western part of the Samoan Islands archipelago in the South Pacific Ocean. Samoa is made up of eleven itumalo (political districts). + GAZ:00003102 San Marino [GAZ:00003102] A country in the Apennine Mountains. It is a landlocked enclave, completely surrounded by Italy. San Marino is an enclave in Italy, on the border between the regioni of Emilia Romagna and Marche. Its topography is dominated by the Apennines mountain range. San Marino is divided into nine municipalities, known locally as Castelli (singular castello). + GAZ:00006927 Sao Tome and Principe [GAZ:00006927] An island nation in the Gulf of Guinea, off the western equatorial coast of Africa. It consists of two islands: Sao Tome and Principe, located about 140 km apart and about 250 and 225 km respectively, off of the northwestern coast of Gabon. Both islands are part of an extinct volcanic mountain range. Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The provinces are further divided into seven districts, six on Sao Tome and one on Principe (with Principe having self-government since 1995-04-29). + GAZ:00005279 Saudi Arabia [GAZ:00005279] A country on the Arabian Peninsula. It is bordered by Jordan on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, and the United Arab Emirates on the east, Oman on the southeast, and Yemen on the south. The Persian Gulf lies to the northeast and the Red Sea to its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; singular mintaqah). Each is then divided into Governorates. + GAZ:00000913 Senegal [GAZ:00000913] A country south of the Senegal River in western Africa. Senegal is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies almost entirely within Senegal, surrounded on the north, east and south; from its western coast Gambia's territory follows the Gambia River more than 300 km inland. Dakar is the capital city of Senegal, located on the Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided into 11 regions and further subdivided into 34 Departements, 103 Arrondissements (neither of which have administrative function) and by Collectivites Locales. + GAZ:00002957 Serbia [GAZ:00002957] A landlocked country in Central and Southeastern Europe, covering the southern part of the Pannonian Plain and the central part of the Balkan Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria to the east; Republic of Macedonia, Montenegro to the south; Croatia and Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided into 29 districts plus the City of Belgrade. The districts and the city of Belgrade are further divided into municipalities. Serbia has two autonomous provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), and Vojvodina in the north (7 districts, 46 municipalities). + GAZ:00006922 Seychelles [GAZ:00006922] An archipelagic island country in the Indian Ocean at the eastern edge of the Somali Sea. It consists of 115 islands. + GAZ:00000914 Sierra Leone [GAZ:00000914] A country in West Africa. It is bordered by Guinea in the north and east, Liberia in the southeast, and the Atlantic Ocean in the southwest and west. The Republic of Sierra Leone is composed of 3 provinces and one area called the Western Area; the provinces are further divided into 12 districts. The Western Area is also divided into 2 districts. + GAZ:00003923 Singapore [GAZ:00003923] An island nation located at the southern tip of the Malay Peninsula. It lies 137 km north of the Equator, south of the Malaysian State of Johor and north of Indonesia's Riau Islands. Singapore consists of 63 islands, including mainland Singapore. There are two man-made connections to Johor, Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in the west. Since 2001-11-24, Singapore has had an administrative subdivision into 5 districts. It is also divided into five Regions, urban planning subdivisions with no administrative role. + GAZ:00012579 Sint Maarten [GAZ:00012579] One of five island areas (Eilandgebieden) of the Netherlands Antilles, encompassing the southern half of the island of Saint Martin/Sint Maarten. + GAZ:00002956 Slovakia [GAZ:00002956] A landlocked country in Central Europe. The Slovak Republic borders the Czech Republic and Austria to the west, Poland to the north, Ukraine to the east and Hungary to the south. The largest city is its capital, Bratislava. Slovakia is subdivided into 8 kraje (singular - kraj, usually translated as regions. The kraje are subdivided into many okresy (singular okres, usually translated as districts). Slovakia currently has 79 districts. + GAZ:00002955 Slovenia [GAZ:00002955] A country in southern Central Europe bordering Italy to the west, the Adriatic Sea to the southwest, Croatia to the south and east, Hungary to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. As of 2005-05 Slovenia is divided into 12 statistical regions for legal and statistical purposes. Slovenia is divided into 210 local municipalities, eleven of which have urban status. + GAZ:00005275 Solomon Islands [GAZ:00005275] A nation in Melanesia, east of Papua New Guinea, consisting of nearly one thousand islands. Together they cover a land mass of 28,400 km2. The capital is Honiara, located on the island of Guadalcanal. + GAZ:00001104 Somalia [GAZ:00001104] A country located in the Horn of Africa. It is bordered by Djibouti to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on its north, the Indian Ocean at its east, and Ethiopia to the west. Prior to the civil war, Somalia was divided into eighteen regions (gobollada, singular gobol), which were in turn subdivided into districts. On a de facto basis, northern Somalia is now divided up among the quasi-independent states of Puntland, Somaliland, Galmudug and Maakhir. + GAZ:00001094 South Africa [GAZ:00001094] A country located at the southern tip of Africa. It borders the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, Swaziland, and Lesotho, an independent enclave surrounded by South African territory. It is divided into nine provinces which are further subdivided into 52 districts: 6 metropolitan and 46 district municipalities. The 46 district municipalities are further subdivided into 231 local municipalities. The district municipalities also contain 20 district management areas (mostly game parks) that are directly governed by the district municipalities. The six metropolitan municipalities perform the functions of both district and local municipalities. + GAZ:00003990 South Georgia and the South Sandwich Islands [GAZ:00003990] A British overseas territory in the southern Atlantic Ocean. It iconsists of South Georgia and the Sandwich Islands, some 640 km to the SE. + GAZ:00002802 South Korea [GAZ:00002802] A republic in East Asia, occupying the southern half of the Korean Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 special city (teukbyeolsi). These are further subdivided into a variety of smaller entities, including cities (si), counties (gun), districts (gu), towns (eup), townships (myeon), neighborhoods (dong) and villages (ri). + GAZ:00233439 South Sudan [GAZ:00233439] A state located in Africa with Juba as its capital city. It's bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic of the Congo to the south, and the Central African Republic to the west and Sudan to the North. Southern Sudan includes the vast swamp region of the Sudd formed by the White Nile, locally called the Bahr el Jebel. + GAZ:00003936 Spain [GAZ:00003936] That part of the Kingdom of Spain that occupies the Iberian Peninsula plus the Balaeric Islands. The Spanish mainland is bordered to the south and east almost entirely by the Mediterranean Sea (except for a small land boundary with Gibraltar); to the north by France, Andorra, and the Bay of Biscay; and to the west by the Atlantic Ocean and Portugal. + GAZ:00010831 Spratly Islands [GAZ:00010831] A group of >100 islands located in the Southeastern Asian group of reefs and islands in the South China Sea, about two-thirds of the way from southern Vietnam to the southern Philippines. + GAZ:00003924 Sri Lanka [GAZ:00003924] An island nation in South Asia, located about 31 km off the southern coast of India. Sri Lanka is divided into 9 provinces and 25 districts. Districts are divided into Divisional Secretariats. + GAZ:00002475 State of Palestine [GAZ:00002475] The territory under the administration of the Palestine National Authority, as established by the Oslo Accords. The PNA divides the Palestinian territories into 16 governorates. + GAZ:00000560 Sudan [GAZ:00000560] A country in North Africa. It is bordered by Egypt to the north, the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and Uganda to the southeast, Democratic Republic of the Congo and the Central African Republic to the southwest, Chad to the west and Libya to the northwest. Sudan is divided into twenty-six states (wilayat, singular