continued template refinement, issue #79

ark.all_attributes.csv

@@ -16,11 +16,11 @@
 "platform","The specific version (manufacturer, model, etc.) of a technology that is used to carry out a laboratory or computational experiment. Specify where applicable for experimental data files, else enter 'none'. In most cases only a single label is expected, however multiple selections can be provided in comma-delimited list where applicable e.g., for 10x Genomics fastq files please specify both the 10x instrument and the sequencing platform.","BD FACSAria Fusion cell sorter, BD FACSAria III, BD FACSCanto, BD FACSCanto II, BD FACSDiscover A8, BD FACSDiscover S8, BD FACSLyric Clinical, BD FACSMelody, BD FACSymphony S6, BD LSRFortessa, Chromium Controller, Chromium GEM-X Single Cell 3' Chip v4, Chromium Next GEM Chip G, Chromium Next GEM Chip H, Chromium Next GEM Chip K, Chromium Next GEM Chip M, Chromium Next GEM Chip Q, Chromium X, Chromium Xo, Chromium iX, CyTOF XT, Cytek Aurora, Cytek Aurora Evo, Fluidigm BioMark, GEM-X Flex Gene Expression Chip, GEM-X OCM 5' Chip, Helios Mass Cytometer, Hyperion, Illumina HiSeq 2500, Illumina HiSeq X Ten, Illumina NextSeq 500, Illumina NovaSeq 6000, Illumina NovaSeq X, Not Applicable, Olink Signature Q100, Sony MA900, Thermo Fisher Attune CytPix, Thermo Fisher Attune NxT, Thermo Fisher Attune Xenith, Visium CytAssist, Xenium, none, unknown","","","True","","","","list like error","string"
 "specimenModality","Label assigned to experimental data files indicating whether the data contained corresponds to a single or multiple biospecimens","multispecimen, single specimen","","","True","","","","","string"
 "individualID","Unique identifier assigned to each study participant. For multi-specimen data files provide all IDs in a comma-separated list.","","","","True","","","","#ClinicalMetadataTemplate unique error^^#BiospecimenMetadataTemplate str^^list like error","string"
-"biospecimenID","A unique identifier assigned to specimens collected from study participants. For multi-specimen data files provide all IDs in a comma-separated list.","","","","True","","","","#BiospecimenMetadataTemplate unique error^^#OlinkBiospecimenMetadataTemplate unique error^^list like error","string"
+"biospecimenID","A unique identifier assigned to specimens collected from study participants. For multi-specimen data files provide all IDs in a comma-separated list.","","","","True","","","","#BiospecimenMetadataTemplate unique error^^list like error","string"
 "parentBiospecimenID","The biospecimenID associated with the originating biospecimen for derived or child biospecimens.","","","","False","","","","","string"
 "biospecimenType","A label indicating the biological material collected for experimentation and data collection. Where applicable, provide all types in a comma-separated list.","PBMCs, cell line, fibroblast-like synoviocyte, kidney biopsy, none, plasma, primary cell culture, saliva, salivary gland, serum, skin biopsy, skin swab, stool, suction blister cells, suction blister fluid, synovial fluid, synovial tissue, total leukocytes, urine, uvea, whole blood","","","True","","","","#BiospecimenMetadataTemplate str^^#InVitroBiospecimenMetadataTemplate^^list like error","string"
 "primaryCellSource","A label indicating the biological source material from which a primary cell culture was derived.","PBMCs, kidney, pannus-derived dermis, pannus-derived epidermis, salivary gland, synovial tissue, total leukocytes, urine, uvea, whole blood","","","True","","","","","string"
-"metadataType","A label further classifying the content of metadata resource.","assay, biospecimen, cell coordinates, data dictionary, file manifest, medication, other, phenotype, protocol, single-cell metadata, target panel, template, tissue multiarray map, user manual","","","True","","","","","string"
+"metadataType","A label further classifying the content of metadata resource.","assay, biospecimen, cell coordinates, data dictionary, file manifest, medication, other, phenotype, protocol, single-cell metadata, target panel, template, tissue microarray map, tissue multiarray map, user manual","","","True","","","","","string"
