diff --git a/ark.all_attributes.csv b/ark.all_attributes.csv index edf8df4..07bd61f 100644 --- a/ark.all_attributes.csv +++ b/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" diff --git a/model_contexts/biospecimen/ark.biospecimen_context.csv b/model_contexts/biospecimen/ark.biospecimen_context.csv index e43d207..918c8ca 100644 --- a/model_contexts/biospecimen/ark.biospecimen_context.csv +++ b/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 \ No newline at end of file diff --git a/model_contexts/biospecimen/ark.biospecimen_model.csv b/model_contexts/biospecimen/ark.biospecimen_model.csv index c60f1dd..3bd6ae0 100644 --- a/model_contexts/biospecimen/ark.biospecimen_model.csv +++ b/model_contexts/biospecimen/ark.biospecimen_model.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 @@ "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","Unique identifier assigned to each study participant. For multi-specimen data files provide all IDs in a comma-separated list.","","","","FALSE","","","","#BiospecimenMetadataTemplate required^^","string" @@ -32,11 +31,11 @@ "custom10xProbeSetSynID","If custom modified probe sets were used for collecting 10x Chromium Flex scRNA-seq data, then the probe reference files should be grouped as a zip or tar archive and uploaded as metadata. This attribute links the experimental data back to the probe set archive file via a synapse ID.","","","","True","","","","regex search ^syn[0-9]{8} error","string" "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" -"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" @@ -75,14 +74,14 @@ "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" @@ -100,9 +99,9 @@ "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" @@ -112,6 +111,7 @@ "sequencingSpikeIn","Pre-made sequencing libraries may be added to your sequencing run to improve sequencing results. If such a 'spike-in' library was used, this attribute specifies the name of the library and the percentage of the spike-in library used in the sequencing run.","","","","False","","","","","string" "librarySpikeIn","Pre-made collections of nucleic acid fragments can be added to samples during the library construction process to improve downstream quantification and statistical analyses. If such a 'spike-in' was used, this attribute specifies the name and manufacturer of the spike-in.","","","","False","","","","","string" "readLength","The number of base pairs (bp) sequenced for reads in a fastq file.","","","","False","","","","int error","integer" +"plateID","An identifier assigned to a multi-well plate. Certain data types and assays 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.","","","","False","","","","","string" "PMCID","Pubmed Central Identifier, formatted as a compact URI string that will automatically resolve into a URL based on the Synapse bioregistry; e.g., pmc:PMCxxxxxxxx","","","","False","","","","regex search ^pmc:PMC[0-9]{8} error","string" "processedDataType","A label used for file annotations to provide a brief description of the processed data file.","barcode counts, differential expression results, epigenomic peaks, gene counts","","","False","","","","list like error","string" "eventCount","The total number of events detected and captured in the corresponding FCS file. In cytometry, an event corresponds to particles detected and measured by the instrument. This number corresponds to the number of rows in the FCS file and is expected to be a whole integer number.","","","","False","","","","int error","integer" @@ -119,5 +119,5 @@ "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" diff --git a/model_contexts/biospecimen/ark.biospecimen_model.jsonld b/model_contexts/biospecimen/ark.biospecimen_model.jsonld index 246e131..8717f4c 100644 --- a/model_contexts/biospecimen/ark.biospecimen_model.jsonld +++ b/model_contexts/biospecimen/ark.biospecimen_model.jsonld @@ -50,9 +50,6 @@ { "@id": "bts:BiospecimenSubtype" }, - { - "@id": "bts:PlateID" - }, { "@id": "bts:Notes" } @@ -182,7 +179,6 @@ "sms:required": "sms:true", "sms:validationRules": { "BiospecimenMetadataTemplate": "unique error", - "OlinkBiospecimenMetadataTemplate": "unique error", "all_other_components": "list like error" } }, @@ -352,23 +348,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:PlateID", - "@type": "rdfs:Class", - "rdfs:comment": "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.", - "rdfs:label": "PlateID", - "rdfs:subClassOf": [ - { - "@id": "bts:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "plateID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, { "@id": "bts:Notes", "@type": "rdfs:Class", @@ -429,9 +408,6 @@ { "@id": "bts:BiospecimenSubtype" }, - { - "@id": "bts:PlateID" - }, { "@id": "bts:Treatment" }, @@ -794,7 +770,7 @@ { "@id": "bts:KrennInflammatory", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennInflammatory", "rdfs:subClassOf": [ { @@ -832,7 +808,7 @@ { "@id": "bts:KrennStroma", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennStroma", "rdfs:subClassOf": [ { @@ -4775,6 +4751,9 @@ { "@id": "bts:Template" }, + { + "@id": "bts:Tissuemicroarraymap" + }, { "@id": "bts:Tissuemultiarraymap" }, @@ -4979,6 +4958,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Tissuemicroarraymap", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Tissuemicroarraymap", + "rdfs:subClassOf": [ + { + "@id": "bts:MetadataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "tissue microarray map", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Tissuemultiarraymap", "@type": "rdfs:Class", @@ -9210,7 +9206,7 @@ { "@id": "bts:Age", "@type": "rdfs:Class", - "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event.", + "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event. If value unknown, enter '-1'.", "rdfs:label": "Age", "rdfs:subClassOf": [ { @@ -9715,7 +9711,7 @@ { "@id": "bts:Weight", "@type": "rdfs:Class", - "rdfs:comment": "Weight of subject.", + "rdfs:comment": "Weight of subject. If value unknown, enter '-1'.", "rdfs:label": "Weight", "rdfs:subClassOf": [ { @@ -10628,6 +10624,23 @@ "int error" ] }, + { + "@id": "bts:PlateID", + "@type": "rdfs:Class", + "rdfs:comment": "An identifier assigned to a multi-well plate. Certain data types and assays 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.", + "rdfs:label": "PlateID", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "plateID", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:PMCID", "@type": "rdfs:Class", @@ -10809,7 +10822,7 @@ { "@id": "bts:SlideID", "@type": "rdfs:Class", - "rdfs:comment": "A library label or name, unique within an experiment, used to distinguish imaging slides.", + "rdfs:comment": "A distinct label or name, unique within an experiment, assigned to an imaging slides.", "rdfs:label": "SlideID", "rdfs:subClassOf": [ { diff --git a/model_contexts/clinical/ark.clinical_model.csv b/model_contexts/clinical/ark.clinical_model.csv index ed93235..d6498c3 100644 --- a/model_contexts/clinical/ark.clinical_model.csv +++ b/model_contexts/clinical/ark.clinical_model.csv @@ -23,11 +23,11 @@ "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" @@ -66,14 +66,14 @@ "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" @@ -91,9 +91,9 @@ "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" @@ -111,5 +111,5 @@ "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" diff --git a/model_contexts/clinical/ark.clinical_model.jsonld b/model_contexts/clinical/ark.clinical_model.jsonld index fa8edbb..88b517c 100644 --- a/model_contexts/clinical/ark.clinical_model.jsonld +++ b/model_contexts/clinical/ark.clinical_model.jsonld @@ -270,7 +270,7 @@ { "@id": "bts:Age", "@type": "rdfs:Class", - "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event.", + "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event. If value unknown, enter '-1'.", "rdfs:label": "Age", "rdfs:subClassOf": [ { @@ -469,7 +469,7 @@ { "@id": "bts:Weight", "@type": "rdfs:Class", - "rdfs:comment": "Weight of subject.", + "rdfs:comment": "Weight of subject. If value unknown, enter '-1'.", "rdfs:label": "Weight", "rdfs:subClassOf": [ { @@ -4185,7 +4185,6 @@ "sms:required": "sms:true", "sms:validationRules": { "BiospecimenMetadataTemplate": "unique error", - "OlinkBiospecimenMetadataTemplate": "unique error", "all_other_components": "list like error" } }, @@ -4803,6 +4802,9 @@ { "@id": "bts:Template" }, + { + "@id": "bts:Tissuemicroarraymap" + }, { "@id": "bts:Tissuemultiarraymap" }, @@ -5007,6 +5009,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Tissuemicroarraymap", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Tissuemicroarraymap", + "rdfs:subClassOf": [ + { + "@id": "bts:MetadataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "tissue microarray map", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Tissuemultiarraymap", "@type": "rdfs:Class", @@ -10047,7 +10066,7 @@ { "@id": "bts:KrennInflammatory", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennInflammatory", "rdfs:subClassOf": [ { @@ -10085,7 +10104,7 @@ { "@id": "bts:KrennStroma", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennStroma", "rdfs:subClassOf": [ { @@ -10671,7 +10690,7 @@ { "@id": "bts:SlideID", "@type": "rdfs:Class", - "rdfs:comment": "A library label or name, unique within an experiment, used to distinguish imaging slides.", + "rdfs:comment": "A distinct label or name, unique within an experiment, assigned to an imaging slides.", "rdfs:label": "SlideID", "rdfs:subClassOf": [ { diff --git a/model_contexts/fastq/ark.fastq_model.csv b/model_contexts/fastq/ark.fastq_model.csv index b60447f..acf53d7 100644 --- a/model_contexts/fastq/ark.fastq_model.csv +++ b/model_contexts/fastq/ark.fastq_model.csv @@ -23,11 +23,11 @@ "custom10xProbeSetSynID","If custom modified probe sets were used for collecting 10x Chromium Flex scRNA-seq data, then the probe reference files should be grouped as a zip or tar archive and uploaded as metadata. This attribute links the experimental data back to the probe set archive file via a synapse ID.","","","","True","","","","regex search ^syn[0-9]{8} 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" @@ -66,14 +66,14 @@ "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" @@ -91,9 +91,9 @@ "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" @@ -111,5 +111,5 @@ "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" diff --git a/model_contexts/fastq/ark.fastq_model.jsonld b/model_contexts/fastq/ark.fastq_model.jsonld index f656fea..87c2230 100644 --- a/model_contexts/fastq/ark.fastq_model.jsonld +++ b/model_contexts/fastq/ark.fastq_model.jsonld @@ -998,7 +998,6 @@ "sms:required": "sms:true", "sms:validationRules": { "BiospecimenMetadataTemplate": "unique error", - "OlinkBiospecimenMetadataTemplate": "unique error", "all_other_components": "list like error" } }, @@ -2943,6 +2942,9 @@ { "@id": "bts:Template" }, + { + "@id": "bts:Tissuemicroarraymap" + }, { "@id": "bts:Tissuemultiarraymap" }, @@ -3147,6 +3149,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Tissuemicroarraymap", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Tissuemicroarraymap", + "rdfs:subClassOf": [ + { + "@id": "bts:MetadataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "tissue microarray map", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Tissuemultiarraymap", "@type": "rdfs:Class", @@ -7276,7 +7295,7 @@ { "@id": "bts:Age", "@type": "rdfs:Class", - "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event.", + "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event. If value unknown, enter '-1'.", "rdfs:label": "Age", "rdfs:subClassOf": [ { @@ -7781,7 +7800,7 @@ { "@id": "bts:Weight", "@type": "rdfs:Class", - "rdfs:comment": "Weight of subject.", + "rdfs:comment": "Weight of subject. If value unknown, enter '-1'.", "rdfs:label": "Weight", "rdfs:subClassOf": [ { @@ -8443,7 +8462,7 @@ { "@id": "bts:KrennInflammatory", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennInflammatory", "rdfs:subClassOf": [ { @@ -8481,7 +8500,7 @@ { "@id": "bts:KrennStroma", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennStroma", "rdfs:subClassOf": [ { @@ -9048,7 +9067,7 @@ { "@id": "bts:SlideID", "@type": "rdfs:Class", - "rdfs:comment": "A library label or name, unique within an experiment, used to distinguish imaging slides.", + "rdfs:comment": "A distinct label or name, unique within an experiment, assigned to an imaging slides.", "rdfs:label": "SlideID", "rdfs:subClassOf": [ { diff --git a/model_contexts/fcs/ark.fcs_model.csv b/model_contexts/fcs/ark.fcs_model.csv index b5b7610..9887e20 100644 --- a/model_contexts/fcs/ark.fcs_model.csv +++ b/model_contexts/fcs/ark.fcs_model.csv @@ -22,11 +22,11 @@ "custom10xProbeSetSynID","If custom modified probe sets were used for collecting 10x Chromium Flex scRNA-seq data, then the probe reference files should be grouped as a zip or tar archive and uploaded as metadata. This attribute links the experimental data back to the probe set archive file via a synapse ID.","","","","True","","","","regex search ^syn[0-9]{8} 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" @@ -65,14 +65,14 @@ "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" @@ -90,9 +90,9 @@ "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" @@ -110,5 +110,5 @@ "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" diff --git a/model_contexts/fcs/ark.fcs_model.jsonld b/model_contexts/fcs/ark.fcs_model.jsonld index 98d2bc6..85cc1f5 100644 --- a/model_contexts/fcs/ark.fcs_model.jsonld +++ b/model_contexts/fcs/ark.fcs_model.jsonld @@ -812,7 +812,6 @@ "sms:required": "sms:true", "sms:validationRules": { "BiospecimenMetadataTemplate": "unique error", - "OlinkBiospecimenMetadataTemplate": "unique error", "all_other_components": "list like error" } }, @@ -2584,6 +2583,9 @@ { "@id": "bts:Template" }, + { + "@id": "bts:Tissuemicroarraymap" + }, { "@id": "bts:Tissuemultiarraymap" }, @@ -2788,6 +2790,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Tissuemicroarraymap", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Tissuemicroarraymap", + "rdfs:subClassOf": [ + { + "@id": "bts:MetadataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "tissue microarray map", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Tissuemultiarraymap", "@type": "rdfs:Class", @@ -7158,7 +7177,7 @@ { "@id": "bts:Age", "@type": "rdfs:Class", - "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event.", + "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event. If value unknown, enter '-1'.", "rdfs:label": "Age", "rdfs:subClassOf": [ { @@ -7663,7 +7682,7 @@ { "@id": "bts:Weight", "@type": "rdfs:Class", - "rdfs:comment": "Weight of subject.", + "rdfs:comment": "Weight of subject. If value unknown, enter '-1'.", "rdfs:label": "Weight", "rdfs:subClassOf": [ { @@ -8325,7 +8344,7 @@ { "@id": "bts:KrennInflammatory", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennInflammatory", "rdfs:subClassOf": [ { @@ -8363,7 +8382,7 @@ { "@id": "bts:KrennStroma", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennStroma", "rdfs:subClassOf": [ { @@ -8896,7 +8915,7 @@ { "@id": "bts:SlideID", "@type": "rdfs:Class", - "rdfs:comment": "A library label or name, unique within an experiment, used to distinguish imaging slides.", + "rdfs:comment": "A distinct label or name, unique within an experiment, assigned to an imaging slides.", "rdfs:label": "SlideID", "rdfs:subClassOf": [ { diff --git a/model_contexts/main/ark.main_model.csv b/model_contexts/main/ark.main_model.csv index e6f18be..d2ddf07 100644 --- a/model_contexts/main/ark.main_model.csv +++ b/model_contexts/main/ark.main_model.csv @@ -29,11 +29,11 @@ "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" @@ -72,14 +72,14 @@ "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" @@ -97,9 +97,9 @@ "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" @@ -118,5 +118,5 @@ "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" diff --git a/model_contexts/main/ark.main_model.jsonld b/model_contexts/main/ark.main_model.jsonld index bdda8ef..2ded422 100644 --- a/model_contexts/main/ark.main_model.jsonld +++ b/model_contexts/main/ark.main_model.jsonld @@ -2223,7 +2223,6 @@ "sms:required": "sms:true", "sms:validationRules": { "BiospecimenMetadataTemplate": "unique error", - "OlinkBiospecimenMetadataTemplate": "unique error", "all_other_components": "list like error" } }, @@ -2357,6 +2356,9 @@ { "@id": "bts:Template" }, + { + "@id": "bts:Tissuemicroarraymap" + }, { "@id": "bts:Tissuemultiarraymap" }, @@ -5865,6 +5867,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Tissuemicroarraymap", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Tissuemicroarraymap", + "rdfs:subClassOf": [ + { + "@id": "bts:MetadataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "tissue microarray map", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Tissuemultiarraymap", "@type": "rdfs:Class", @@ -9519,7 +9538,7 @@ { "@id": "bts:Age", "@type": "rdfs:Class", - "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event.", + "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event. If value unknown, enter '-1'.", "rdfs:label": "Age", "rdfs:subClassOf": [ { @@ -10024,7 +10043,7 @@ { "@id": "bts:Weight", "@type": "rdfs:Class", - "rdfs:comment": "Weight of subject.", + "rdfs:comment": "Weight of subject. If value unknown, enter '-1'.", "rdfs:label": "Weight", "rdfs:subClassOf": [ { @@ -10591,7 +10610,7 @@ { "@id": "bts:KrennInflammatory", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennInflammatory", "rdfs:subClassOf": [ { @@ -10629,7 +10648,7 @@ { "@id": "bts:KrennStroma", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennStroma", "rdfs:subClassOf": [ { @@ -11103,7 +11122,7 @@ { "@id": "bts:SlideID", "@type": "rdfs:Class", - "rdfs:comment": "A library label or name, unique within an experiment, used to distinguish imaging slides.", + "rdfs:comment": "A distinct label or name, unique within an experiment, assigned to an imaging slides.", "rdfs:label": "SlideID", "rdfs:subClassOf": [ { diff --git a/model_contexts/olink/ark.olink_model.csv b/model_contexts/olink/ark.olink_model.csv index d62f3c5..ee7cba1 100644 --- a/model_contexts/olink/ark.olink_model.csv +++ b/model_contexts/olink/ark.olink_model.csv @@ -22,11 +22,11 @@ "custom10xProbeSetSynID","If custom modified probe sets were used for collecting 10x Chromium Flex scRNA-seq data, then the probe reference files should be grouped as a zip or tar archive and uploaded as metadata. This attribute links the experimental data back to the probe set archive file via a synapse ID.","","","","True","","","","regex search ^syn[0-9]{8} 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" @@ -65,14 +65,14 @@ "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" @@ -90,9 +90,9 @@ "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" @@ -109,5 +109,5 @@ "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" diff --git a/model_contexts/olink/ark.olink_model.jsonld b/model_contexts/olink/ark.olink_model.jsonld index c0106f6..9b1f748 100644 --- a/model_contexts/olink/ark.olink_model.jsonld +++ b/model_contexts/olink/ark.olink_model.jsonld @@ -2574,7 +2574,6 @@ "sms:required": "sms:true", "sms:validationRules": { "BiospecimenMetadataTemplate": "unique error", - "OlinkBiospecimenMetadataTemplate": "unique error", "all_other_components": "list like error" } }, @@ -3106,6 +3105,9 @@ { "@id": "bts:Template" }, + { + "@id": "bts:Tissuemicroarraymap" + }, { "@id": "bts:Tissuemultiarraymap" }, @@ -3310,6 +3312,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Tissuemicroarraymap", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Tissuemicroarraymap", + "rdfs:subClassOf": [ + { + "@id": "bts:MetadataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "tissue microarray map", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Tissuemultiarraymap", "@type": "rdfs:Class", @@ -7671,7 +7690,7 @@ { "@id": "bts:Age", "@type": "rdfs:Class", - "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event.", + "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event. If value unknown, enter '-1'.", "rdfs:label": "Age", "rdfs:subClassOf": [ { @@ -8176,7 +8195,7 @@ { "@id": "bts:Weight", "@type": "rdfs:Class", - "rdfs:comment": "Weight of subject.", + "rdfs:comment": "Weight of subject. If value unknown, enter '-1'.", "rdfs:label": "Weight", "rdfs:subClassOf": [ { @@ -8838,7 +8857,7 @@ { "@id": "bts:KrennInflammatory", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennInflammatory", "rdfs:subClassOf": [ { @@ -8876,7 +8895,7 @@ { "@id": "bts:KrennStroma", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennStroma", "rdfs:subClassOf": [ { @@ -9445,7 +9464,7 @@ { "@id": "bts:SlideID", "@type": "rdfs:Class", - "rdfs:comment": "A library label or name, unique within an experiment, used to distinguish imaging slides.", + "rdfs:comment": "A distinct label or name, unique within an experiment, assigned to an imaging slides.", "rdfs:label": "SlideID", "rdfs:subClassOf": [ { diff --git a/model_contexts/singlecell/ark.singlecell_model.csv b/model_contexts/singlecell/ark.singlecell_model.csv index 3edb1b3..6264d59 100644 --- a/model_contexts/singlecell/ark.singlecell_model.csv +++ b/model_contexts/singlecell/ark.singlecell_model.csv @@ -32,7 +32,7 @@ "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" @@ -74,14 +74,14 @@ "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" @@ -99,9 +99,9 @@ "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" @@ -119,5 +119,5 @@ "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" diff --git a/model_contexts/singlecell/ark.singlecell_model.jsonld b/model_contexts/singlecell/ark.singlecell_model.jsonld index 8bc4ae5..ba96461 100644 --- a/model_contexts/singlecell/ark.singlecell_model.jsonld +++ b/model_contexts/singlecell/ark.singlecell_model.jsonld @@ -49,7 +49,6 @@ "sms:required": "sms:true", "sms:validationRules": { "BiospecimenMetadataTemplate": "unique error", - "OlinkBiospecimenMetadataTemplate": "unique error", "all_other_components": "list like error" } }, @@ -8746,7 +8745,7 @@ { "@id": "bts:Age", "@type": "rdfs:Class", - "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event.", + "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event. If value unknown, enter '-1'.", "rdfs:label": "Age", "rdfs:subClassOf": [ { @@ -9271,7 +9270,7 @@ { "@id": "bts:Weight", "@type": "rdfs:Class", - "rdfs:comment": "Weight of subject.", + "rdfs:comment": "Weight of subject. If value unknown, enter '-1'.", "rdfs:label": "Weight", "rdfs:subClassOf": [ { @@ -9933,7 +9932,7 @@ { "@id": "bts:KrennInflammatory", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennInflammatory", "rdfs:subClassOf": [ { @@ -9971,7 +9970,7 @@ { "@id": "bts:KrennStroma", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennStroma", "rdfs:subClassOf": [ { @@ -10524,7 +10523,7 @@ { "@id": "bts:SlideID", "@type": "rdfs:Class", - "rdfs:comment": "A library label or name, unique within an experiment, used to distinguish imaging slides.", + "rdfs:comment": "A distinct label or name, unique within an experiment, assigned to an imaging slides.", "rdfs:label": "SlideID", "rdfs:subClassOf": [ { diff --git a/model_contexts/spatial/ark.spatial_context.csv b/model_contexts/spatial/ark.spatial_context.csv index a142ecf..5d63277 100644 --- a/model_contexts/spatial/ark.spatial_context.csv +++ b/model_contexts/spatial/ark.spatial_context.csv @@ -1,14 +1,14 @@ Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType -Spatial Assay Metadata Template,A template outlining metadata to be collected for each slide in a spatial transcriptomic or imaging based dataset.,,"Component, assay, specimenModality, sampleProcessingBatch, dataCollectionBatch, targetPanel, targetPanelSynID, targetPanelSize",,,,,,, +Spatial Imaging Assay Metadata Template,A template outlining metadata to be collected for each slide in a spatial transcriptomic or imaging based dataset.,,"Component, assay, specimenModality, sampleProcessingBatch, dataCollectionBatch, targetPanel, targetPanelSynID, targetPanelSize",,,,,,, Spatial Imaging File Annotation Template,A data contributor template outlining metadata to be collected as file annotations for imaging-based data files.,,"Component, fileFormat, assay, resourceType, specimenModality",,,,,,, BDM Spatial Imaging File Annotations,A template outlining as file annotations for imaging-based data files to be compiled by ARK BDM.,,"Component, fileFormat, assay, resourceType, specimenModality, parentBiospecimenID, biospecimenType, biospecimenSubtype, dataType, dataSubtype, diagnosis, visitID, targetPanel, targetPanelSynID, targetPanelSize, program, project, species",,,,,,, -single specimen,Is a valid value of `specimenModality` that triggers conditional dependencies for additional attributes.,,"biospecimenID, individualID",,,,,,, +single specimen,Is a valid value of `specimenModality` that triggers conditional dependencies for additional attributes.,,biospecimenID,,,,,,, multispecimen,Is a valid value of `specimenModality` that triggers conditional dependencies for additional attributes.,,slideID,,,,,,, resourceType,,"experimental data, metadata",,,TRUE,,,,list like error,string -assay,,"Xenium, CosMX, GenePS SeqFISH, imaging