wilayah) which in turn are subdivided into 133 districts. + GAZ:00002525 Suriname [GAZ:00002525] A country in northern South America. It is situated between French Guiana to the east and Guyana to the west. The southern border is shared with Brazil and the northern border is the Atlantic coast. The southernmost border with French Guiana is disputed along the Marowijne river. Suriname is divided into 10 districts, each of which is divided into Ressorten. + GAZ:00005396 Svalbard [GAZ:00005396] An archipelago of continental islands lying in the Arctic Ocean north of mainland Europe, about midway between Norway and the North Pole. + GAZ:00001099 Swaziland [GAZ:00001099] A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla). + GAZ:00002729 Sweden [GAZ:00002729] A Nordic country on the Scandinavian Peninsula in Northern Europe. It has borders with Norway (west and north) and Finland (northeast). Sweden is a unitary state, currently divided into twenty-one counties (lan). Each county further divides into a number of municipalities or kommuner, with a total of 290 municipalities in 2004. + GAZ:00002941 Switzerland [GAZ:00002941] A federal republic in Europe. Switzerland is bordered by Germany, France, Italy, Austria and Liechtenstein. The Swiss Confederation consists of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within Switzerland there are two enclaves: Busingen belongs to Germany, Campione d'Italia belongs to Italy. + GAZ:00002474 Syria [GAZ:00002474] A country in Southwest Asia, bordering Lebanon, the Mediterranean Sea and the island of Cyprus to the west, Israel to the southwest, Jordan to the south, Iraq to the east, and Turkey to the north. Syria has fourteen governorates, or muhafazat (singular: muhafazah). The governorates are divided into sixty districts, or manatiq (singular: mintaqah), which are further divided into sub-districts, or nawahi (singular: nahia). + GAZ:00005341 Taiwan [GAZ:00005341] A state in East Asia with de facto rule of the island of Tawain and adjacent territory. The Republic of China currently administers two historical provinces of China (one completely and a small part of another one) and centrally administers two direct-controlled municipalities. + GAZ:00006912 Tajikistan [GAZ:00006912] A mountainous landlocked country in Central Asia. Afghanistan borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and People's Republic of China to the east. Tajikistan consists of 4 administrative divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly known as Karotegin Province). Each region is divided into several districts (nohiya or raion). + GAZ:00001103 Tanzania [GAZ:00001103] A country in East Africa bordered by Kenya and Uganda on the north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, and Zambia, Malawi and Mozambique on the south. To the east it borders the Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight districts (wilaya), each with at least one council, have been created to further increase local authority; the councils are also known as local government authorities. Currently there are 114 councils operating in 99 districts; 22 are urban and 92 are rural. The 22 urban units are further classified as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) or town councils (the remaining eleven communities). + GAZ:00003744 Thailand [GAZ:00003744] A country in Southeast Asia. To its east lie Laos and Cambodia; to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided into 75 provinces (changwat), which are gathered into 5 groups of provinces by location. There are also 2 special governed districts: the capital Bangkok (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial level and thus often counted as a 76th province. + GAZ:00006913 Timor-Leste [GAZ:00006913] A country in Southeast Asia. It comprises the eastern half of the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, an exclave on the northwestern side of the island, within Indonesian West Timor. The small country of 15,410 km2 is located about 640 km northwest of Darwin, Australia. East Timor is divided into thirteen administrative districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, villages and hamlets. + GAZ:00000915 Togo [GAZ:00000915] A country in West Africa bordering Ghana in the west, Benin in the east and Burkina Faso in the north. In the south, it has a short Gulf of Guinea coast, on which the capital Lome is located. + GAZ:00260188 Tokelau [GAZ:00260188] A dependent territory of New Zealand in the southern Pacific Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and Fakaofo. They have a combined land area of 10 km2 (4 sq mi). + GAZ:00006916 Tonga [GAZ:00006916] A Polynesian country, and also an archipelago comprising 169 islands, of which 36 are inhabited. The archipelago's total surface area is about 750 square kilometres (290 sq mi) scattered over 700,000 square kilometres (270,000 sq mi) of the southern Pacific Ocean. + GAZ:00003767 Trinidad and Tobago [GAZ:00003767] An archipelagic state in the southern Caribbean, lying northeast of the South American nation of Venezuela and south of Grenada in the Lesser Antilles. It also shares maritime boundaries with Barbados to the northeast and Guyana to the southeast. The country covers an area of 5,128 km2and consists of two main islands, Trinidad and Tobago, and 21 smaller islands. + GAZ:00005812 Tromelin Island [GAZ:00005812] A low, flat 0.8 km2 island in the Indian Ocean, about 350 km east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 m long and 700 m wide, surrounded by coral reefs. The island is 7 m high at its highest point. + GAZ:00000562 Tunisia [GAZ:00000562] A country situated on the Mediterranean coast of North Africa. It is bordered by Algeria to the west and Libya to the southeast. Tunisia is subdivided into 24 governorates, divided into 262 "delegations" or "districts" (mutamadiyat), and further subdivided into municipalities (shaykhats). + GAZ:00000558 Turkey [GAZ:00000558] A Eurasian country that stretches across the Anatolian peninsula in western Asia and Thrace (Rumelia) in the Balkan region of southeastern Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago are to the west; and the Black Sea is to the north. Separating Anatolia and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus and the Dardanelles), which are commonly reckoned to delineate the border between Asia and Europe, thereby making Turkey transcontinental. The territory of Turkey is subdivided into 81 provinces for administrative purposes. The provinces are organized into 7 regions for census purposes; however, they do not represent an administrative structure. Each province is divided into districts, for a total of 923 districts. + GAZ:00005018 Turkmenistan [GAZ:00005018] A country in Central Asia. It is bordered by Afghanistan to the southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan to the northwest, and the Caspian Sea to the west. It was a constituent republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan is divided into five provinces or welayatlar (singular - welayat) and one independent city. + GAZ:00003955 Turks and Caicos Islands [GAZ:00003955] A British Overseas Territory consisting of two groups of tropical islands in the West Indies. The Turks and Caicos Islands are divided into six administrative districts (two in the Turks Islands and four in the Caicos Islands. + GAZ:00009715 Tuvalu [GAZ:00009715] A Polynesian island nation located in the Pacific Ocean midway between Hawaii and Australia. + GAZ:00002459 United States of America [GAZ:00002459] A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into "census areas"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a "charter township", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county. + GAZ:00001102 Uganda [GAZ:00001102] A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties. + GAZ:00002724 Ukraine [GAZ:00002724] A country in Eastern Europe. It borders Russia to the east, Belarus to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine is subdivided into twenty-four oblasts (provinces) and one autonomous republic (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, and Sevastopol, both have a special legal status. The 24 oblasts and Crimea are subdivided into 490 raions (districts), or second-level administrative units. + GAZ:00005282 United Arab Emirates [GAZ:00005282] A Middle Eastern federation of seven states situated in the southeast of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain. + GAZ:00002637 United Kingdom [GAZ:00002637] A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel. + GAZ:00002930 Uruguay [GAZ:00002930] A country located in the southeastern part of South America. It is bordered by Brazil to the north, by Argentina across the bank of both the Uruguay