 "codingLanguage","The coding, aka programming, language(s) contained in the file marked with `resourceType = code`. Select all that apply.","C, C#, C++, Fortan, Java, Julia, Matlab, Python, R, Ruby, SAS","","","True","","","","","string"
 "visitID","Ordinal ID distinguishing different patient visits.","","","","True","","","","","string"
 "softwareAndVersion","Relevant software and version used to generate the data file.","BD FACSDiva 8.0.1, Cell Ranger 9.0.1, Cell Ranger ATAC v1.1.0, Cell Ranger v3.0.0, Cell Ranger v3.0.1, Cell Ranger v3.0.2, Cell Ranger v3.1.0, Cell Ranger v4.0.0, Cell Ranger v5.0.0, Cell Ranger v5.0.1, Cell Ranger v6.0.0, Cell Ranger v6.0.1, Cell Ranger v6.0.2, Cell Ranger v6.1.0, Cell Ranger v6.1.1, Cell Ranger v6.1.2, Cell Ranger v7.0.0, Cell Ranger v7.0.1, Cell Ranger v7.1.0, Cell Ranger v7.2.0, Cell Ranger v8.0.0, Cell Ranger v8.0.1, Cell Ranger v9.0.0, Space Ranger 3.0.0, Space Ranger 3.0.1, Space Ranger 3.1.0, Space Ranger 3.1.1, Space Ranger 3.1.2, Space Ranger 3.1.3, demuxlet","","","False","","","","","string"
@@ -59,14 +59,14 @@
 "vitiligoPhenotype","Classification of vitiligo lesions which correlate with autoimmune activity and result in specific skin and depigmentation manifestations at the lesion site. If N/A please select 'none'. Multiple selections can be provided in a comma-delimited list.","active, confetti, inflammatory, none, trichrome","","","True","","","","list like error","string"
 "psoriasisType","General type classification of psoriasis disease manifestation.","erythrodermic, guttate, inverse, plaque, pustular","","","False","","","","","string"
 "ageDiagnosis","Age at which subject was diagnosed with `diagnosis`. If providing this value be sure the unit matches that used for `age`.","","","","False","","","","num error","number"
-"age","Age at which subject was enrolled in study or age at corresponding visit and data collection event.","","","","True","","","","num error","number"
+"age","Age at which subject was enrolled in study or age at corresponding visit and data collection event. If value unknown, enter '-1'.","","","","True","","","","num error","number"
 "ageUnits","The unit of measure used for `ageEnrollment` and `ageDiagnosis`","months, years","","","True","","","","","string"
 "sex","A textual description of a person's sex at birth.","female, intersex, male, unknown","","","True","","","","","string"
 "height","Standing height of subject.","","","","True","","","","num error","number"
 "race","A textual description of a person's race.","American Indian or Alaska Native, Asian, Black or African American, Hispanic, Mixed Race, Native Hawaiian or Other Pacific Islander, White, other, unknown","","","False","","","","","string"
 "ethnicity","The ethnicity of a person.","Hispanic or Latino, Not Hispanic or Latino, unknown","","","False","","","","","string"
 "heightUnits","Unit of measure of value provided for `height`.","centimeters, feet, inches, meters","","","True","","","","","string"
-"weight","Weight of subject.","","","","True","","","","num error","number"
+"weight","Weight of subject. If value unknown, enter '-1'.","","","","True","","","","num error","number"
 "weightUnits","Abbreviated unit of measure of value provided for `weight`.","g, kg, lb, oz","","","True","","","","","string"
 "comorbidities","Any diseases or medical condition that is simultaneously present in addition to `diagnosis`.","Hashimoto's Thyroiditis, autoimmune thyroid disease, cardiovascular disease, diabetes, inflammatory bowel disease, multiple sclerosis, other, psoriasis, psoriatic arthritis, pulmonary disease, rheumatoid arthritis, systemic lupus erythematosus","","","False","","","","list like error","string"
 "diabetesType","Type of diabetes mellitus.","gestational, type 1, type 2, unknown","","","False","","","","","string"
@@ -84,9 +84,9 @@
 "cellOntologyID","Cell Ontology CL identifier that best describes a biopsecimen used to generate data, e.g., CL:0000084 for T cell.","","","","False","","","","regex search ^CL: error","string"