mass cytometry, Visium, H&E, serial IHC",,,,,,,, -Rds,Is a valid value of 'fileFormat' that triggers conditional dependencies for additional attributes.,,RObjectClass,,,,,,, -experimental data,Is a valid value of 'resourceType' that triggers conditional dependencies for additional attributes.,,processedDataType,,,,,,, +assay,,"Xenium, CosMX, GenePS SeqFISH, imaging mass cytometry, Visium, H&E, serial IHC",,,TRUE,,,,,string +Rds,Is a valid value of 'fileFormat' that triggers conditional dependencies for additional attributes.,,RObjectClass,,FALSE,,,,, +experimental data,Is a valid value of 'resourceType' that triggers conditional dependencies for additional attributes.,,processedDataType,,FALSE,,,,, metadata,"Is a valid value of Resource Type that triggers conditional dependencies for additional attributes. Any file that contains curated data describing an experiment and experimental-derived data, including metadata about study subjects, biospecimens, protocols, assay reagents, marker panels, and ID mappings",,metadataType,,FALSE,,,,, -metadataType,,"single-cell metadata, cell coordinates, target panel, tissue multiarray map, other",,,TRUE,,,,,string -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,,,,,,, \ No newline at end of file +metadataType,,"single-cell metadata, cell coordinates, target panel, tissue microarray map, other",,,TRUE,,,,,string +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,,FALSE,,,,, +AMP AIM,Accelerating Medicines Partnership Autoimmune and Immune-Mediated Diseases. Is a valid value for 'program' that triggers conditional dependencies for additional attributes.,,visitID,,FALSE,,,,, \ No newline at end of file diff --git a/model_contexts/spatial/ark.spatial_model.csv b/model_contexts/spatial/ark.spatial_model.csv index dd1725c..97ab2e8 100644 --- a/model_contexts/spatial/ark.spatial_model.csv +++ b/model_contexts/spatial/ark.spatial_model.csv @@ -1,17 +1,17 @@ "Attribute","Description","Valid Values","DependsOn","Properties","Required","Parent","DependsOn Component","Source","Validation Rules","columnType" -"Spatial Assay Metadata Template","A template outlining metadata to be collected for each slide in a spatial transcriptomic or imaging based dataset.","","Component, assay, specimenModality, sampleProcessingBatch, dataCollectionBatch, targetPanel, targetPanelSynID, targetPanelSize","","","","","","","" +"Spatial Imaging Assay Metadata Template","A template outlining metadata to be collected for each slide in a spatial transcriptomic or imaging based dataset.","","Component, assay, specimenModality, sampleProcessingBatch, dataCollectionBatch, targetPanel, targetPanelSynID, targetPanelSize","","","","","","","" "Spatial Imaging File Annotation Template","A data contributor template outlining metadata to be collected as file annotations for imaging-based data files.","","Component, fileFormat, assay, resourceType, specimenModality","","","","","","","" "BDM Spatial Imaging File Annotations","A template outlining as file annotations for imaging-based data files to be compiled by ARK BDM.","","Component, fileFormat, assay, resourceType, specimenModality, parentBiospecimenID, biospecimenType, biospecimenSubtype, dataType, dataSubtype, diagnosis, visitID, targetPanel, targetPanelSynID, targetPanelSize, program, project, species","","","","","","","" -"single specimen","Is a valid value of `specimenModality` that triggers conditional dependencies for additional attributes.","","biospecimenID, individualID","","","","","","","" +"single specimen","Is a valid value of `specimenModality` that triggers conditional dependencies for additional attributes.","","biospecimenID","","","","","","","" "multispecimen","Is a valid value of `specimenModality` that triggers conditional dependencies for additional attributes.","","slideID","","","","","","","" "resourceType","High-level classification of the file content","experimental data, metadata","","","TRUE","","","","list like error","string" -"assay","The technology used to generate the data in this file. For multimodal datasets with concomitant profiling of biospecimen select all assays that apply. e.g., the GEX files from a CITE-seq experiment should be labeled with both 'scRNASeq' and 'CITESeq'.","Xenium, CosMX, GenePS SeqFISH, imaging mass cytometry, Visium, H&E, serial IHC","","","","","","","","" -"Rds","Is a valid value of 'fileFormat' that triggers conditional dependencies for additional attributes.","","RObjectClass","","","","","","","" -"experimental data","Is a valid value of 'resourceType' that triggers conditional dependencies for additional attributes.","","processedDataType","","","","","","","" +"assay","The technology used to generate the data in this file. For multimodal datasets with concomitant profiling of biospecimen select all assays that apply. e.g., the GEX files from a CITE-seq experiment should be labeled with both 'scRNASeq' and 'CITESeq'.","Xenium, CosMX, GenePS SeqFISH, imaging mass cytometry, Visium, H&E, serial IHC","","","TRUE","","","","","string" +"Rds","Is a valid value of 'fileFormat' that triggers conditional dependencies for additional attributes.","","RObjectClass","","FALSE","","","","","" +"experimental data","Is a valid value of 'resourceType' that triggers conditional dependencies for additional attributes.","","processedDataType","","FALSE","","","","","" "metadata","Is a valid value of Resource Type that triggers conditional dependencies for additional attributes. Any file that contains curated data describing an experiment and experimental-derived data, including metadata about study subjects, biospecimens, protocols, assay reagents, marker panels, and ID mappings","","metadataType","","FALSE","","","","","" -"metadataType","A label further classifying the content of metadata resource.","single-cell metadata, cell coordinates, target panel, tissue multiarray map, other","","","TRUE","","","","","string" -"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","","","","","","","" +"metadataType","A label further classifying the content of metadata resource.","single-cell metadata, cell coordinates, target panel, tissue microarray map, other","","","TRUE","","","","","string" +"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","","FALSE","","","","","" +"AMP AIM","Accelerating Medicines Partnership Autoimmune and Immune-Mediated Diseases. Is a valid value for 'program' that triggers conditional dependencies for additional attributes.","","visitID","","FALSE","","","","","" "Component","A high-level attribute for grouping attributes into templates.","","","","True","","","","","string" "fileFormat","Standard file format name or file extension","bai, bam, bed, bim, csv, czi, docx, dose, erate, fam, fastq, fcs, geojson, h5, h5ad, info, mcd, mtx, parquet, pdf, rds, rec, svs, tbi, tgz, tsv, txt, vcf, xls, xlsx, zip","","","True","","","","","string" "publicationSynID","The synID of the corresponding Synapse entity that stores metadata about the publication. This is used to differentiate publication-specific files, often consisting of level 4 processed data and expanded subject metadata, in a publication dataset that also includes raw or minimally processed files from experimental datasets. This provides an easy way to distinguish and select for the publication-specific data from which the research findings were derived. When this attribute is used to annotate a Dataset it serves as a way to directly link the Dataset entity with the publication metadata stored in Synapse.","","","","False","","","","regex search ^syn[0-9]{8} error","string" @@ -27,7 +27,7 @@ "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" @@ -69,14 +69,14 @@ "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" @@ -94,9 +94,9 @@ "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" @@ -114,5 +114,5 @@ "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" diff --git a/model_contexts/spatial/ark.spatial_model.jsonld b/model_contexts/spatial/ark.spatial_model.jsonld index afc326d..af83d4a 100644 --- a/model_contexts/spatial/ark.spatial_model.jsonld +++ b/model_contexts/spatial/ark.spatial_model.jsonld @@ -8,10 +8,10 @@ }, "@graph": [ { - "@id": "bts:SpatialAssayMetadataTemplate", + "@id": "bts:SpatialImagingAssayMetadataTemplate", "@type": "rdfs:Class", "rdfs:comment": "A template outlining metadata to be collected for each slide in a spatial transcriptomic or imaging based dataset.", - "rdfs:label": "SpatialAssayMetadataTemplate", + "rdfs:label": "SpatialImagingAssayMetadataTemplate", "rdfs:subClassOf": [ { "@id": "bts:Thing" @@ -20,7 +20,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spatial Assay Metadata Template", + "sms:displayName": "Spatial Imaging Assay Metadata Template", "sms:required": "sms:false", "sms:requiresDependency": [ { @@ -104,7 +104,7 @@ } ], "sms:displayName": "assay", - "sms:required": "sms:false", + "sms:required": "sms:true", "sms:validationRules": [] }, { @@ -902,9 +902,6 @@ "sms:requiresDependency": [ { "@id": "bts:BiospecimenID" - }, - { - "@id": "bts:IndividualID" } ], "sms:validationRules": [] @@ -926,28 +923,6 @@ "sms:required": "sms:true", "sms:validationRules": { "BiospecimenMetadataTemplate": "unique error", - "OlinkBiospecimenMetadataTemplate": "unique error", - "all_other_components": "list like error" - } - }, - { - "@id": "bts:IndividualID", - "@type": "rdfs:Class", - "rdfs:comment": "Unique identifier assigned to each study participant. For multi-specimen data files provide all IDs in a comma-separated list.", - "rdfs:label": "IndividualID", - "rdfs:subClassOf": [ - { - "@id": "bts:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "individualID", - "sms:required": "sms:true", - "sms:validationRules": { - "BiospecimenMetadataTemplate": "str", - "ClinicalMetadataTemplate": "unique error", "all_other_components": "list like error" } }, @@ -976,7 +951,7 @@ { "@id": "bts:SlideID", "@type": "rdfs:Class", - "rdfs:comment": "A library label or name, unique within an experiment, used to distinguish imaging slides.", + "rdfs:comment": "A distinct label or name, unique within an experiment, assigned to an imaging slides.", "rdfs:label": "SlideID", "rdfs:subClassOf": [ { @@ -1281,7 +1256,7 @@ "@id": "bts:Targetpanel" }, { - "@id": "bts:Tissuemultiarraymap" + "@id": "bts:Tissuemicroarraymap" }, { "@id": "bts:Other" @@ -1343,10 +1318,10 @@ "sms:validationRules": [] }, { - "@id": "bts:Tissuemultiarraymap", + "@id": "bts:Tissuemicroarraymap", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Tissuemultiarraymap", + "rdfs:label": "Tissuemicroarraymap", "rdfs:subClassOf": [ { "@id": "bts:MetadataType" @@ -1355,7 +1330,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "tissue multiarray map", + "sms:displayName": "tissue microarray map", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3624,6 +3599,27 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:IndividualID", + "@type": "rdfs:Class", + "rdfs:comment": "Unique identifier assigned to each study participant. For multi-specimen data files provide all IDs in a comma-separated list.", + "rdfs:label": "IndividualID", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "individualID", + "sms:required": "sms:true", + "sms:validationRules": { + "BiospecimenMetadataTemplate": "str", + "ClinicalMetadataTemplate": "unique error", + "all_other_components": "list like error" + } + }, { "@id": "bts:PBMCs", "@type": "rdfs:Class", @@ -8303,7 +8299,7 @@ { "@id": "bts:Age", "@type": "rdfs:Class", - "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event.", + "rdfs:comment": "Age at which subject was enrolled in study or age at corresponding visit and data collection event. If value unknown, enter '-1'.", "rdfs:label": "Age", "rdfs:subClassOf": [ { @@ -8808,7 +8804,7 @@ { "@id": "bts:Weight", "@type": "rdfs:Class", - "rdfs:comment": "Weight of subject.", + "rdfs:comment": "Weight of subject. If value unknown, enter '-1'.", "rdfs:label": "Weight", "rdfs:subClassOf": [ { @@ -9470,7 +9466,7 @@ { "@id": "bts:KrennInflammatory", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennInflammatory", "rdfs:subClassOf": [ { @@ -9508,7 +9504,7 @@ { "@id": "bts:KrennStroma", "@type": "rdfs:Class", - "rdfs:comment": "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'.", + "rdfs:comment": "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'.", "rdfs:label": "KrennStroma", "rdfs:subClassOf": [ { diff --git a/model_contexts/spatial/ark.spatial_templates.txt b/model_contexts/spatial/ark.spatial_templates.txt index 3dc6b98..e8deaef 100644 --- a/model_contexts/spatial/ark.spatial_templates.txt +++ b/model_contexts/spatial/ark.spatial_templates.txt @@ -1,3 +1,3 @@ BDMSpatialImagingFileAnnotations spatial -SpatialAssayMetadataTemplate spatial +SpatialImagingAssayMetadataTemplate spatial SpatialImagingFileAnnotationTemplate spatial diff --git a/model_json_schema/ark.BiospecimenMetadataTemplate.schema.json b/model_json_schema/ark.BiospecimenMetadataTemplate.schema.json index 3f3e5aa..9b61b1c 100644 --- a/model_json_schema/ark.BiospecimenMetadataTemplate.schema.json +++ b/model_json_schema/ark.BiospecimenMetadataTemplate.schema.json @@ -4,21 +4,28 @@ "title": "ark", "type": "object", "properties": { + "biospecimenID": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "altSampleID": {}, "biospecimenSubtype": { "enum": [ + "supernatant", "frozen tissue", - "PFA-fixed tissue", + "nuclei suspension", + "fresh tissue", "cell or tissue lysate", + "PFA-fixed tissue", "cell suspension", - "supernatant", - "nuclei suspension", "flow-sorted cells", "FFPE tissue", - "fresh tissue", "" ] }, - "biospecimenID": { + "individualID": { "not": { "type": "null" }, @@ -28,51 +35,49 @@ "type": "array", "items": { "enum": [ - "ELLIPSS", - "STAMP", + "AIM for RA", "V-CoRT", - "LOCKIT", + "ELLIPSS", + "RA", "SLE", - "AIM for RA", - "RA" + "LOCKIT", + "STAMP" ] }, "maxItems": 7 }, - "parentBiospecimenID": {}, + "notes": {}, "biospecimenType": { "enum": [ - "synovial fluid", + "none", + "uvea", + "salivary gland", + "total leukocytes", + "cell line", + "stool", + "primary cell culture", "PBMCs", "kidney biopsy", - "stool", - "suction blister fluid", - "salivary gland", + "synovial tissue", + "skin swab", + "plasma", "serum", "fibroblast-like synoviocyte", - "skin swab", - "saliva", "skin biopsy", - "synovial tissue", - "suction blister cells", - "cell line", - "plasma", + "saliva", + "suction blister fluid", "urine", - "primary cell culture", - "none", - "total leukocytes", - "uvea", + "synovial fluid", + "suction blister cells", "whole blood" ] }, - "notes": {}, "Component": { "not": { "type": "null" }, "minLength": 1 }, - "altSampleID": {}, "program": { "enum": [ "AMP RA/SLE", @@ -80,83 +85,72 @@ "Community Contribution" ] }, - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "plateID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, + "parentBiospecimenID": {}, "cellType": {}, - "cellOntologyID": {}, "userDefinedCellType": {}, + "cellOntologyID": {}, "FACSPopulation": {}, - "synovialCollectionProcedure": { + "primaryCellSource": { "enum": [ - "biopsy", - "synovectomy", - "arthroplasty", - "unknown", + "pannus-derived epidermis", + "urine", + "uvea", + "salivary gland", + "PBMCs", + "total leukocytes", + "pannus-derived dermis", + "whole blood", + "synovial tissue", + "kidney", "" ] }, + "krennStroma": {}, + "krennSynovitisScore": {}, "anatomicalSite": { "enum": [ - "left hip joint", - "left knee joint", "right 1st MTP joint", - "right 3rd MCP joint", + "right wrist joint", "right hip joint", "left ankle joint", - "left 2nd MCP joint", "other site", + "unknown", + "left knee joint", "left wrist joint", - "right 2nd MCP joint", "right 2nd MTP joint", - "right knee joint", - "right wrist joint", + "right 3rd MCP joint", "right ankle joint", + "right 2nd MCP joint", + "left hip joint", + "right knee joint", + "left 2nd MCP joint", + "" + ] + }, + "krennLining": {}, + "krennInflammatory": {}, + "synovialCollectionProcedure": { + "enum": [ + "arthroplasty", "unknown", + "biopsy", + "synovectomy", "" ] }, "skinSiteStatus": { "enum": [ - "lesional", - "healthy control", "lesional proximal", + "healthy control", + "lesional", "non-lesional", "" ] }, "salivaCollectionProcedure": { "enum": [ - "unstimulated", "stimulated", - "" - ] - }, - "krennStroma": {}, - "krennSynovitisScore": {}, - "krennLining": {}, - "krennInflammatory": {}, - "primaryCellSource": { - "enum": [ - "PBMCs", - "total leukocytes", - "pannus-derived dermis", - "salivary gland", - "uvea", - "pannus-derived epidermis", - "kidney", - "whole blood", - "urine", - "synovial tissue", + "unstimulated", "" ] }, @@ -164,12 +158,11 @@ }, "required": [ "biospecimenID", + "individualID", "project", "biospecimenType", "Component", - "program", - "individualID", - "plateID" + "program" ], "allOf": [ { @@ -275,10 +268,10 @@ }, "then": { "properties": { - "cellOntologyID": {} + "userDefinedCellType": {} }, "required": [ - "cellOntologyID" + "userDefinedCellType" ] } }, @@ -297,24 +290,24 @@ }, "then": { "properties": { - "cellOntologyID": {} + "userDefinedCellType": {} }, "required": [ - "cellOntologyID" + "userDefinedCellType" ] } }, { "if": { "properties": { - "biospecimenType": { + "biospecimenSubtype": { "enum": [ - "cell line" + "cell suspension" ] } }, "required": [ - "biospecimenType" + "biospecimenSubtype" ] }, "then": { @@ -329,14 +322,14 @@ { "if": { "properties": { - "biospecimenType": { + "biospecimenSubtype": { "enum": [ - "primary cell culture" + "flow-sorted cells" ] } }, "required": [ - "biospecimenType" + "biospecimenSubtype" ] }, "then": { @@ -351,44 +344,44 @@ { "if": { "properties": { - "biospecimenSubtype": { + "biospecimenType": { "enum": [ - "cell suspension" + "cell line" ] } }, "required": [ - "biospecimenSubtype" + "biospecimenType" ] }, "then": { "properties": { - "userDefinedCellType": {} + "cellOntologyID": {} }, "required": [ - "userDefinedCellType" + "cellOntologyID" ] } }, { "if": { "properties": { - "biospecimenSubtype": { + "biospecimenType": { "enum": [ - "flow-sorted cells" + "primary cell culture" ] } }, "required": [ - "biospecimenSubtype" + "biospecimenType" ] }, "then": { "properties": { - "userDefinedCellType": {} + "cellOntologyID": {} }, "required": [ - "userDefinedCellType" + "cellOntologyID" ] } }, @@ -424,7 +417,7 @@ "properties": { "biospecimenType": { "enum": [ - "synovial fluid" + "primary cell culture" ] } }, @@ -434,121 +427,186 @@ }, "then": { "properties": { - "synovialCollectionProcedure": { + "primaryCellSource": { "enum": [ - "biopsy", - "synovectomy", - "arthroplasty", - "unknown" + "pannus-derived epidermis", + "urine", + "uvea", + "salivary gland", + "PBMCs", + "total leukocytes", + "pannus-derived dermis", + "whole blood", + "synovial tissue", + "kidney" ] } }, "required": [ - "synovialCollectionProcedure" + "primaryCellSource" ] } }, { "if": { "properties": { - "biospecimenType": { + "primaryCellSource": { "enum": [ "synovial tissue" ] } }, "required": [ - "biospecimenType" + "primaryCellSource" ] }, "then": { "properties": { - "synovialCollectionProcedure": { - "enum": [ - "biopsy", - "synovectomy", - "arthroplasty", - "unknown" - ] - } + "krennStroma": {} }, "required": [ - "synovialCollectionProcedure" + "krennStroma" ] } }, { "if": { "properties": { - "biospecimenType": { + "primaryCellSource": { "enum": [ - "synovial fluid" + "synovial tissue" ] } }, "required": [ - "biospecimenType" + "primaryCellSource" ] }, "then": { "properties": { - "anatomicalSite": { + "krennStroma": {} + }, + "required": [ + "krennStroma" + ] + } + }, + { + "if": { + "properties": { + "primaryCellSource": { "enum": [ - "left hip joint", - "left knee joint", - "right 1st MTP joint", - "right 3rd MCP joint", - "right hip joint", - "left ankle joint", - "left 2nd MCP joint", - "other site", - "left wrist joint", - "right 2nd MCP joint", - "right 2nd MTP joint", - "right knee joint", - "right wrist joint", - "right ankle joint", - "unknown" + "synovial tissue" ] } }, "required": [ - "anatomicalSite" + "primaryCellSource" + ] + }, + "then": { + "properties": { + "krennSynovitisScore": {} + }, + "required": [ + "krennSynovitisScore" ] } }, { "if": { "properties": { - "biospecimenType": { + "primaryCellSource": { "enum": [ - "suction blister fluid" + "synovial tissue" ] } }, "required": [ - "biospecimenType" + "primaryCellSource" + ] + }, + "then": { + "properties": { + "krennSynovitisScore": {} + }, + "required": [ + "krennSynovitisScore" + ] + } + }, + { + "if": { + "properties": { + "primaryCellSource": { + "enum": [ + "synovial tissue" + ] + } + }, + "required": [ + "primaryCellSource" ] }, "then": { "properties": { "anatomicalSite": { "enum": [ - "left hip joint", - "left knee joint", "right 1st MTP joint", - "right 3rd MCP joint", + "right wrist joint", "right hip joint", "left ankle joint", - "left 2nd MCP joint", "other site", + "unknown", + "left knee joint", "left wrist joint", - "right 2nd MCP joint", "right 2nd MTP joint", + "right 3rd MCP joint", + "right ankle joint", + "right 2nd MCP joint", + "left hip joint", "right knee joint", + "left 2nd MCP joint" + ] + } + }, + "required": [ + "anatomicalSite" + ] + } + }, + { + "if": { + "properties": { + "primaryCellSource": { + "enum": [ + "synovial tissue" + ] + } + }, + "required": [ + "primaryCellSource" + ] + }, + "then": { + "properties": { + "anatomicalSite": { + "enum": [ + "right 1st MTP joint", "right wrist joint", + "right hip joint", + "left ankle joint", + "other site", + "unknown", + "left knee joint", + "left wrist joint", + "right 2nd MTP joint", + "right 3rd MCP joint", "right ankle joint", - "unknown" + "right 2nd MCP joint", + "left hip joint", + "right knee joint", + "left 2nd MCP joint" ] } }, @@ -574,21 +632,21 @@ "properties": { "anatomicalSite": { "enum": [ - "left hip joint", - "left knee joint", "right 1st MTP joint", - "right 3rd MCP joint", + "right wrist joint", "right hip joint", "left ankle joint", - "left 2nd MCP joint", "other site", + "unknown", + "left knee joint", "left wrist joint", - "right 2nd MCP joint", "right 2nd MTP joint", - "right knee joint", - "right wrist joint", + "right 3rd MCP joint", "right ankle joint", - "unknown" + "right 2nd MCP joint", + "left hip joint", + "right knee joint", + "left 2nd MCP joint" ] } }, @@ -614,21 +672,21 @@ "properties": { "anatomicalSite": { "enum": [ - "left hip joint", - "left knee joint", "right 1st MTP joint", - "right 3rd MCP joint", + "right wrist joint", "right hip joint", "left ankle joint", - "left 2nd MCP joint", "other site", + "unknown", + "left knee joint", "left wrist joint", - "right 2nd MCP joint", "right 2nd MTP joint", - "right knee joint", - "right wrist joint", + "right 3rd MCP joint", "right ankle joint", - "unknown" + "right 2nd MCP joint", + "left hip joint", + "right knee joint", + "left 2nd MCP joint" ] } }, @@ -642,7 +700,7 @@ "properties": { "biospecimenType": { "enum": [ - "synovial tissue" + "suction blister fluid" ] } }, @@ -654,21 +712,61 @@ "properties": { "anatomicalSite": { "enum": [ - "left hip joint", - "left knee joint", "right 1st MTP joint", - "right 3rd MCP joint", + "right wrist joint", "right hip joint", "left ankle joint", - "left 2nd MCP joint", "other site", + "unknown", + "left knee joint", "left wrist joint", - "right 2nd MCP joint", "right 2nd MTP joint", + "right 3rd MCP joint", + "right ankle joint", + "right 2nd MCP joint", + "left hip joint", "right knee joint", + "left 2nd MCP joint" + ] + } + }, + "required": [ + "anatomicalSite" + ] + } + }, + { + "if": { + "properties": { + "biospecimenType": { + "enum": [ + "synovial fluid" + ] + } + }, + "required": [ + "biospecimenType" + ] + }, + "then": { + "properties": { + "anatomicalSite": { + "enum": [ + "right 1st MTP joint", "right wrist joint", + "right hip joint", + "left ankle joint", + "other site", + "unknown", + "left knee joint", + "left wrist joint", + "right 2nd MTP joint", + "right 3rd MCP joint", "right ankle joint", - "unknown" + "right 2nd MCP joint", + "left hip joint", + "right knee joint", + "left 2nd MCP joint" ] } }, @@ -694,21 +792,21 @@ "properties": { "anatomicalSite": { "enum": [ - "left hip joint", - "left knee joint", "right 1st MTP joint", - "right 3rd MCP joint", + "right wrist joint", "right hip joint", "left ankle joint", - "left 2nd MCP joint", "other site", + "unknown", + "left knee joint", "left wrist joint", - "right 2nd MCP joint", "right 2nd MTP joint", - "right knee joint", - "right wrist joint", + "right 3rd MCP joint", "right ankle joint", - "unknown" + "right 2nd MCP joint", + "left hip joint", + "right knee joint", + "left 2nd MCP joint" ] } }, @@ -720,116 +818,146 @@ { "if": { "properties": { - "biospecimenType": { + "primaryCellSource": { "enum": [ - "suction blister fluid" + "synovial tissue" ] } }, "required": [ - "biospecimenType" + "primaryCellSource" ] }, "then": { "properties": { - "skinSiteStatus": { + "krennLining": {} + }, + "required": [ + "krennLining" + ] + } + }, + { + "if": { + "properties": { + "primaryCellSource": { "enum": [ - "lesional", - "healthy control", - "lesional proximal", - "non-lesional" + "synovial tissue" ] } }, "required": [ - "skinSiteStatus" + "primaryCellSource" + ] + }, + "then": { + "properties": { + "krennLining": {} + }, + "required": [ + "krennLining" ] } }, { "if": { "properties": { - "biospecimenType": { + "primaryCellSource": { "enum": [ - "skin swab" + "synovial tissue" ] } }, "required": [ - "biospecimenType" + "primaryCellSource" ] }, "then": { "properties": { - "skinSiteStatus": { + "krennInflammatory": {} + }, + "required": [ + "krennInflammatory" + ] + } + }, + { + "if": { + "properties": { + "primaryCellSource": { "enum": [ - "lesional", - "healthy control", - "lesional proximal", - "non-lesional" + "synovial tissue" ] } }, "required": [ - "skinSiteStatus" + "primaryCellSource" + ] + }, + "then": { + "properties": { + "krennInflammatory": {} + }, + "required": [ + "krennInflammatory" ] } }, { "if": { "properties": { - "biospecimenType": { + "primaryCellSource": { "enum": [ - "skin biopsy" + "synovial tissue" ] } }, "required": [ - "biospecimenType" + "primaryCellSource" ] }, "then": { "properties": { - "skinSiteStatus": { + "synovialCollectionProcedure": { "enum": [ - "lesional", - "healthy control", - "lesional proximal", - "non-lesional" + "arthroplasty", + "unknown", + "biopsy", + "synovectomy" ] } }, "required": [ - "skinSiteStatus" + "synovialCollectionProcedure" ] } }, { "if": { "properties": { - "biospecimenType": { + "primaryCellSource": { "enum": [ - "suction blister cells" + "synovial tissue" ] } }, "required": [ - "biospecimenType" + "primaryCellSource" ] }, "then": { "properties": { - "skinSiteStatus": { + "synovialCollectionProcedure": { "enum": [ - "lesional", - "healthy control", - "lesional proximal", - "non-lesional" + "arthroplasty", + "unknown", + "biopsy", + "synovectomy" ] } }, "required": [ - "skinSiteStatus" + "synovialCollectionProcedure" ] } }, @@ -838,7 +966,7 @@ "properties": { "biospecimenType": { "enum": [ - "saliva" + "synovial fluid" ] } }, @@ -848,15 +976,17 @@ }, "then": { "properties": { - "salivaCollectionProcedure": { + "synovialCollectionProcedure": { "enum": [ - "unstimulated", - "stimulated" + "arthroplasty", + "unknown", + "biopsy", + "synovectomy" ] } }, "required": [ - "salivaCollectionProcedure" + "synovialCollectionProcedure" ] } }, @@ -865,7 +995,7 @@ "properties": { "biospecimenType": { "enum": [ - "synovial tissue" + "skin swab" ] } }, @@ -875,10 +1005,17 @@ }, "then": { "properties": { - "krennStroma": {} + "skinSiteStatus": { + "enum": [ + "lesional proximal", + "healthy control", + "lesional", + "non-lesional" + ] + } }, "required": [ - "krennStroma" + "skinSiteStatus" ] } }, @@ -887,7 +1024,7 @@ "properties": { "biospecimenType": { "enum": [ - "synovial tissue" + "skin biopsy" ] } }, @@ -897,10 +1034,17 @@ }, "then": { "properties": { - "krennSynovitisScore": {} + "skinSiteStatus": { + "enum": [ + "lesional proximal", + "healthy control", + "lesional", + "non-lesional" + ] + } }, "required": [ - "krennSynovitisScore" + "skinSiteStatus" ] } }, @@ -909,7 +1053,7 @@ "properties": { "biospecimenType": { "enum": [ - "synovial tissue" + "suction blister fluid" ] } }, @@ -919,10 +1063,17 @@ }, "then": { "properties": { - "krennLining": {} + "skinSiteStatus": { + "enum": [ + "lesional proximal", + "healthy control", + "lesional", + "non-lesional" + ] + } }, "required": [ - "krennLining" + "skinSiteStatus" ] } }, @@ -931,7 +1082,7 @@ "properties": { "biospecimenType": { "enum": [ - "synovial tissue" + "suction blister cells" ] } }, @@ -941,10 +1092,17 @@ }, "then": { "properties": { - "krennInflammatory": {} + "skinSiteStatus": { + "enum": [ + "lesional proximal", + "healthy control", + "lesional", + "non-lesional" + ] + } }, "required": [ - "krennInflammatory" + "skinSiteStatus" ] } }, @@ -953,7 +1111,7 @@ "properties": { "biospecimenType": { "enum": [ - "primary cell culture" + "saliva" ] } }, @@ -963,23 +1121,15 @@ }, "then": { "properties": { - "primaryCellSource": { + "salivaCollectionProcedure": { "enum": [ - "PBMCs", - "total leukocytes", - "pannus-derived dermis", - "salivary gland", - "uvea", - "pannus-derived epidermis", - "kidney", - "whole blood", - "urine", - "synovial tissue" + "stimulated", + "unstimulated" ] } }, "required": [ - "primaryCellSource" + "salivaCollectionProcedure" ] } }, diff --git a/model_json_schema/ark.BulkATAC-seqAssayMetadataTemplate.schema.json b/model_json_schema/ark.BulkATAC-seqAssayMetadataTemplate.schema.json index 1fb2d83..02b0468 100644 --- a/model_json_schema/ark.BulkATAC-seqAssayMetadataTemplate.schema.json +++ b/model_json_schema/ark.BulkATAC-seqAssayMetadataTemplate.schema.json @@ -4,266 +4,269 @@ "title": "ark", "type": "object", "properties": { - "alignmentReference": { + "libraryPrepMethod": { "enum": [ - "unknown", - "10x Cell Ranger Human GRCh38 2020-A", - "vdj_GRCh38_alts_ensembl-4.0.0", - "modified GRCh38", - "10x Cell Ranger Human GRCh38 2024-A" + "10x Chromium GEM-X Single Cell 3' v4", + "Takara Human TCR profiling for Illumina", + "10x GEM-X Universal 5? Gene Expression v3", + "TruSeq Stranded mRNA", + "SMARTer Stranded Total RNA v2", + "Chromium Next GEM Single Cell ATAC v1.1", + "CEL-Seq2", + "NEBNext Ultra II Directional RNA Library", + "Takara Human TCRv2 profiling for Illumina", + "Takara Human BCR profiling for Illumina", + "10x GEM-X Flex Gene Expression Human", + "10x Chromium Single Cell Human TCR", + "Nextera XT DNA", + "SMART-Seq Human BCR with UMI", + "10x Chromium Fixed RNA Human Transcriptome", + "Nextera XT", + "10x Chromium Next GEM Single Cell 3'", + "SMART-Seq Human TCR with UMI", + "Takara Human scTCR profiling for Illumina", + "10x Chromium Single Cell Human BCR", + "10x Chromium Next GEM Single Cell 5' v2", + "10x Chromium Next GEM Single Cell 3' 3.1", + "10x Chromium Next GEM Single Cell 5' v1.1", + "QIAseq miRNA Library", + "in-house library prep", + "NEBNext Human Immune Sequencing Kit", + "SMART-Seq v4 Ultra Low Input RNA", + "Fluidigm C1 HT", + "10x Chromium Next GEM Single Cell ATAC v2", + "custom DASH-treatment", + "10x Chromium GEM-X Single Cell 5' v3" ] }, "softwareAndVersion": { "enum": [ - "Cell Ranger v6.0.2", - "Cell Ranger v3.0.1", - "Cell Ranger v7.2.0", - "Cell Ranger v5.0.0", - "Cell Ranger v8.0.1", - "Cell Ranger v3.0.2", + "Cell Ranger v7.0.0", "BD FACSDiva 8.0.1", - "demuxlet", - "Cell Ranger v6.0.0", + "Cell Ranger v3.0.2", + "Cell Ranger v6.1.1", + "Cell Ranger v3.1.0", + "Space Ranger 3.1.1", + "Cell Ranger v7.2.0", "Space Ranger 3.1.0", + "Cell Ranger v7.0.1", + "demuxlet", + "Cell Ranger v5.0.0", + "Cell Ranger v6.0.1", "Cell Ranger v6.1.0", - "Cell Ranger v7.1.0", "Cell Ranger v9.0.0", - "Space Ranger 3.1.3", - "Cell Ranger v7.0.1", - "Space Ranger 3.0.0", "Cell Ranger v4.0.0", - "Cell Ranger v7.0.0", - "Space Ranger 3.1.1", - "Cell Ranger 9.0.1", + "Cell Ranger ATAC v1.1.0", + "Space Ranger 3.1.3", + "Space Ranger 3.0.1", + "Cell Ranger v3.0.0", + "Space Ranger 3.1.2", "Cell Ranger v5.0.1", - "Cell Ranger v6.0.1", + "Cell Ranger v6.0.2", + "Cell Ranger v7.1.0", + "Cell Ranger v8.0.1", + "Space Ranger 3.0.0", + "Cell Ranger v6.0.0", "Cell Ranger v8.0.0", - "Cell Ranger v6.1.1", + "Cell Ranger 9.0.1", "Cell Ranger v6.1.2", - "Cell Ranger v3.1.0", - "Space Ranger 3.1.2", - "Space Ranger 3.0.1", - "Cell Ranger v3.0.0", - "Cell Ranger ATAC v1.1.0", + "Cell Ranger v3.0.1", "" ] }, - "specimenModality": { - "enum": [ - "multispecimen", - "single specimen" - ] + "totalReads": { + "not": { + "type": "null" + }, + "minLength": 1 }, - "nucleicAcidSource": { + "assay": { "type": "array", "items": { "enum": [ - "BCR mRNA", - "poly(A) RNA", - "CRISPR protospacer feature barcode", - "surface protein feature barcode", - "globin-depleted RNA", - "gDNA", - "multiplexing oligo", - "rRNA-depleted RNA", - "intracellular protein feature barcode", - "TCR mRNA", - "Tn5-accessible gDNA", - "antigen capture barcode" + "Olink Target 48", + "LC-MS/MS", + "multiplexed ELISA", + "Olink Explore HT", + "CITESeq", + "RNASeq", + "VDJSeq", + "Olink Target 96", + "Xenium", + "flow cytometry", + "kiloplex", + "scVDJSeq", + "ASAPSeq", + "snATACSeq", + "serial IHC", + "GenePS SeqFISH", + "NULISA", + "imaging mass cytometry", + "Olink Flex", + "scRNASeq", + "WGS", + "WES", + "CE-MS", + "feature barcode sequencing", + "CosMX", + "SomaScan", + "Olink Focus", + "Visium", + "snRNASeq", + "Olink Reveal", + "CyTOF", + "imaging mass spectrometry", + "H&E", + "SNP array" ] }, - "maxItems": 12 + "maxItems": 34 }, "platform": { "type": "array", "items": { "enum": [ - "BD FACSDiscover A8", + "Illumina NextSeq 500", + "BD FACSMelody", + "CyTOF XT", + "Chromium Next GEM Chip Q", + "Hyperion", + "Illumina NovaSeq 6000", + "Chromium iX", + "Not Applicable", + "BD FACSymphony S6", + "BD FACSLyric Clinical", + "BD FACSCanto", "Chromium Next GEM Chip G", - "Chromium GEM-X Single Cell 3' Chip v4", - "GEM-X Flex Gene Expression Chip", - "Chromium Next GEM Chip M", - "BD FACSDiscover S8", + "Illumina HiSeq 2500", + "Chromium X", + "Olink Signature Q100", "Xenium", - "BD LSRFortessa", - "Fluidigm BioMark", - "Thermo Fisher Attune Xenith", + "GEM-X OCM 5' Chip", + "Sony MA900", + "BD FACSCanto II", + "BD FACSDiscover S8", "Chromium Controller", - "Visium CytAssist", - "BD FACSAria III", - "Helios Mass Cytometer", - "Illumina HiSeq 2500", + "Fluidigm BioMark", "Illumina NovaSeq X", - "none", + "BD FACSAria III", + "unknown", + "BD LSRFortessa", "Chromium Xo", - "Hyperion", - "Chromium Next GEM Chip K", - "GEM-X OCM 5' Chip", - "BD FACSCanto II", - "Illumina NextSeq 500", + "Cytek Aurora", "Illumina HiSeq X Ten", - "Olink Signature Q100", - "Illumina NovaSeq 6000", + "Thermo Fisher Attune CytPix", + "Chromium Next GEM Chip K", "Thermo Fisher Attune NxT", - "Chromium Next GEM Chip H", - "Chromium iX", - "Cytek Aurora", - "BD FACSCanto", - "unknown", - "Chromium X", - "BD FACSLyric Clinical", - "Cytek Aurora Evo", - "Not Applicable", - "CyTOF XT", + "Visium CytAssist", + "GEM-X Flex Gene Expression Chip", + "BD FACSDiscover A8", + "Chromium Next GEM Chip M", "BD FACSAria Fusion cell sorter", - "BD FACSMelody", - "BD FACSymphony S6", - "Sony MA900", - "Chromium Next GEM Chip Q", - "Thermo Fisher Attune CytPix" + "none", + "Helios Mass Cytometer", + "Thermo Fisher Attune Xenith", + "Cytek Aurora Evo", + "Chromium Next GEM Chip H", + "Chromium GEM-X Single Cell 3' Chip v4" ] }, "maxItems": 43 }, + "alignmentReference": { + "enum": [ + "modified GRCh38", + "10x Cell Ranger Human GRCh38 2024-A", + "unknown", + "vdj_GRCh38_alts_ensembl-4.0.0", + "10x Cell Ranger Human GRCh38 2020-A" + ] + }, + "dataCollectionBatch": {}, "Component": { "not": { "type": "null" }, "minLength": 1 }, - "totalReads": { - "not": { - "type": "null" - }, - "minLength": 1 + "specimenModality": { + "enum": [ + "multispecimen", + "single specimen" + ] }, - "assay": { + "nucleicAcidSource": { "type": "array", "items": { "enum": [ - "Olink Flex", - "Xenium", - "imaging mass spectrometry", - "scVDJSeq", - "Olink Focus", - "imaging mass cytometry", - "snATACSeq", - "Olink Explore HT", - "flow cytometry", - "Olink Reveal", - "RNASeq", - "H&E", - "scRNASeq", - "kiloplex", - "CosMX", - "CyTOF", - "CITESeq", - "snRNASeq", - "Olink Target 48", - "WGS", - "feature barcode sequencing", - "multiplexed ELISA", - "GenePS SeqFISH", - "ASAPSeq", - "NULISA", - "serial IHC", - "SomaScan", - "SNP array", - "Visium", - "LC-MS/MS", - "Olink Target 96", - "CE-MS", - "VDJSeq", - "WES" + "BCR mRNA", + "TCR mRNA", + "antigen capture barcode", + "gDNA", + "globin-depleted RNA", + "intracellular protein feature barcode", + "CRISPR protospacer feature barcode", + "surface protein feature barcode", + "Tn5-accessible gDNA", + "multiplexing oligo", + "poly(A) RNA", + "rRNA-depleted RNA" ] }, - "maxItems": 34 + "maxItems": 12 }, "sampleProcessingBatch": {}, - "dataCollectionBatch": {}, - "libraryPrepMethod": { - "enum": [ - "TruSeq Stranded mRNA", - "10x Chromium Next GEM Single Cell 5' v2", - "Takara Human TCR profiling for Illumina", - "NEBNext Human Immune Sequencing Kit", - "Chromium Next GEM Single Cell ATAC v1.1", - "Takara Human scTCR profiling for Illumina", - "Nextera XT DNA", - "10x GEM-X Universal 5? Gene Expression v3", - "custom DASH-treatment", - "10x Chromium Next GEM Single Cell ATAC v2", - "SMART-Seq Human BCR with UMI", - "QIAseq miRNA Library", - "SMARTer Stranded Total RNA v2", - "10x GEM-X Flex Gene Expression Human", - "10x Chromium GEM-X Single Cell 5' v3", - "10x Chromium Single Cell Human BCR", - "10x Chromium Next GEM Single Cell 5' v1.1", - "10x Chromium Next GEM Single Cell 3'", - "10x Chromium Single Cell Human TCR", - "10x Chromium Fixed RNA Human Transcriptome", - "10x Chromium Next GEM Single Cell 3' 3.1", - "Takara Human TCRv2 profiling for Illumina", - "CEL-Seq2", - "Nextera XT", - "Fluidigm