River to the west and the estuary of Rio de la Plata to the southwest, and the South Atlantic Ocean to the southeast. Uraguay consists of 19 departments (departamentos, singular - departamento). + GAZ:00004979 Uzbekistan [GAZ:00004979] A doubly landlocked country in Central Asia, formerly part of the Soviet Union. It shares borders with Kazakhstan to the west and to the north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one autonomous republic (respublika and one independent city (shahar). + GAZ:00006918 Vanuatu [GAZ:00006918] An island country located in the South Pacific Ocean. The archipelago, which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New Guinea, southeast of the Solomon Islands, and west of Fiji. + GAZ:00002931 Venezuela [GAZ:00002931] A country on the northern coast of South America. The country comprises a continental mainland and numerous islands located off the Venezuelan coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses borders with Guyana to the east, Brazil to the south, and Colombia to the west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just north, off the Venezuelan coast. Venezuela is divided into twenty-three states (Estados), a capital district (distrito capital) corresponding to the city of Caracas, the Federal Dependencies (Dependencias Federales, a special territory), and Guayana Esequiba (claimed in a border dispute with Guyana). Venezuela is further subdivided into 335 municipalities (municipios); these are subdivided into over one thousand parishes (parroquias). + GAZ:00003756 Viet Nam [GAZ:00003756] The easternmost country on the Indochina Peninsula in Southeast Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, alongside China, Laos, and Cambodia. + GAZ:00003959 Virgin Islands [GAZ:00003959] A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts. + GAZ:00007111 Wake Island [GAZ:00007111] A coral atoll (despite its name) having a coastline of 19 km in the North Pacific Ocean, located about two-thirds of the way from Honolulu (3,700 km west) to Guam (2,430 km east). + GAZ:00007191 Wallis and Futuna [GAZ:00007191] A Polynesian French island territory (but not part of, or even contiguous with, French Polynesia) in the South Pacific between Fiji and Samoa. It is made up of three main volcanic tropical islands and a number of tiny islets. + GAZ:00009572 West Bank [GAZ:00009572] A landlocked territory near the Mediterranean coast of Western Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the south, west and north.[2] Under Israeli occupation since 1967, the area is split into 167 Palestinian "islands" under partial Palestinian National Authority civil rule, and 230 Israeli settlements into which Israeli law is "pipelined". + GAZ:00000564 Western Sahara [GAZ:00000564] A territory of northwestern Africa, bordered by Morocco to the north, Algeria in the northeast, Mauritania to the east and south, and the Atlantic Ocean on the west. Western Sahara is administratively divided into four regions. + GAZ:00005284 Yemen [GAZ:00005284] A country located on the Arabian Peninsula in Southwest Asia. Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's territory includes over 200 islands, the largest of which is Socotra, about 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen is divided into twenty governorates (muhafazah) and one municipality. The population of each governorate is listed in the table below. The governorates of Yemen are divided into 333 districts (muderiah). The districts are subdivided into 2,210 sub-districts, and then into 38,284 villages (as of 2001). + GAZ:00001107 Zambia [GAZ:00001107] A landlocked country in Southern Africa. The neighbouring countries are the Democratic Republic of the Congo to the north, Tanzania to the north-east, Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, and Angola to the west. The capital city is Lusaka. Zambia is divided into nine provinces. Each province is subdivided into several districts with a total of 73 districts. + GAZ:00001106 Zimbabwe [GAZ:00001106] A landlocked country in the southern part of the continent of Africa, between the Zambezi and Limpopo rivers. It is bordered by South Africa to the south, Botswana to the southwest, Zambia to the northwest, and Mozambique to the east. Zimbabwe is divided into eight provinces and two cities with provincial status. The provinces are subdivided into 59 districts and 1,200 municipalities. + \ No newline at end of file diff --git a/web/templates/hpai/schema_slots.tsv b/web/templates/hpai/schema_slots.tsv new file mode 100644 index 00000000..d0a14efd --- /dev/null +++ b/web/templates/hpai/schema_slots.tsv @@ -0,0 +1,283 @@ +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_BIOSAMPLE_Enterics EXPORT_VirusSeq_Portal +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001122 Database Identifiers +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0001123 specimen_collector_sample_ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. ASDFG123 sample_name +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0100752 specimen_collector_subsample_ID specimen_collector_subsample_id WhitespaceMinimizedString The user-defined identifier assigned to a portion of the original sample. Store the ID for the subsample/aliquot. ASDFG123_12 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0100996 pooled_sample_ID pooled_sample_id WhitespaceMinimizedString The user-defined identifier assigned to a combined (pooled) set of samples. If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID. 12345AYZ +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0100760 sampling_site_ID sampling_site_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific location from which samples are taken. Store the ID for the site from which a sample was taken. The "site" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID. Site 12A +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0100761 sampling_event_ID sampling_event_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites. Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site. Event 120522.1 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0001136 BioProject_accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 bioproject_accession +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0001139 BioSample_accession biosample_accession WhitespaceMinimizedString TRUE {UPPER_CASE} {UPPER_CASE} The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD SAMN14180202, SAMD00000001 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. ERR123456, DRR123456, CRR123456 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001150 Sample collection and processing +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100762 sample_collection_data_steward_name sample_collection_data_steward_name WhitespaceMinimizedString The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the name of the sample collection data steward. Joe Bloggs +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101107 sample_collection_data_steward_contact_email sample_collection_data_steward_contact_email WhitespaceMinimizedString The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the "sample collector contact email". bloggsj@aglab.ca +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by WhitespaceMinimizedString null value menu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada collected_by +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001156 sample_collector_contact_email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca WaterTester@facility.ca +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001181 geo_loc_name_(country) geo_loc_name_country geo_loc_name_(country) menu null value menu TRUE The country of origin of the sample. If known, select a value from the pick list. Canada geo_loc_name +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001185 geo_loc_name_(state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString null value menu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga Western Cape geo_loc_name +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100280 geo_loc_name_(county/region) geo_loc_name_county_region WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001189 geo_loc_name_(city) geo_loc_name_city WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100436 geo_loc_name_(site) geo_loc_name_site__ WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100309 geo_loc_latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100310 geo_loc_longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001191 organism organism organism menu null value menu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae organism +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101108 influenza_subtype influenza_subtype influenza_subsubtype menu TRUE TRUE +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101109 influenza_subtyping_scheme_name influenza_subtyping_scheme_name influenza_subtyping_scheme_name menu +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process taxonomic_identification_process menu +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101110 virus_identifier virus_identifier WhitespaceMinimizedString +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101111 WHO/OIE/FAO_H5_clade who_oie_fao_h5_clade WhitespaceMinimizedString +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date date null value menu TRUE The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 collection_date +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101071 sample_collection_end_date sample_collection_end_date date null value menu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101072 sample_collection_start_time sample_collection_start_time time null value menu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101073 sample_collection_end_time sample_collection_end_time time null value menu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100765 sample_collection_time_of_day sample_collection_time_of_day sample_collection_time_of_day menu null value menu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100766 sample_collection_time_duration_value sample_collection_time_duration_value WhitespaceMinimizedString null value menu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 4 +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100767 sample_collection_time_duration_unit sample_collection_time_duration_unit sample_collection_duration_unit menu null value menu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date null value menu The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date null value menu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 +HPAI;HPAIHost Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country geo_loc_name (country) menu null value menu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] +HPAI;HPAIFood Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country geo_loc_name (country) menu null value menu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin +HPAI;HPAIFood Sample collection and processing GENEPIO:0100444 food_product food_product food_product menu null value menu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product isolation_source;food_product_type +HPAI;HPAIFood Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties food_product_properties menu null value menu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source +HPAI;HPAIFood Sample collection and processing GENEPIO:0100447 food_packaging food_packaging food_packaging menu null value menu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap +HPAI;HPAIFood Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date date A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date +HPAI;HPAIFood Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date date A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 +HPAI;HPAIWW;HPAIEnviro;HPAIFood Sample collection and processing GENEPIO:0001232 environmental_site environmental_site environmental_site menu null value menu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env +HPAI;HPAIWW;HPAIEnviro;HPAIFood Sample collection and processing GENEPIO:0001223 environmental_material environmental_material environmental_material menu null value menu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material isolation_source +HPAI;HPAIHost Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material anatomical_material menu null value menu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;isolation_source +HPAI;HPAIHost Sample collection and processing GENEPIO:0001216 body_product body_product body_product menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;isolation_source +HPAI;HPAIHost Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part anatomical_part menu null value menu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part isolation_source +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001234 collection_device collection_device collection_device menu null value menu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device samp_collect_device;isolation_source +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001241 collection_method collection_method collection_method menu null value menu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method isolation_source +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100768 sample_volume_measurement_value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit sample_volume_measurement_unit menu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status residual_sample_status menu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling purpose_of_sampling menu null value menu TRUE TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Public health surveillance purpose_of_sampling +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity presampling_activity menu null value menu TRUE The activities or variables upstream of sample collection that may affect the sample. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Agricultural activity +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100434 presampling_activity_details presampling_activity_details WhitespaceMinimizedString null value menu The details of the activities or variables that affected the sample collected. Briefly describe the presampling activities using free text. Agricultural waste from large farm contributes waste to the site sampled. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100448 sample_storage_method sample_storage_method WhitespaceMinimizedString The process used to store the sample. Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here. The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100449 sample_storage_medium sample_storage_medium WhitespaceMinimizedString The medium in which a sample is stored. Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write "None". Cary-Blair transport medium +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101014 sample_storage_duration_value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit sample_storage_duration_unit menu null value menu The units of a measured sample storage duration. Provide the units from the pick list. Day +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001253 specimen_processing specimen_processing specimen_processing menu null value menu TRUE Any processing applied to the sample during or after receiving the sample. Select processes from the picklist that were applied to this sample. Centrifugation +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100311 specimen_processing_details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101029 experimental_protocol experimental_protocol WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type experimental_specimen_role_type menu null value menu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101112 experimental_specimen_details experimental_specimen_details WhitespaceMinimizedString +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100690 available_data_types available_data_types available_data_types menu null value menu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101023 available_data_type_details available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria +HPAI;HPAIHost GENEPIO:0001268 Host information +HPAI;HPAIHost Host information GENEPIO:0001386 host_(common_name) host_common_name host (common name) menu null value menu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host +HPAI;HPAIHost Host information GENEPIO:0001387 host_(scientific_name) host_scientific_name host (scientific name) menu null value menu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host +HPAI;HPAIHost Host information GENEPIO:0100450 host_(ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety +HPAI;HPAIHost Host information GENEPIO:0100451 host_(breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed +HPAI;HPAIHost Host information GENEPIO:0100452 host_(food production name) host_food_production_name host (food production name) menu null value menu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host +HPAI;HPAIHost Host Information GENEPIO:0001392 host_age host_age decimal null value menu TRUE 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age +HPAI;HPAIHost Host Information GENEPIO:0001393 host_age_unit host_age_unit host_age_unit menu null value menu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] +HPAI;HPAIHost Host information GENEPIO:0001394 host_age_bin host_age_bin host_age_bin menu null value menu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age + host_gender host_gender +HPAI;HPAIHost