 "cellType","The cell type name from Cell Ontology for the corresponding CL identifier.","","","","False","","","","","string"
 "userDefinedCellType","User-defined label of a cell type. Contributors are provided this option to use preferred or custom cell type labels that may vary from options and standards set by Cell Ontology.","","","","False","","","","","string"
-"krennInflammatory","A standardized, semi-quantitative measure of the degree of inflammatory infiltrate in synovial specimen. This is one of three measures used to derive the Krenn Synovitis Score (KSS) which is a histological scoring system used to quantify inflammation in synovial tissue biopsies, particularly in the context of inflammatory arthritis like rheumatoid arthritis. If value unknown, use '-1'.","","","","False","","","https://doi.org/10.1111/j.1365-2559.2006.02508.x","num error","number"
+"krennInflammatory","A standardized, semi-quantitative measure of the degree of inflammatory infiltrate in synovial specimen. This is one of three measures used to derive the Krenn Synovitis Score (KSS) which is a histological scoring system used to quantify inflammation in synovial tissue biopsies, particularly in the context of inflammatory arthritis like rheumatoid arthritis. If value unknown, enter '-1'.","","","","False","","","https://doi.org/10.1111/j.1365-2559.2006.02508.x","num error","number"
 "krennLining","A standardized, semi-quantitative measure of the degree of hyperplasia/enlargement of the synovial lining layer of synovial specimen. This is one of three measures used to derive the Krenn Synovitis Score (KSS) which is a histological scoring system used to quantify inflammation in synovial tissue biopsies, particularly in the context of inflammatory arthritis like rheumatoid arthritis. If value unknown, use '-1'.","","","","False","","","https://doi.org/10.1111/j.1365-2559.2006.02508.x","num error","number"
-"krennStroma","A standardized, semi-quantitative measure of stromal cell density of synovial specimen. This is one of three measures used to derive the Krenn Synovitis Score (KSS) which is a histological scoring system used to quantify inflammation in synovial tissue biopsies, particularly in the context of inflammatory arthritis like rheumatoid arthritis. If value unknown, use '-1'.","","","","False","","","https://doi.org/10.1111/j.1365-2559.2006.02508.x","num error","number"
+"krennStroma","A standardized, semi-quantitative measure of stromal cell density of synovial specimen. This is one of three measures used to derive the Krenn Synovitis Score (KSS) which is a histological scoring system used to quantify inflammation in synovial tissue biopsies, particularly in the context of inflammatory arthritis like rheumatoid arthritis. If value unknown, enter '-1'.","","","","False","","","https://doi.org/10.1111/j.1365-2559.2006.02508.x","num error","number"
 "krennSynovitisScore","The Krenn Synovitis Score (KSS) is a histological scoring system used to quantify inflammation in synovial tissue biopsies, particularly in the context of inflammatory arthritis like rheumatoid arthritis. If value unknown, use '-1'.","","","","False","","","https://doi.org/10.1111/j.1365-2559.2006.02508.x","num error","number"
 "datasetStatus","A categorical label indicating the status of an ARK Portal dataset. This is applied to improve downstream management of datasets as well as various ETL workflows.","deprecated, released, test, under peer review, unreleased","","","True","","","","","string"
 "sampleProcessingBatch","A label indicating batching of sample processing or preparation that occurs prior to data collection.","","","","False","","","","","string"
@@ -105,5 +105,5 @@
 "species","The genus species of sample or subject origin.","Homo sapiens","","","True","","","","","string"
 "treatment","A short descriptive label indicating what experimental treatments have been applied to a biospecimen before data capture. Please include the word 'control' to indicate specific treatments that are intended to serve as a control group.","","","","True","","","","","string"