C1 HT", - "SMART-Seq v4 Ultra Low Input RNA", - "SMART-Seq Human TCR with UMI", - "in-house library prep", - "NEBNext Ultra II Directional RNA Library", - "10x Chromium GEM-X Single Cell 3' v4", - "Takara Human BCR profiling for Illumina" - ] - }, - "libraryID": {}, - "biospecimenID": {}, "10xProbeSetReference": { "enum": [ "Flex Human Transcriptome Probe Set v1.0.1", - "Visium Human Transcriptome v2", - "Flex Human Transcriptome Probe Set v1.1.0", "Visium Human Transcriptome v1", "custom probe set", + "Flex Human Transcriptome Probe Set v1.1.0", + "Visium Human Transcriptome v2", "" ] - } + }, + "libraryID": {}, + "biospecimenID": {} }, "required": [ - "alignmentReference", - "specimenModality", - "nucleicAcidSource", - "platform", - "Component", + "libraryPrepMethod", "totalReads", "assay", - "libraryPrepMethod" + "platform", + "alignmentReference", + "Component", + "specimenModality", + "nucleicAcidSource" ], "allOf": [ { "if": { "properties": { - "specimenModality": { + "libraryPrepMethod": { "enum": [ - "multispecimen" + "10x GEM-X Flex Gene Expression Human" ] } }, "required": [ - "specimenModality" + "libraryPrepMethod" ] }, "then": { "properties": { - "libraryID": { - "not": { - "type": "null" - }, - "minLength": 1 + "10xProbeSetReference": { + "enum": [ + "Flex Human Transcriptome Probe Set v1.0.1", + "Visium Human Transcriptome v1", + "custom probe set", + "Flex Human Transcriptome Probe Set v1.1.0", + "Visium Human Transcriptome v2" + ] } }, "required": [ - "libraryID" + "10xProbeSetReference" ] } }, @@ -272,7 +275,7 @@ "properties": { "specimenModality": { "enum": [ - "single specimen" + "multispecimen" ] } }, @@ -282,7 +285,7 @@ }, "then": { "properties": { - "biospecimenID": { + "libraryID": { "not": { "type": "null" }, @@ -290,37 +293,34 @@ } }, "required": [ - "biospecimenID" + "libraryID" ] } }, { "if": { "properties": { - "libraryPrepMethod": { + "specimenModality": { "enum": [ - "10x GEM-X Flex Gene Expression Human" + "single specimen" ] } }, "required": [ - "libraryPrepMethod" + "specimenModality" ] }, "then": { "properties": { - "10xProbeSetReference": { - "enum": [ - "Flex Human Transcriptome Probe Set v1.0.1", - "Visium Human Transcriptome v2", - "Flex Human Transcriptome Probe Set v1.1.0", - "Visium Human Transcriptome v1", - "custom probe set" - ] + "biospecimenID": { + "not": { + "type": "null" + }, + "minLength": 1 } }, "required": [ - "10xProbeSetReference" + "biospecimenID" ] } } diff --git a/model_json_schema/ark.BulkRNA-seqAssayMetadataTemplate.schema.json b/model_json_schema/ark.BulkRNA-seqAssayMetadataTemplate.schema.json index c9de9a9..acecb85 100644 --- a/model_json_schema/ark.BulkRNA-seqAssayMetadataTemplate.schema.json +++ b/model_json_schema/ark.BulkRNA-seqAssayMetadataTemplate.schema.json @@ -4,103 +4,6 @@ "title": "ark", "type": "object", "properties": { - "libraryPrepMethod": { - "enum": [ - "Nextera XT DNA", - "10x Chromium GEM-X Single Cell 5' v3", - "CEL-Seq2", - "Takara Human scTCR profiling for Illumina", - "10x Chromium Next GEM Single Cell 3' 3.1", - "10x Chromium Next GEM Single Cell 5' v1.1", - "10x Chromium GEM-X Single Cell 3' v4", - "Chromium Next GEM Single Cell ATAC v1.1", - "NEBNext Human Immune Sequencing Kit", - "10x Chromium Next GEM Single Cell 5' v2", - "10x Chromium Next GEM Single Cell ATAC v2", - "Takara Human BCR profiling for Illumina", - "Fluidigm C1 HT", - "10x GEM-X Flex Gene Expression Human", - "Takara Human TCRv2 profiling for Illumina", - "10x Chromium Single Cell Human TCR", - "SMART-Seq Human TCR with UMI", - "Takara Human TCR profiling for Illumina", - "SMART-Seq v4 Ultra Low Input RNA", - "10x Chromium Fixed RNA Human Transcriptome", - "Nextera XT", - "QIAseq miRNA Library", - "SMARTer Stranded Total RNA v2", - "10x GEM-X Universal 5? Gene Expression v3", - "10x Chromium Next GEM Single Cell 3'", - "in-house library prep", - "TruSeq Stranded mRNA", - "SMART-Seq Human BCR with UMI", - "NEBNext Ultra II Directional RNA Library", - "10x Chromium Single Cell Human BCR", - "custom DASH-treatment" - ] - }, - "Component": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "softwareAndVersion": { - "enum": [ - "Cell Ranger ATAC v1.1.0", - "Space Ranger 3.0.0", - "Cell Ranger v6.1.1", - "Space Ranger 3.1.2", - "Cell Ranger v5.0.1", - "Cell Ranger v6.1.0", - "Cell Ranger v3.1.0", - "Cell Ranger v6.0.1", - "Cell Ranger v7.1.0", - "Cell Ranger 9.0.1", - "Space Ranger 3.0.1", - "BD FACSDiva 8.0.1", - "Cell Ranger v6.0.2", - "Space Ranger 3.1.1", - "Space Ranger 3.1.3", - "Cell Ranger v9.0.0", - "Cell Ranger v7.0.1", - "Cell Ranger v5.0.0", - "Cell Ranger v3.0.0", - "Cell Ranger v3.0.2", - "Cell Ranger v8.0.0", - "Cell Ranger v6.1.2", - "demuxlet", - "Cell Ranger v7.0.0", - "Cell Ranger v8.0.1", - "Space Ranger 3.1.0", - "Cell Ranger v3.0.1", - "Cell Ranger v6.0.0", - "Cell Ranger v4.0.0", - "Cell Ranger v7.2.0", - "" - ] - }, - "dataCollectionBatch": {}, - "nucleicAcidSource": { - "type": "array", - "items": { - "enum": [ - "BCR mRNA", - "poly(A) RNA", - "rRNA-depleted RNA", - "gDNA", - "multiplexing oligo", - "globin-depleted RNA", - "surface protein feature barcode", - "CRISPR protospacer feature barcode", - "Tn5-accessible gDNA", - "antigen capture barcode", - "TCR mRNA", - "intracellular protein feature barcode" - ] - }, - "maxItems": 12 - }, "totalReads": { "not": { "type": "null" @@ -111,162 +14,256 @@ "type": "array", "items": { "enum": [ - "imaging mass spectrometry", - "SNP array", - "SomaScan", - "VDJSeq", - "multiplexed ELISA", "CyTOF", - "CITESeq", - "ASAPSeq", - "scRNASeq", - "Olink Target 96", - "RNASeq", + "GenePS SeqFISH", + "Olink Flex", "CE-MS", - "LC-MS/MS", + "Visium", "WGS", + "SNP array", + "flow cytometry", "kiloplex", - "Olink Flex", - "Olink Reveal", + "CITESeq", "H&E", + "Olink Reveal", + "scRNASeq", + "imaging mass cytometry", + "snATACSeq", + "LC-MS/MS", + "Olink Focus", "scVDJSeq", - "Olink Explore HT", - "Olink Target 48", - "GenePS SeqFISH", - "feature barcode sequencing", - "flow cytometry", - "serial IHC", "WES", - "CosMX", - "snATACSeq", + "Olink Target 96", + "Olink Explore HT", "snRNASeq", "NULISA", - "Visium", - "Xenium", - "imaging mass cytometry", - "Olink Focus" + "SomaScan", + "serial IHC", + "ASAPSeq", + "multiplexed ELISA", + "Olink Target 48", + "RNASeq", + "imaging mass spectrometry", + "CosMX", + "feature barcode sequencing", + "VDJSeq", + "Xenium" ] }, "maxItems": 34 }, - "sampleProcessingBatch": {}, "alignmentReference": { "enum": [ - "10x Cell Ranger Human GRCh38 2024-A", "unknown", - "modified GRCh38", "10x Cell Ranger Human GRCh38 2020-A", - "vdj_GRCh38_alts_ensembl-4.0.0" + "modified GRCh38", + "vdj_GRCh38_alts_ensembl-4.0.0", + "10x Cell Ranger Human GRCh38 2024-A" ] }, + "Component": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "nucleicAcidSource": { + "type": "array", + "items": { + "enum": [ + "Tn5-accessible gDNA", + "globin-depleted RNA", + "multiplexing oligo", + "gDNA", + "CRISPR protospacer feature barcode", + "antigen capture barcode", + "poly(A) RNA", + "intracellular protein feature barcode", + "BCR mRNA", + "TCR mRNA", + "rRNA-depleted RNA", + "surface protein feature barcode" + ] + }, + "maxItems": 12 + }, "specimenModality": { "enum": [ "single specimen", "multispecimen" ] }, + "libraryPrepMethod": { + "enum": [ + "Nextera XT DNA", + "TruSeq Stranded mRNA", + "10x Chromium Next GEM Single Cell 3'", + "NEBNext Ultra II Directional RNA Library", + "10x Chromium Next GEM Single Cell 5' v2", + "10x GEM-X Universal 5? Gene Expression v3", + "Nextera XT", + "Takara Human TCR profiling for Illumina", + "10x GEM-X Flex Gene Expression Human", + "QIAseq miRNA Library", + "10x Chromium GEM-X Single Cell 5' v3", + "custom DASH-treatment", + "10x Chromium Next GEM Single Cell 5' v1.1", + "NEBNext Human Immune Sequencing Kit", + "Takara Human TCRv2 profiling for Illumina", + "Fluidigm C1 HT", + "10x Chromium GEM-X Single Cell 3' v4", + "CEL-Seq2", + "in-house library prep", + "10x Chromium Single Cell Human TCR", + "SMART-Seq Human BCR with UMI", + "10x Chromium Next GEM Single Cell ATAC v2", + "10x Chromium Next GEM Single Cell 3' 3.1", + "Chromium Next GEM Single Cell ATAC v1.1", + "10x Chromium Single Cell Human BCR", + "SMART-Seq v4 Ultra Low Input RNA", + "SMARTer Stranded Total RNA v2", + "10x Chromium Fixed RNA Human Transcriptome", + "SMART-Seq Human TCR with UMI", + "Takara Human BCR profiling for Illumina", + "Takara Human scTCR profiling for Illumina" + ] + }, + "dataCollectionBatch": {}, + "sampleProcessingBatch": {}, + "softwareAndVersion": { + "enum": [ + "Cell Ranger v6.1.0", + "Cell Ranger v7.1.0", + "Cell Ranger v3.0.0", + "Cell Ranger v7.0.0", + "Cell Ranger v5.0.0", + "BD FACSDiva 8.0.1", + "Space Ranger 3.1.0", + "Cell Ranger 9.0.1", + "Space Ranger 3.1.3", + "Cell Ranger v7.2.0", + "Cell Ranger v8.0.1", + "Cell Ranger v5.0.1", + "demuxlet", + "Cell Ranger v9.0.0", + "Space Ranger 3.1.2", + "Space Ranger 3.0.0", + "Space Ranger 3.0.1", + "Space Ranger 3.1.1", + "Cell Ranger v7.0.1", + "Cell Ranger v6.0.0", + "Cell Ranger v3.1.0", + "Cell Ranger v4.0.0", + "Cell Ranger ATAC v1.1.0", + "Cell Ranger v6.0.1", + "Cell Ranger v6.1.2", + "Cell Ranger v3.0.1", + "Cell Ranger v8.0.0", + "Cell Ranger v6.1.1", + "Cell Ranger v6.0.2", + "Cell Ranger v3.0.2", + "" + ] + }, "platform": { "type": "array", "items": { "enum": [ - "Illumina NovaSeq 6000", - "Chromium Next GEM Chip G", - "none", - "Chromium Next GEM Chip M", - "GEM-X Flex Gene Expression Chip", - "Chromium Next GEM Chip Q", - "Illumina HiSeq X Ten", - "BD FACSCanto II", - "Chromium Controller", - "Illumina NextSeq 500", - "BD LSRFortessa", - "BD FACSCanto", "Chromium Next GEM Chip H", - "Sony MA900", - "Thermo Fisher Attune CytPix", - "Chromium Xo", - "CyTOF XT", - "BD FACSymphony S6", - "BD FACSMelody", + "Olink Signature Q100", "unknown", + "Illumina HiSeq X Ten", + "CyTOF XT", + "Illumina NovaSeq X", + "BD FACSAria III", + "Helios Mass Cytometer", "Thermo Fisher Attune Xenith", - "Thermo Fisher Attune NxT", "Chromium iX", + "Thermo Fisher Attune CytPix", + "Fluidigm BioMark", + "BD FACSAria Fusion cell sorter", + "Chromium GEM-X Single Cell 3' Chip v4", + "Chromium Next GEM Chip Q", + "Chromium X", "Hyperion", + "BD FACSMelody", + "Chromium Xo", + "Cytek Aurora Evo", + "GEM-X Flex Gene Expression Chip", + "Sony MA900", + "BD FACSLyric Clinical", "Illumina HiSeq 2500", "Visium CytAssist", - "Chromium X", - "Helios Mass Cytometer", - "Illumina NovaSeq X", + "BD LSRFortessa", + "BD FACSymphony S6", + "Chromium Next GEM Chip G", + "Chromium Controller", + "BD FACSCanto II", "GEM-X OCM 5' Chip", + "BD FACSCanto", + "Thermo Fisher Attune NxT", "BD FACSDiscover S8", + "Cytek Aurora", "Not Applicable", - "Olink Signature Q100", - "Chromium GEM-X Single Cell 3' Chip v4", - "BD FACSDiscover A8", - "Fluidigm BioMark", - "BD FACSAria Fusion cell sorter", - "BD FACSLyric Clinical", - "BD FACSAria III", + "Illumina NextSeq 500", + "Illumina NovaSeq 6000", + "Chromium Next GEM Chip M", "Chromium Next GEM Chip K", - "Cytek Aurora Evo", - "Cytek Aurora", + "BD FACSDiscover A8", + "none", "Xenium" ] }, "maxItems": 43 }, + "biospecimenID": {}, + "libraryID": {}, "10xProbeSetReference": { "enum": [ - "Visium Human Transcriptome v1", "Flex Human Transcriptome Probe Set v1.0.1", + "Visium Human Transcriptome v1", + "custom probe set", "Visium Human Transcriptome v2", "Flex Human Transcriptome Probe Set v1.1.0", - "custom probe set", "" ] - }, - "biospecimenID": {}, - "libraryID": {} + } }, "required": [ - "libraryPrepMethod", - "Component", - "nucleicAcidSource", "totalReads", "assay", "alignmentReference", + "Component", + "nucleicAcidSource", "specimenModality", + "libraryPrepMethod", "platform" ], "allOf": [ { "if": { "properties": { - "libraryPrepMethod": { + "specimenModality": { "enum": [ - "10x GEM-X Flex Gene Expression Human" + "single specimen" ] } }, "required": [ - "libraryPrepMethod" + "specimenModality" ] }, "then": { "properties": { - "10xProbeSetReference": { - "enum": [ - "Visium Human Transcriptome v1", - "Flex Human Transcriptome Probe Set v1.0.1", - "Visium Human Transcriptome v2", - "Flex Human Transcriptome Probe Set v1.1.0", - "custom probe set" - ] + "biospecimenID": { + "not": { + "type": "null" + }, + "minLength": 1 } }, "required": [ - "10xProbeSetReference" + "biospecimenID" ] } }, @@ -275,7 +272,7 @@ "properties": { "specimenModality": { "enum": [ - "single specimen" + "multispecimen" ] } }, @@ -285,7 +282,7 @@ }, "then": { "properties": { - "biospecimenID": { + "libraryID": { "not": { "type": "null" }, @@ -293,34 +290,37 @@ } }, "required": [ - "biospecimenID" + "libraryID" ] } }, { "if": { "properties": { - "specimenModality": { + "libraryPrepMethod": { "enum": [ - "multispecimen" + "10x GEM-X Flex Gene Expression Human" ] } }, "required": [ - "specimenModality" + "libraryPrepMethod" ] }, "then": { "properties": { - "libraryID": { - "not": { - "type": "null" - }, - "minLength": 1 + "10xProbeSetReference": { + "enum": [ + "Flex Human Transcriptome Probe Set v1.0.1", + "Visium Human Transcriptome v1", + "custom probe set", + "Visium Human Transcriptome v2", + "Flex Human Transcriptome Probe Set v1.1.0" + ] } }, "required": [ - "libraryID" + "10xProbeSetReference" ] } } diff --git a/model_json_schema/ark.ClinicalMetadataTemplate.schema.json b/model_json_schema/ark.ClinicalMetadataTemplate.schema.json index 00e3c96..648e67b 100644 --- a/model_json_schema/ark.ClinicalMetadataTemplate.schema.json +++ b/model_json_schema/ark.ClinicalMetadataTemplate.schema.json @@ -4,52 +4,32 @@ "title": "ark", "type": "object", "properties": { - "diagnosis": { - "type": "array", - "items": { - "enum": [ - "SLE", - "dermatomyositis", - "unknown", - "control", - "Sjogren's disease", - "cutaneous lupus erythematosus", - "scleroderma", - "OA", - "psoriasis", - "At-Risk RA", - "lupus nephritis", - "vitiligo", - "RA", - "psoriatic arthritis" - ] + "individualID": { + "not": { + "type": "null" }, - "maxItems": 14 + "minLength": 1 }, "heightUnits": { "enum": [ - "inches", - "feet", "centimeters", - "meters" + "meters", + "feet", + "inches" ] }, - "individualID": { + "height": { "not": { "type": "null" }, "minLength": 1 }, - "program": { - "enum": [ - "Community Contribution", - "AMP RA/SLE", - "AMP AIM" - ] - }, - "species": { + "weightUnits": { "enum": [ - "Homo sapiens" + "lb", + "kg", + "oz", + "g" ] }, "age": { @@ -58,143 +38,163 @@ }, "minLength": 1 }, - "weight": { - "not": { - "type": "null" + "comorbidities": { + "type": "array", + "items": { + "enum": [ + "Hashimoto's Thyroiditis", + "autoimmune thyroid disease", + "psoriasis", + "cardiovascular disease", + "other", + "multiple sclerosis", + "inflammatory bowel disease", + "psoriatic arthritis", + "pulmonary disease", + "rheumatoid arthritis", + "diabetes", + "systemic lupus erythematosus", + "" + ] }, - "minLength": 1 + "maxItems": 12 }, - "weightUnits": { - "enum": [ - "oz", - "lb", - "kg", - "g" - ] + "diagnosis": { + "type": "array", + "items": { + "enum": [ + "Sjogren's disease", + "OA", + "scleroderma", + "unknown", + "psoriasis", + "dermatomyositis", + "At-Risk RA", + "vitiligo", + "SLE", + "control", + "cutaneous lupus erythematosus", + "psoriatic arthritis", + "lupus nephritis", + "RA" + ] + }, + "maxItems": 14 }, "project": { "type": "array", "items": { "enum": [ + "STAMP", + "AIM for RA", "LOCKIT", "SLE", - "ELLIPSS", - "AIM for RA", "V-CoRT", - "STAMP", + "ELLIPSS", "RA" ] }, "maxItems": 7 }, + "species": { + "enum": [ + "Homo sapiens" + ] + }, + "Component": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "ageUnits": { "enum": [ "years", "months" ] }, + "weight": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "sex": { "enum": [ - "female", - "male", + "unknown", "intersex", - "unknown" + "male", + "female" + ] + }, + "program": { + "enum": [ + "AMP AIM", + "Community Contribution", + "AMP RA/SLE" + ] + }, + "ethnicity": { + "enum": [ + "unknown", + "Hispanic or Latino", + "Not Hispanic or Latino", + "" ] }, "race": { "enum": [ + "White", + "Hispanic", "unknown", "other", - "American Indian or Alaska Native", "Mixed Race", + "American Indian or Alaska Native", "Native Hawaiian or Other Pacific Islander", - "Asian", - "White", - "Hispanic", "Black or African American", + "Asian", "" ] }, - "Component": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "ethnicity": { + "PASI": {}, + "diabetesType": { "enum": [ - "Hispanic or Latino", - "Not Hispanic or Latino", + "type 1", "unknown", + "type 2", + "gestational", "" ] }, - "comorbidities": { - "type": "array", - "items": { - "enum": [ - "rheumatoid arthritis", - "multiple sclerosis", - "other", - "cardiovascular disease", - "Hashimoto's Thyroiditis", - "diabetes", - "autoimmune thyroid disease", - "inflammatory bowel disease", - "psoriasis", - "systemic lupus erythematosus", - "pulmonary disease", - "psoriatic arthritis", - "" - ] - }, - "maxItems": 12 - }, - "height": { - "not": { - "type": "null" - }, - "minLength": 1 - }, "CDASI": {}, - "PASI": {}, + "VASI": {}, + "VIDA": {}, + "VETI": {}, "vitiligoType": { "enum": [ - "unclassified", - "segmental", "non-segmental", + "segmental", "mixed", + "unclassified", "" ] }, - "VASI": {}, - "VETI": {}, - "VIDA": {}, - "visitID": {}, - "diabetesType": { - "enum": [ - "type 1", - "type 2", - "gestational", - "unknown", - "" - ] - } + "visitID": {} }, "required": [ - "diagnosis", - "heightUnits", "individualID", - "program", - "species", - "age", - "weight", + "heightUnits", + "height", "weightUnits", + "age", + "diagnosis", "project", + "species", + "Component", "ageUnits", + "weight", "sex", - "Component", - "height" + "program" ], "allOf": [ { @@ -202,7 +202,7 @@ "properties": { "diagnosis": { "enum": [ - "dermatomyositis" + "psoriasis" ] } }, @@ -212,24 +212,24 @@ }, "then": { "properties": { - "CDASI": {} + "PASI": {} }, "required": [ - "CDASI" + "PASI" ] } }, { "if": { "properties": { - "comorbidities": { + "diagnosis": { "enum": [ "psoriasis" ] } }, "required": [ - "comorbidities" + "diagnosis" ] }, "then": { @@ -244,14 +244,14 @@ { "if": { "properties": { - "comorbidities": { + "diagnosis": { "enum": [ "psoriasis" ] } }, "required": [ - "comorbidities" + "diagnosis" ] }, "then": { @@ -266,14 +266,14 @@ { "if": { "properties": { - "comorbidities": { + "diagnosis": { "enum": [ "psoriasis" ] } }, "required": [ - "comorbidities" + "diagnosis" ] }, "then": { @@ -290,7 +290,7 @@ "properties": { "comorbidities": { "enum": [ - "psoriasis" + "diabetes" ] } }, @@ -300,10 +300,18 @@ }, "then": { "properties": { - "PASI": {} + "diabetesType": { + "enum": [ + "type 1", + "unknown", + "type 2", + "gestational", + "" + ] + } }, "required": [ - "PASI" + "diabetesType" ] } }, @@ -312,7 +320,7 @@ "properties": { "diagnosis": { "enum": [ - "vitiligo" + "dermatomyositis" ] } }, @@ -322,18 +330,10 @@ }, "then": { "properties": { - "vitiligoType": { - "enum": [ - "unclassified", - "segmental", - "non-segmental", - "mixed", - "" - ] - } + "CDASI": {} }, "required": [ - "vitiligoType" + "CDASI" ] } }, @@ -374,10 +374,10 @@ }, "then": { "properties": { - "VETI": {} + "VIDA": {} }, "required": [ - "VETI" + "VIDA" ] } }, @@ -396,37 +396,40 @@ }, "then": { "properties": { - "VIDA": {} + "VETI": {} }, "required": [ - "VIDA" + "VETI" ] } }, { "if": { "properties": { - "program": { + "diagnosis": { "enum": [ - "AMP RA/SLE" + "vitiligo" ] } }, "required": [ - "program" + "diagnosis" ] }, "then": { "properties": { - "visitID": { - "not": { - "type": "null" - }, - "minLength": 1 + "vitiligoType": { + "enum": [ + "non-segmental", + "segmental", + "mixed", + "unclassified", + "" + ] } }, "required": [ - "visitID" + "vitiligoType" ] } }, @@ -460,30 +463,27 @@ { "if": { "properties": { - "comorbidities": { + "program": { "enum": [ - "diabetes" + "AMP RA/SLE" ] } }, "required": [ - "comorbidities" + "program" ] }, "then": { "properties": { - "diabetesType": { - "enum": [ - "type 1", - "type 2", - "gestational", - "unknown", - "" - ] + "visitID": { + "not": { + "type": "null" + }, + "minLength": 1 } }, "required": [ - "diabetesType" + "visitID" ] } } diff --git a/model_json_schema/ark.CyTOFAssayMetadataTemplate.schema.json b/model_json_schema/ark.CyTOFAssayMetadataTemplate.schema.json index cedb4a5..96f21e8 100644 --- a/model_json_schema/ark.CyTOFAssayMetadataTemplate.schema.json +++ b/model_json_schema/ark.CyTOFAssayMetadataTemplate.schema.json @@ -4,131 +4,108 @@ "title": "ark", "type": "object", "properties": { + "targetPanelSynID": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "targetPanel": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "platform": { "type": "array", "items": { "enum": [ - "Illumina NovaSeq X", - "BD FACSDiscover S8", + "Illumina NextSeq 500", + "Chromium Next GEM Chip K", + "Chromium Next GEM Chip M", + "Chromium Controller", "Cytek Aurora", - "BD FACSCanto", - "Chromium Next GEM Chip Q", - "Chromium Next GEM Chip G", "BD FACSAria Fusion cell sorter", - "BD FACSMelody", + "Olink Signature Q100", + "GEM-X Flex Gene Expression Chip", + "Illumina NovaSeq 6000", + "BD FACSDiscover S8", + "Thermo Fisher Attune CytPix", + "BD FACSCanto II", + "Chromium GEM-X Single Cell 3' Chip v4", "BD FACSymphony S6", - "Xenium", - "Chromium Next GEM Chip M", "Cytek Aurora Evo", - "Illumina NextSeq 500", "Chromium Next GEM Chip H", - "Chromium GEM-X Single Cell 3' Chip v4", - "Chromium Xo", - "Helios Mass Cytometer", - "GEM-X Flex Gene Expression Chip", - "Sony MA900", - "Olink Signature Q100", - "Hyperion", - "Visium CytAssist", + "Chromium Next GEM Chip Q", + "Thermo Fisher Attune NxT", + "BD FACSDiscover A8", + "Illumina NovaSeq X", + "BD FACSLyric Clinical", "BD LSRFortessa", - "GEM-X OCM 5' Chip", - "BD FACSCanto II", - "Illumina HiSeq X Ten", + "BD FACSMelody", + "Hyperion", + "unknown", + "Helios Mass Cytometer", "Chromium X", - "Illumina NovaSeq 6000", - "Thermo Fisher Attune CytPix", - "Chromium Next GEM Chip K", "Fluidigm BioMark", - "Thermo Fisher Attune Xenith", "CyTOF XT", + "Not Applicable", + "GEM-X OCM 5' Chip", "none", - "BD FACSDiscover A8", - "unknown", - "Chromium Controller", "BD FACSAria III", - "BD FACSLyric Clinical", - "Chromium iX", - "Thermo Fisher Attune NxT", + "Illumina HiSeq X Ten", "Illumina HiSeq 2500", - "Not Applicable" + "Xenium", + "Chromium Next GEM Chip G", + "Chromium iX", + "Sony MA900", + "Chromium Xo", + "BD FACSCanto", + "Thermo Fisher Attune Xenith", + "Visium CytAssist" ] }, "maxItems": 43 }, - "targetPanelSize": {}, - "softwareAndVersion": { - "enum": [ - "Cell Ranger v9.0.0", - "Space Ranger 3.1.0", - "Cell Ranger v3.0.1", - "Cell Ranger v6.1.1", - "Cell Ranger v7.0.1", - "Cell Ranger ATAC v1.1.0", - "Cell Ranger v8.0.0", - "Cell Ranger v7.1.0", - "Cell Ranger v6.0.1", - "Cell Ranger v6.0.2", - "Cell Ranger v6.0.0", - "Cell Ranger v5.0.1", - "Space Ranger 3.1.1", - "Cell Ranger v6.1.0", - "Cell Ranger v5.0.0", - "Space Ranger 3.1.3", - "Cell Ranger v6.1.2", - "Cell Ranger v7.2.0", - "BD FACSDiva 8.0.1", - "Space Ranger 3.0.1", - "demuxlet", - "Cell Ranger v3.0.0", - "Cell Ranger 9.0.1", - "Cell Ranger v7.0.0", - "Cell Ranger v3.1.0", - "Space Ranger 3.0.0", - "Space Ranger 3.1.2", - "Cell Ranger v3.0.2", - "Cell Ranger v4.0.0", - "Cell Ranger v8.0.1", - "" - ] - }, + "dataCollectionBatch": {}, "assay": { "type": "array", "items": { "enum": [ - "CE-MS", - "WES", - "snATACSeq", - "kiloplex", + "imaging mass cytometry", "CyTOF", - "serial IHC", - "VDJSeq", - "GenePS SeqFISH", - "Olink Reveal", - "Olink Flex", + "Olink Target 96", "SomaScan", - "SNP array", + "CE-MS", + "H&E", + "WGS", + "imaging mass spectrometry", + "Olink Target 48", + "NULISA", + "serial IHC", + "WES", "Olink Explore HT", - "Xenium", - "ASAPSeq", - "CITESeq", - "multiplexed ELISA", - "Olink Target 96", "Olink Focus", - "feature barcode sequencing", + "CITESeq", + "CosMX", + "scRNASeq", "snRNASeq", "RNASeq", - "Visium", - "scVDJSeq", + "ASAPSeq", + "Olink Flex", + "snATACSeq", + "GenePS SeqFISH", + "SNP array", "LC-MS/MS", - "imaging mass spectrometry", - "NULISA", - "scRNASeq", - "Olink Target 48", - "CosMX", - "H&E", - "imaging mass cytometry", + "scVDJSeq", + "multiplexed ELISA", + "feature barcode sequencing", + "kiloplex", + "Olink Reveal", "flow cytometry", - "WGS" + "Xenium", + "VDJSeq", + "Visium" ] }, "maxItems": 34 @@ -139,33 +116,56 @@ }, "minLength": 1 }, - "sampleProcessingBatch": {}, - "biospecimenID": { - "not": { - "type": "null" - }, - "minLength": 1 + "softwareAndVersion": { + "enum": [ + "Cell Ranger v9.0.0", + "Cell Ranger v3.0.1", + "Space Ranger 3.0.1", + "Cell Ranger v6.0.0", + "Cell Ranger v6.0.2", + "demuxlet", + "Cell Ranger v7.1.0", + "Cell Ranger 9.0.1", + "Cell Ranger v3.0.2", + "Space Ranger 3.0.0", + "Space Ranger 3.1.2", + "Cell Ranger v5.0.0", + "Space Ranger 3.1.0", + "Cell Ranger v7.0.1", + "Cell Ranger v7.2.0", + "Cell Ranger v6.1.1", + "Cell Ranger v8.0.0", + "Cell Ranger v3.1.0", + "Space Ranger 3.1.1", + "Cell Ranger v6.0.1", + "Cell Ranger v3.0.0", + "Cell Ranger v4.0.0", + "Cell Ranger v6.1.0", + "Cell Ranger v8.0.1", + "BD FACSDiva 8.0.1", + "Cell Ranger ATAC v1.1.0", + "Cell Ranger v6.1.2", + "Cell Ranger v5.0.1", + "Cell Ranger v7.0.0", + "Space Ranger 3.1.3", + "" + ] }, - "targetPanelSynID": { + "biospecimenID": { "not": { "type": "null" }, "minLength": 