Host information GENEPIO:0001391 host_disease host_disease host_disease menu null value menu The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease +HPAI;HPAIHost Host Information GENEPIO:0001388 host_health_state host_health_state host_health_state menu null value menu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state +HPAI;HPAIHost Host Information GENEPIO:0001389 host_health_status_details host_health_status_details host_health_status_details menu null value menu Further details pertaining to the health or disease status of the host at time of collection. If known, select a value from the pick list. Hospitalized (ICU) [GENEPIO:0100046] +HPAI;HPAIHost Host Information GENEPIO:0001390 host_health_outcome host_health_outcome host_health_outcome menu null value menu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_disease_outcome +HPAI;HPAIHost Host Information GENEPIO:0001398 host_subject_ID host_subject_id WhitespaceMinimizedString A unique identifier by which each host can be referred to e.g. #131 Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward. BCxy123 host_subject_id +HPAI;HPAIHost Host Information GENEPIO:0100281 case_ID case_id WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 +HPAI;HPAIHost Host Information GENEPIO:0001399 symptom_onset_date symptom_onset_date date null value menu The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 +HPAI;HPAIHost Host Information GENEPIO:0001400 signs_and_symptoms signs_and_symptoms signs_and_symptoms menu null value menu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] +HPAI;HPAIHost Host Information GENEPIO:0001401 pre-existing_conditions_and_risk_factors preexisting_conditions_and_risk_factors pre-existing_conditions_and_risk_factors menu null value menu TRUE "Patient pre-existing conditions and risk factors. +Pre-existing condition: A medical condition that existed prior to the current infection. +Risk Factor: A variable associated with an increased risk of disease or infection." Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Asthma [HP:0002099] +HPAI;HPAIHost Host Information GENEPIO:0001402 complications complications complications menu null value menu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. Acute respiratory failure [MONDO:0001208] +HPAI;HPAIHost GENEPIO:0001409 Host exposure information +HPAI;HPAIHost Host exposure information GENEPIO:0001417 exposure event exposure_event exposure event menu null value menu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Social Gathering Additional location information Exposure Event PH_EXPOSURE +HPAI;HPAIHost Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level exposure contact level menu null value menu The exposure transmission contact type. Select direct or indirect exposure from the pick-list. Direct exposure contact level +HPAI;HPAIHost Host exposure information GENEPIO:0001419 host role host_role host role menu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Inpatient PH_HOST_ROLE +HPAI;HPAIHost Host exposure information GENEPIO:0001428 exposure setting exposure_setting exposure setting menu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Healthcare Setting PH_EXPOSURE +HPAI;HPAIHost Host exposure information GENEPIO:0001431 exposure details exposure_details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Case infected family at home PH_EXPOSURE_DETAILS +HPAI;HPAIHost GENEPIO:0001403 Host vaccination information +HPAI;HPAIHost Host vaccination information GENEPIO:0001404 host_vaccination_status host_vaccination_status host_vaccination_status menu null value menu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated [GENEPIO:0100100] prior_sars_cov_2_vaccination +HPAI;HPAIHost Host vaccination information GENEPIO:0001406 number_of_vaccine_doses_received number_of_vaccine_doses_received integer 0 The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 2 +HPAI;HPAIHost Host vaccination information GENEPIO:0100313 vaccination_dose_1_vaccine_name vaccination_dose_1_vaccine_name WhitespaceMinimizedString The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) +HPAI;HPAIHost Host vaccination information GENEPIO:0100314 vaccination_dose_1_vaccination_date vaccination_dose_1_vaccination_date date The date the first dose of a vaccine was administered. Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-03-01 +HPAI;HPAIHost Host vaccination information GENEPIO:0100315 vaccination_dose_2_vaccine_name vaccination_dose_2_vaccine_name WhitespaceMinimizedString The name of the vaccine administered as the second dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) +HPAI;HPAIHost Host vaccination information GENEPIO:0100316 vaccination_dose_2_vaccination_date vaccination_dose_2_vaccination_date date The date the second dose of a vaccine was administered. Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-09-01 +HPAI;HPAIHost Host vaccination information GENEPIO:0100321 vaccination history vaccination_history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 Last vaccinated +HPAI;HPAIHost Host treatment information +HPAI;HPAIHost Host treatment information GENEPIO:0101113 influenza_antiviral_treatment_administration influenza_antiviral_treatment_administration influenza_antiviral_treatment_administration menu null value menu An action of giving or applying an influenza antiviral agent to a patient as part of a treatment regimen. Influenza antiviral treatment administered [GENEPIO:0101194] +HPAI;HPAIHost Host treatment information GENEPIO:0101114 influenza_antiviral_agent influenza_antiviral_agent__ WhitespaceMinimizedString A substance that destroys or inhibits replication of viruses. +HPAI;HPAIHost Host treatment information GENEPIO:0101115 influenza_antiviral_treatment_date influenza_antiviral_treatment_date date The date on which the influenza antiviral agent was administered to a patient as part of treatment "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given. + +" +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100773 water_catchment_area_human_population_measurement_value water_catchment_area_human_population_measurement_value integer null value menu TRUE The numerical value of the human population measurement that contributes to the composition of water in a catchment area. Where known, provide the numerical value of population size, i.e. the number of people. 10,500 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100774 water_catchment_area_human_population_range water_catchment_area_human_population_range water catchment area human population range menu null value menu The human population range of the water catchment that contributes effluent to a wastewater site. Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist. 1,000 - 10,000 people +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100775 water_catchment_area_human_population_measurement_method water_catchment_area_human_population_measurement_method WhitespaceMinimizedString The method by which a water catchment 's human population size was measured or estimated Provide a brief description of how catchment population size was measured or estimated. population of jurisdiction encompassing the wastewater service area +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100776 water catchment area human population density value water_catchment_area_human_population_density_value WhitespaceMinimizedString The numerical value describing the number of humans per geographical area in a water catchment. Provide the numerical value of the population density in the catchement area. 4 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water_catchment_area_human_population_density_unit water catchment area human population density unit menu null value menu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type populated area type menu null value menu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling_weather_conditions sampling weather conditions menu null value menu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling_weather_conditions presampling weather conditions menu null value menu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString null value menu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100440 water_depth water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units water_depth_units menu null value menu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100697 sediment_depth sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units sediment_depth_units menu null value menu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100441 air_temperature air_temperature WhitespaceMinimizedString The temperature of some air. Provide the numerical value for the temperature of the air (without units). 