 "treatmentTimepoint","Where applicable, specify the timepoint relative to treatment to distinguish different sets of samples that have undergone the same treatment but for different lengths of time. REQUIRED: please specify the unit of time, e.g., secs, mins, hrs, days, etc.","","","","False","","","","","string"
-"slideID","A library label or name, unique within an experiment, used to distinguish imaging slides.","","","","True","","","","","string"
+"slideID","A distinct label or name, unique within an experiment, assigned to an imaging slides.","","","","True","","","","","string"
 "altSampleID","An alternate identifier for a sample. With some assays there can be default or alternate sample identifiers entered into the data collection software. If you will be uploading data collected with an alternate identifier please provide that here. In some cases, the ARK BDM team will use this field to capture original but out-dated identifiers for samples.","","","","False","","","","","string"

model_contexts/biospecimen/ark.biospecimen_context.csv

@@ -1,6 +1,6 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType
-Biospecimen Metadata Template,A general template outlining metadata to be collected for biospecimen profiled in a dataset.,,"Component, program, project, individualID, biospecimenID, parentBiospecimenID, altSampleID, biospecimenType, biospecimenSubtype, plateID, notes",,,,,,,
-In Vitro Biospecimen Metadata Template,A template outlining metadata to be collected for biospecimen used for an in vitro experiment.,,"Component, program, project, individualID, biospecimenID, parentBiospecimenID, altSampleID, biospecimenType, biospecimenSubtype, plateID, treatment, treatmentTimepoint, notes",,,,,,,
+Biospecimen Metadata Template,A general template outlining metadata to be collected for biospecimen profiled in a dataset.,,"Component, program, project, individualID, biospecimenID, parentBiospecimenID, altSampleID, biospecimenType, biospecimenSubtype, notes",,,,,,,
+In Vitro Biospecimen Metadata Template,A template outlining metadata to be collected for biospecimen used for an in vitro experiment.,,"Component, program, project, individualID, biospecimenID, parentBiospecimenID, altSampleID, biospecimenType, biospecimenSubtype, treatment, treatmentTimepoint, notes",,,,,,,
 skin swab,Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.,,"skinSiteStatus, anatomicalSite",,,,,,,
 skin biopsy,Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.,,"skinSiteStatus, anatomicalSite",,,,,,,
 suction blister cells,Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.,,"skinSiteStatus, anatomicalSite",,,,,,,
@@ -12,7 +12,6 @@ flow-sorted cells,A valid value of 'biospecimenSubtype' that triggers conditiona
 cell suspension,A valid value of 'biospecimenSubtype' that triggers conditional dependencies for additional attributes.,,"cellOntologyID, cellType, userDefinedCellType",,,,,,,
 AMP RA/SLE,Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus. Is a valid value for 'program' that triggers conditional dependencies for additional attributes.,,visitID,,,,,,,
 AMP AIM,Accelerating Medicines Partnership Autoimmune and Immune-Mediated Diseases. Is a valid value for 'program' that triggers conditional dependencies for additional attributes.,,visitID,,,,,,,
-plateID,"An identifier corresponding to a multi-well plate. Certain data types and assays (e.g., Olink) profile samples using multi-well plates. Knowing which samples were profiled on each plate is important for establishing sample provenance, finding the right data files for a specific set of samples, as well as downstream exploratory data analysis and QC work particularly regarding identification and correction of batch effects. This attribute is required. Please enter 'Not Applicable' if your biospecimen were not profiled in plated batches.",,,,TRUE,,,,,string
 primary cell culture,Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.,,"cellType, cellOntologyID, primaryCellSource",,,,,,,
 cell line,Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.,,"cellType, cellOntologyID",,,,,,,
 individualID,,,,,FALSE,,,,#BiospecimenMetadataTemplate required^^,string