25 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units air_temperature_units menu null value menu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units water_temperature_units menu null value menu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100442 weather_type weather_type weather_type menu null value menu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation_measurement_unit precipitation measurement unit menu null value menu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100913 precipitation measurement method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100935 ambient temperature measurement value ambient_temperature_measurement_value WhitespaceMinimizedString The numerical value of a measurement of the ambient temperature. Provide the numerical value of the measured temperature. 70 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100936 ambient temperature measurement unit ambient_temperature_measurement_unit ambient temperature measurement unit menu null value menu The units of a measurement of the ambient temperature. Provide the units of the measured temperature. degree Celsius (C) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0001736 pH measurement value ph_measurement_value WhitespaceMinimizedString The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution. Provide the numerical value of the measured pH. 7.4 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100781 pH measurement method ph_measurement_method WhitespaceMinimizedString The process used to measure pH value. Provide the name of the procedure or technology used to measure pH. pH test strip (litmus test) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100905 total daily flow rate measurement value total_daily_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured fluid flow rate over the course of a day. Provide the numerical value of the measured flow rate. 10 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100906 total daily flow rate measurement unit total_daily_flow_rate_measurement_unit total daily flow rate measurement unit menu null value menu The units of a measured fluid flow rate over the course of a day. Provide the units of the measured flow rate by selecting a value from the pick list. million gallons per day (MGD) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100907 total daily flow rate measurement method total_daily_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure total daily fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100908 instantaneous flow rate measurement value instantaneous_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured instantaneous fluid flow rate. Provide the numerical value of the measured flow rate. 25 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100909 instantaneous flow rate measurement unit instantaneous_flow_rate_measurement_unit instantaneous flow rate measurement unit menu null value menu The units of a measured instantaneous fluid flow rate. Provide the units of the measured flow rate by selecting a value from the pick list. cubic meter per hour (m^3/h) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100910 instantaneous flow rate measurement method instantaneous_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure instantaneous fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100783 turbidity measurement value turbidity_measurement_value WhitespaceMinimizedString TRUE The numerical value of a measurement of turbidity. Provide the numerical value of the measured turbidity. 0.02 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100914 turbidity measurement unit turbidity_measurement_unit turbidity measurement unit menu null value menu TRUE The units of a measurement of turbidity. Provide the units of the measured turbidity by selecting a value from the pick list. nephelometric turbidity unit (NTU) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101013 turbidity measurement method turbidity_measurement_method WhitespaceMinimizedString The process used to measure turbidity. Provide the name of the procedure or technology used to measure turbidity. Nephelometric method +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100915 dissolved oxygen measurement value dissolved_oxygen_measurement_value WhitespaceMinimizedString The numerical value of a measurement of dissolved oxygen. Provide the numerical value of the measured dissolved oxygen. 5 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100784 dissolved oxygen measurement unit dissolved_oxygen_measurement_unit dissolved oxygen measurement unit menu null value menu The units of a measurement of dissolved oxygen. Provide the units of the measured dissolved oxygen by selecting a value from the pick list. part per million (ppm) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100785 dissolved oxygen measurement method dissolved_oxygen_measurement_method WhitespaceMinimizedString The method used to measure dissolved oxygen. Provide the name of the procedure or technology used to measure dissolved oxygen. Dissolved oxygen meter in vertical direction +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100917 oxygen reduction potential (ORP) measurement value oxygen_reduction_potential_orp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of oxygen reduction potential (ORP). Provide the numerical value of the measured oxygen reduction potential. -50 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100786 oxygen reduction potential (ORP) measurement unit oxygen_reduction_potential_orp_measurement_unit oxygen reduction potential (ORP) measurement unit menu null value menu The units of a measurement of oxygen reduction potential (ORP). Provide the units of the measured oxygen reduction potential by selecting a value from the pick list. milliVolt (mV) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100787 oxygen reduction potential (ORP) measurement method oxygen_reduction_potential_orp_measurement_method WhitespaceMinimizedString The method used to measure oxygen reduction potential (ORP). Provide the name of the procedure or technology used to measure oxygen reduction potential. ORP sensor +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100788 chemical oxygen demand (COD) measurement value chemical_oxygen_demand_cod_measurement_value WhitespaceMinimizedString The measured value from a chemical oxygen demand (COD) test. Provide the numerical value of the COD test result. 26 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100789 chemical oxygen demand (COD) measurement unit chemical_oxygen_demand_cod_measurement_unit chemical oxygen demand (COD) measurement unit menu null value menu The units associated with a value from a chemical oxygen demand (COD) test. Provide the units of the COD test result. milligram per liter (mg/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100790 chemical oxygen demand (COD) measurement method chemical_oxygen_demand_cod_measurement_method WhitespaceMinimizedString The method used to measure chemical oxygen demand (COD). Provide the name of the procedure or technology used to measure COD. Hach LCK test kit +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100791 carbonaceous biochemical oxygen demand (CBOD) measurement value carbonaceous_biochemical_oxygen_demand_cbod_measurement_value WhitespaceMinimizedString The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the numerical value of the measured CBOD. 20 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100792 carbonaceous biochemical oxygen demand (CBOD) measurement unit carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit carbonaceous biochemical oxygen demand (CBOD) measurement unit menu null value menu The units of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the units of the measured CBOD by selecting a value from the pick list. milligram per liter (mg/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100793 carbonaceous biochemical oxygen demand (CBOD) measurement method carbonaceous_biochemical_oxygen_demand_cbod_measurement_method WhitespaceMinimizedString The method used to measure carbonaceous biochemical oxygen demand (CBOD). Provide the name of the procedure or technology used to measure CBOD. CBOD measurement by optical probe +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100794 total suspended solids (TSS) measurement value total_suspended_solids_tss_measurement_value WhitespaceMinimizedString The numerical value from a total suspended solids (TSS) test. Provide the numerical value of the measured TSS. 8 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100795 total suspended solids (TSS) measurement unit total_suspended_solids_tss_measurement_unit total suspended solids (TSS) measurement unit menu null value menu The units associated with a value from a total suspended solids (TSS) test. Provide the units of the measured TSS. percent (%) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100796 total suspended solids (TSS) measurement method total_suspended_solids_tss_measurement_method WhitespaceMinimizedString The method used to measure total suspended solids (TSS). Provide the name of the procedure or technology used to measure TSS. Vacuum filter through a 2-micron filter, then oven-dried and weighed sample +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100797 total dissolved solids (TDS) measurement value total_dissolved_solids_tds_measurement_value WhitespaceMinimizedString The numerical value from a total dissolved solids (TDS) test. Provide the numerical value of the measured TDS. 2 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100798 total dissolved solids (TDS) measurement unit total_dissolved_solids_tds_measurement_unit total dissolved solids (TDS) measurement unit menu null value menu The units associated with a value from a total dissolved solids (TDS) test. Provide the units of the measured TDS. percent (%) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100799 total dissolved solids (TDS) measurement method total_dissolved_solids_tds_measurement_method WhitespaceMinimizedString The method used to measure total dissolved solids (TDS). Provide the name of the procedure or technology used to measure TDS. Subtract calculated TSS from calculated TS +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100800 total solids (TS) measurement value total_solids_ts_measurement_value WhitespaceMinimizedString The numerical value from a total solids (TS) test. Provide the numerical value of the measured TS. 10 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100801 total solids (TS) measurement unit total_solids_ts_measurement_unit total solids (TS) measurement unit menu null value menu The units associated with a value from a total solids (TS) test. Provide the units of the measured TS. percent (%) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100802 total solids (TS) measurement method total_solids_ts_measurement_method WhitespaceMinimizedString The method used to measure total solids (TS). Provide the name of the procedure or technology used to measure TS. Gravimetric method by oven drying, then weighing +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100878 alkalinity measurement value alkalinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of alkalinity. Provide the numerical value of the measured alkalinity. 3 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100879 alkalinity measurement unit alkalinity_measurement_unit alkalinity measurement unit menu null value menu The units of a measurement of alkalinity. Provide the units of the measured alkalinity. milligram per liter of calcium carbonate (mg/L CaCO3) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100880 alkalinity measurement method alkalinity_measurement_method WhitespaceMinimizedString The process used to measure alkalinity. Provide the name of the procedure or technology used to measure alkalinity. Titration method +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100916 conductivity measurement value conductivity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of conductivity. Provide the numerical value of the measured conductivity. 1412 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100803 conductivity measurement unit conductivity_measurement_unit conductivity measurement unit menu null value menu The units of a measurement of conductivity. Provide the units of the measured conductivity. microSiemen per centimeter (μS/cm) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100804 conductivity measurement method conductivity_measurement_method WhitespaceMinimizedString The method used to measure conductivity. Provide the name of the procedure or technology used to measure conductivity. Conductivity electrode and meter +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100805 salinity measurement value salinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of salinity. Provide the numerical value of the measured salinity. 35 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100806 salinity measurement unit salinity_measurement_unit salinity measurement unit menu null value menu The units of a measurement of salinity. Provide the units of the measured salinity. practical salinity unit (PSU) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100807 salinity measurement method salinity_measurement_method WhitespaceMinimizedString The method used to measure salinity. Provide the name of the procedure or technology used to measure salinity. conductivity meter +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100808 total nitrogen (TN) measurement value total_nitrogen_tn_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total nitrogen (TN). Provide the numerical value of the measured TN. 120 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total_nitrogen_tn_measurement_unit total nitrogen (TN) measurement unit menu null value menu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100810 total nitrogen (TN) measurement method total_nitrogen_tn_measurement_method WhitespaceMinimizedString The method used to measure total nitrogen (TN). Provide the name of the procedure or technology used to measure TN. Hach total nitrogen spectrophotometric test +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100811 total phosphorus (TP) measurement value total_phosphorus_tp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total phosphorus (TP). Provide the numerical value of the measured TP. 2 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit total phosphorus (TP) measurement unit menu null value menu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100813 total phosphorus (TP) measurement method total_phosphorus_tp_measurement_method WhitespaceMinimizedString The method used to measure total phosphorus (TP). Provide the name of the procedure or technology used to measure TP. Merck phosphate spectrophotometric test kit +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal_contamination_indicator_ fecal contamination indicator menu null value menu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100815 fecal contamination value fecal_contamination_value WhitespaceMinimizedString TRUE The numerical value of a measurement of fecal contamination. Provide the numerical value of the measured fecal contamination. 10 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100816 fecal contamination unit fecal_contamination_unit fecal contamination unit menu null value menu TRUE The units of a measurement of fecal contamination. Provide the units of the measured fecal contamination. cycle threshold (Ct) / quantification cycle (Cq) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100817 fecal contamination method fecal_contamination_method WhitespaceMinimizedString The method used to measure fecal contamination. Provide the name of the procedure or technology used to measure fecal contamination. quantitative PCR assay +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100818 fecal coliform count value fecal_coliform_count_value WhitespaceMinimizedString The numerical value of a measurement of fecal coliforms within a sample. Provide the numerical value of the measured fecal coliforms. 3 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100819 fecal coliform count unit fecal_coliform_count_unit fecal coliform count unit menu null value menu The units of a measurement of fecal coliforms. Provide the units of the measured fecal coliforms. most probable number per milliliter (MPN/mL) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100820 fecal coliform count method fecal_coliform_count_method WhitespaceMinimizedString The method used to measure fecal coliforms. Provide the name of the procedure or technology used to measure fecal coliforms. MPN method via serial dilutions until lack of growth +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100837 urinary contamination indicator urinary_contamination_indicator urinary contamination indicator menu null value menu A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination. If a urinary contamination indicator was measured, select it from the picklist. urobilin +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100838 urinary contamination value urinary_contamination_value WhitespaceMinimizedString The numerical value of a measurement of urinary contamination. Provide the numerical value of the measured urinary contamination. 3 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100839 urinary contamination unit urinary_contamination_unit urinary contamination unit menu null value menu The units of a measurement of urinary contamination. Provide the units of the measured urinary contamination. nanograms per liter +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100840 urinary contamination method urinary_contamination_method WhitespaceMinimizedString The method used to measure urinary contamination. Provide the name of the procedure or technology used to measure urinary contamination. Urobilin Concentration Test +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100821 sample temperature value (at collection) sample_temperature_value_at_collection WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample at collection. Provide the numerical value of the measured temperature. 20 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100822 sample temperature unit (at collection) sample_temperature_unit_at_collection sample temperature unit (at collection) menu null value menu The units of a measurement of temperature of a sample at the time of collection. Provide the units of the measured temperature. degree Celsius (C) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100823 sample temperature value (when received) sample_temperature_value_when_received WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample upon receipt. Provide the numerical value of the measured temperature. 22 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100824 sample temperature unit (when received) sample_temperature_unit_when_received sample temperature unit (when received) menu null value menu The units of a measurement of temperature of a sample at the time upon receipt. Provide the units of the measured temperature. degree Celsius (C) +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001441 Sequence information +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type sequencing_assay_type menu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001447 sequencing_date sequencing_date date {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing__ purpose_of_sequencing menu null value menu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001446 purpose_of_sequencing_details purpose_of_sequencing_details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100416 sequenced_by sequenced_by WhitespaceMinimizedString null value menu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100470 sequenced_by_laboratory_name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100471 sequenced_by_contact_name sequenced_by_contact_name WhitespaceMinimizedString null value menu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString null value menu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by WhitespaceMinimizedString null value menu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001165 sequence_submitter_contact_email sequence_submitter_contact_email WhitespaceMinimizedString null value menu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100939 nucleic_acid_extraction_method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100772 nucleic_acid_extraction_kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100472 sequencing_project_name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform sequencing_platform menu null value menu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument sequencing_instrument menu null value menu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001450 library_preparation_kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100843 DNA_fragment_length dna_fragment_length Integer The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100966 genomic_target_enrichment_method genomic_target_enrichment_method genomic_target_enrichment_method menu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100967 genomic_target_enrichment_method_details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information). enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001456 amplicon_pcr_primer_scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001449 amplicon_size amplicon_size Integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0101102 sequencing_flow_cell_version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001454 sequencing_protocol sequencing_protocol WhitespaceMinimizedString The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001476 r1_fastq_filename r1_fastq_filename WhitespaceMinimizedString The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001477 r2_fastq_filename r2_fastq_filename WhitespaceMinimizedString The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001480 fast5_filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. batch1a_sequences.fast5 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString The name of the sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001461 assembly_filename assembly_filename WhitespaceMinimizedString The user-defined filename of the FASTA file. Provide the FASTA filename. pathogenassembly123.fasta +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001457 Bioinformatics and QC metrics +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination quality_control_determination menu null value menu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues quality_control_issues menu null value menu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString null value menu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString null value menu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString null value menu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString null value menu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString null value menu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString null value menu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination_ integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0101082 Taxonomic identification information +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001506 Pathogen diagnostic testing +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101116 genetic target name genetic_target_name WhitespaceMinimizedString null value menu The name of the genetic marker used for testing. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101117 genetic target region genetic_target_region WhitespaceMinimizedString The specific region or segment of a genetic sequence used for testing or analysis. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101118 genetic target region reference genome genetic_target_region_reference_genome WhitespaceMinimizedString The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100962 diagnostic target presence diagnostic_target_presence diagnostic target presence menu null value menu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100963 diagnostic measurement value diagnostic_measurement_value WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100964 diagnostic measurement unit diagnostic_measurement_unit diagnostic measurement unit menu null value menu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100965 diagnostic measurement method diagnostic_measurement_method diagnostic measurement method menu null value menu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101104 diagnostic testing threshold value diagnostic_testing_threshold_value integer The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101105 diagnostic testing threshold units diagnostic_testing_threshold_units WhitespaceMinimizedString The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101106 diagnostic testing details diagnostic_testing_details WhitespaceMinimizedString Describe any details of the diagnsotic testing. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0100478 Risk assessment information +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100480 prevalence_metrics prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100481 prevalence_metrics_details prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production stage_of_production menu null value menu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention experimental_intervention menu null value menu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100484 experiment_intervention_details experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed + \ No newline at end of file diff --git a/web/templates/menu.json b/web/templates/menu.json index 5117e66f..735a7e07 100644 --- a/web/templates/menu.json +++ b/web/templates/menu.json @@ -83,5 +83,32 @@ "status": "published", "display": true } + }, + "hpai": { + "HPAI": { + "name": "HPAI", + "status": "published", + "display": true + }, + "HPAIFood": { + "name": "HPAIFood", + "status": "published", + "display": true + }, + "HPAIWW": { + "name": "HPAIWW", + "status": "published", + "display": true + }, + "HPAIEnviro": { + "name": "HPAIEnviro", + "status": "published", + "display": true + }, + "HPAIHost": { + "name": "HPAIHost", + "status": "published", + "display": true + } } } \ No newline at end of file