1 }, - "dataCollectionBatch": {}, - "targetPanel": { - "not": { - "type": "null" - }, - "minLength": 1 - } + "targetPanelSize": {}, + "sampleProcessingBatch": {} }, "required": [ + "targetPanelSynID", + "targetPanel", "platform", "assay", "Component", - "biospecimenID", - "targetPanelSynID", - "targetPanel" + "biospecimenID" ] } \ No newline at end of file diff --git a/model_json_schema/ark.DatasetAnnotationTemplate.schema.json b/model_json_schema/ark.DatasetAnnotationTemplate.schema.json index 70d803e..16a1ed6 100644 --- a/model_json_schema/ark.DatasetAnnotationTemplate.schema.json +++ b/model_json_schema/ark.DatasetAnnotationTemplate.schema.json @@ -4,80 +4,74 @@ "title": "ark", "type": "object", "properties": { - "associatedCodeURL": {}, + "Component": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "datasetType": { "enum": [ "publication", "experimental" ] }, - "ImmPortAccession": {}, - "project": { + "diagnosis": { "type": "array", "items": { "enum": [ - "V-CoRT", - "ELLIPSS", - "SLE", + "OA", "RA", - "LOCKIT", - "AIM for RA", - "STAMP" + "control", + "cutaneous lupus erythematosus", + "psoriatic arthritis", + "scleroderma", + "SLE", + "lupus nephritis", + "At-Risk RA", + "Sjogren's disease", + "vitiligo", + "psoriasis", + "dermatomyositis", + "unknown" ] }, - "maxItems": 7 - }, - "biospecimenSubtype": { - "enum": [ - "nuclei suspension", - "flow-sorted cells", - "fresh tissue", - "supernatant", - "PFA-fixed tissue", - "cell or tissue lysate", - "frozen tissue", - "cell suspension", - "FFPE tissue", - "" - ] - }, - "publicationSynID": {}, - "dbGapAccession": {}, - "species": { - "enum": [ - "Homo sapiens" - ] + "maxItems": 14 }, - "acknowledgmentStatement": { + "datasetStatus": { "enum": [ - "syn26710600/wiki/619685" + "deprecated", + "released", + "unreleased", + "test", + "under peer review" ] }, "biospecimenType": { "type": "array", "items": { "enum": [ - "none", - "skin biopsy", + "synovial tissue", + "urine", + "primary cell culture", "suction blister cells", + "skin biopsy", "salivary gland", - "suction blister fluid", - "fibroblast-like synoviocyte", - "primary cell culture", - "saliva", - "PBMCs", "serum", - "stool", - "plasma", - "skin swab", "kidney biopsy", - "total leukocytes", - "cell line", - "synovial tissue", "uvea", + "cell line", + "fibroblast-like synoviocyte", + "skin swab", + "none", + "plasma", "whole blood", - "urine", - "synovial fluid" + "synovial fluid", + "PBMCs", + "suction blister fluid", + "stool", + "total leukocytes", + "saliva" ] }, "maxItems": 21 @@ -86,153 +80,159 @@ "type": "array", "items": { "enum": [ - "NULISA", - "CITESeq", - "SNP array", + "WGS", + "CE-MS", + "Xenium", + "SomaScan", + "Olink Target 96", "VDJSeq", - "snRNASeq", "imaging mass cytometry", + "WES", + "kiloplex", + "scRNASeq", + "imaging mass spectrometry", + "snRNASeq", + "Olink Reveal", "RNASeq", - "CyTOF", - "H&E", "scVDJSeq", - "Olink Reveal", - "multiplexed ELISA", - "Visium", - "Xenium", - "snATACSeq", + "flow cytometry", + "CITESeq", + "NULISA", "feature barcode sequencing", - "scRNASeq", - "Olink Flex", - "Olink Explore HT", - "CE-MS", "CosMX", - "ASAPSeq", - "WGS", + "H&E", + "CyTOF", + "multiplexed ELISA", + "Olink Focus", "serial IHC", - "flow cytometry", + "snATACSeq", "GenePS SeqFISH", - "imaging mass spectrometry", - "LC-MS/MS", - "kiloplex", + "Olink Flex", + "ASAPSeq", "Olink Target 48", - "WES", - "Olink Focus", - "SomaScan", - "Olink Target 96" + "Visium", + "Olink Explore HT", + "LC-MS/MS", + "SNP array" ] }, "maxItems": 34 }, - "program": { - "enum": [ - "AMP AIM", - "AMP RA/SLE", - "Community Contribution" - ] - }, "datasetDescription": { "not": { "type": "null" }, "minLength": 1 }, - "associatedDataset": {}, - "Component": { - "not": { - "type": "null" - }, - "minLength": 1 + "acknowledgmentStatement": { + "enum": [ + "syn26710600/wiki/619685" + ] }, - "diagnosis": { - "type": "array", - "items": { - "enum": [ - "psoriasis", - "lupus nephritis", - "control", - "dermatomyositis", - "At-Risk RA", - "SLE", - "RA", - "unknown", - "Sjogren's disease", - "OA", - "psoriatic arthritis", - "scleroderma", - "vitiligo", - "cutaneous lupus erythematosus" - ] - }, - "maxItems": 14 + "biospecimenSubtype": { + "enum": [ + "nuclei suspension", + "FFPE tissue", + "fresh tissue", + "PFA-fixed tissue", + "flow-sorted cells", + "cell suspension", + "supernatant", + "cell or tissue lysate", + "frozen tissue", + "" + ] }, - "datasetStatus": { + "dbGapAccession": {}, + "species": { "enum": [ - "unreleased", - "under peer review", - "released", - "deprecated", - "test" + "Homo sapiens" ] }, + "associatedCodeURL": {}, "dataType": { "type": "array", "items": { "enum": [ + "transcriptomics", + "lipidomics", "cytometry", - "metabolomics", - "immunostaining", - "proteomics", - "multimodal", "epigenomics", - "lipidomics", - "immune repertoire profiling", - "histology", + "proteomics", "microbiome", "genomics", - "transcriptomics" + "immune repertoire profiling", + "multimodal", + "immunostaining", + "histology", + "metabolomics" ] }, "maxItems": 12 }, - "dataSubtype": { + "publicationSynID": {}, + "project": { "type": "array", "items": { "enum": [ - "none", - "pseudobulk", - "single-nucleus", - "spatial", - "single-cell", - "bulk" + "RA", + "LOCKIT", + "V-CoRT", + "SLE", + "ELLIPSS", + "STAMP", + "AIM for RA" ] }, - "maxItems": 6 + "maxItems": 7 }, + "program": { + "enum": [ + "Community Contribution", + "AMP AIM", + "AMP RA/SLE" + ] + }, + "associatedDataset": {}, "ARKRelease": { "enum": [ - "2025.07.R1", - "2025.02.R1", + "2024.07.R1", "2024.08.R1", - "1.0", - "2024.12.R1", - "2025.05.R1", - "2024.10.R1", - "2025.04.R1", - "2025.09.R1", - "2025.01.R1", - "2024.06.R1", - "2025.12.R1", - "2024.09.R1", + "2.0", "2025.08.R1", "2025.06.R1", - "2025.10.R1", - "2024.07.R1", + "2024.06.R1", + "2025.09.R1", "2025.03.R1", - "2.0", - "2025.11.R1" + "2025.07.R1", + "2025.05.R1", + "2025.11.R1", + "2024.12.R1", + "2025.01.R1", + "1.0", + "2025.10.R1", + "2025.02.R1", + "2025.04.R1", + "2024.10.R1", + "2024.09.R1", + "2025.12.R1" ] }, + "ImmPortAccession": {}, + "dataSubtype": { + "type": "array", + "items": { + "enum": [ + "pseudobulk", + "bulk", + "single-cell", + "single-nucleus", + "none", + "spatial" + ] + }, + "maxItems": 6 + }, "programPhase": { "type": "array", "items": { @@ -246,20 +246,20 @@ } }, "required": [ + "Component", "datasetType", - "project", - "species", - "acknowledgmentStatement", + "diagnosis", + "datasetStatus", "biospecimenType", "assay", - "program", "datasetDescription", - "Component", - "diagnosis", - "datasetStatus", + "acknowledgmentStatement", + "species", "dataType", - "dataSubtype", - "ARKRelease" + "project", + "program", + "ARKRelease", + "dataSubtype" ], "allOf": [ { diff --git a/model_json_schema/ark.FCSFileAnnotationTemplate.schema.json b/model_json_schema/ark.FCSFileAnnotationTemplate.schema.json index edb9672..b739e07 100644 --- a/model_json_schema/ark.FCSFileAnnotationTemplate.schema.json +++ b/model_json_schema/ark.FCSFileAnnotationTemplate.schema.json @@ -6,15 +6,14 @@ "properties": { "specimenModality": { "enum": [ - "multispecimen", - "single specimen" + "single specimen", + "multispecimen" ] }, - "eventCount": {}, - "fileFormat": { + "assay": { "enum": [ - "fcs", - "" + "CyTOF", + "flow cytometry" ] }, "Component": { @@ -23,21 +22,22 @@ }, "minLength": 1 }, - "assay": { + "fileFormat": { "enum": [ - "flow cytometry", - "CyTOF" + "fcs", + "" ] }, - "dataCollectionBatch": {}, - "sampleProcessingBatch": {}, + "eventCount": {}, + "biospecimenID": {}, "individualID": {}, - "biospecimenID": {} + "sampleProcessingBatch": {}, + "dataCollectionBatch": {} }, "required": [ "specimenModality", - "Component", - "assay" + "assay", + "Component" ], "allOf": [ { @@ -45,7 +45,7 @@ "properties": { "specimenModality": { "enum": [ - "multispecimen" + "single specimen" ] } }, @@ -55,10 +55,15 @@ }, "then": { "properties": { - "dataCollectionBatch": {} + "biospecimenID": { + "not": { + "type": "null" + }, + "minLength": 1 + } }, "required": [ - "dataCollectionBatch" + "biospecimenID" ] } }, @@ -67,7 +72,7 @@ "properties": { "specimenModality": { "enum": [ - "multispecimen" + "single specimen" ] } }, @@ -77,10 +82,15 @@ }, "then": { "properties": { - "sampleProcessingBatch": {} + "individualID": { + "not": { + "type": "null" + }, + "minLength": 1 + } }, "required": [ - "sampleProcessingBatch" + "individualID" ] } }, @@ -89,7 +99,7 @@ "properties": { "specimenModality": { "enum": [ - "single specimen" + "multispecimen" ] } }, @@ -99,15 +109,10 @@ }, "then": { "properties": { - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 - } + "sampleProcessingBatch": {} }, "required": [ - "individualID" + "sampleProcessingBatch" ] } }, @@ -116,7 +121,7 @@ "properties": { "specimenModality": { "enum": [ - "single specimen" + "multispecimen" ] } }, @@ -126,15 +131,10 @@ }, "then": { "properties": { - "biospecimenID": { - "not": { - "type": "null" - }, - "minLength": 1 - } + "dataCollectionBatch": {} }, "required": [ - "biospecimenID" + "dataCollectionBatch" ] } } diff --git a/model_json_schema/ark.FastqFileAnnotationTemplate.schema.json b/model_json_schema/ark.FastqFileAnnotationTemplate.schema.json index f6b975a..675a961 100644 --- a/model_json_schema/ark.FastqFileAnnotationTemplate.schema.json +++ b/model_json_schema/ark.FastqFileAnnotationTemplate.schema.json @@ -4,55 +4,55 @@ "title": "ark", "type": "object", "properties": { - "Component": { - "not": { - "type": "null" - }, - "minLength": 1 - }, + "readLength": {}, "assay": { "type": "array", "items": { "enum": [ - "snRNASeq", - "WGS", - "WES", + "scVDJSeq", "feature barcode sequencing", - "CITESeq", + "WGS", "VDJSeq", - "scVDJSeq", + "CITESeq", + "WES", "RNASeq", "ASAPSeq", - "scRNASeq", - "snATACSeq" + "snATACSeq", + "snRNASeq", + "scRNASeq" ] }, "maxItems": 11 }, - "specimenModality": { + "fileFormat": { "enum": [ - "single specimen", - "multispecimen" + "fastq" ] }, - "fileFormat": { + "Component": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "specimenModality": { "enum": [ - "fastq" + "single specimen", + "multispecimen" ] }, - "readLength": {}, + "targetPanel": {}, "targetPanelSynID": {}, "targetPanelSize": {}, - "targetPanel": {}, "biospecimenID": {}, "individualID": {}, "libraryID": {} }, "required": [ - "Component", "assay", - "specimenModality", - "fileFormat" + "fileFormat", + "Component", + "specimenModality" ], "allOf": [ { @@ -70,7 +70,7 @@ }, "then": { "properties": { - "targetPanelSynID": { + "targetPanel": { "not": { "type": "null" }, @@ -78,7 +78,7 @@ } }, "required": [ - "targetPanelSynID" + "targetPanel" ] } }, @@ -97,10 +97,15 @@ }, "then": { "properties": { - "targetPanelSize": {} + "targetPanelSynID": { + "not": { + "type": "null" + }, + "minLength": 1 + } }, "required": [ - "targetPanelSize" + "targetPanelSynID" ] } }, @@ -119,15 +124,10 @@ }, "then": { "properties": { - "targetPanel": { - "not": { - "type": "null" - }, - "minLength": 1 - } + "targetPanelSize": {} }, "required": [ - "targetPanel" + "targetPanelSize" ] } }, diff --git a/model_json_schema/ark.InVitroBiospecimenMetadataTemplate.schema.json b/model_json_schema/ark.InVitroBiospecimenMetadataTemplate.schema.json index 4954345..38d321c 100644 --- a/model_json_schema/ark.InVitroBiospecimenMetadataTemplate.schema.json +++ b/model_json_schema/ark.InVitroBiospecimenMetadataTemplate.schema.json @@ -4,14 +4,12 @@ "title": "ark", "type": "object", "properties": { - "individualID": {}, "treatment": { "not": { "type": "null" }, "minLength": 1 }, - "altSampleID": {}, "project": { "type": "array", "items": { @@ -19,212 +17,202 @@ "STAMP", "V-CoRT", "AIM for RA", - "LOCKIT", + "ELLIPSS", "RA", - "SLE", - "ELLIPSS" + "LOCKIT", + "SLE" ] }, "maxItems": 7 }, - "notes": {}, "biospecimenID": { "not": { "type": "null" }, "minLength": 1 }, - "program": { - "enum": [ - "Community Contribution", - "AMP AIM", - "AMP RA/SLE" - ] - }, + "notes": {}, + "parentBiospecimenID": {}, + "altSampleID": {}, "Component": { "not": { "type": "null" }, "minLength": 1 }, - "parentBiospecimenID": {}, "biospecimenType": { "enum": [ - "suction blister cells", - "uvea", - "skin biopsy", - "urine", - "cell line", - "none", - "PBMCs", - "synovial tissue", - "synovial fluid", - "kidney biopsy", - "serum", + "total leukocytes", "whole blood", - "fibroblast-like synoviocyte", - "skin swab", - "stool", "saliva", + "synovial tissue", + "fibroblast-like synoviocyte", + "serum", "primary cell culture", - "suction blister fluid", - "total leukocytes", + "kidney biopsy", + "uvea", + "skin swab", + "synovial fluid", + "urine", + "salivary gland", "plasma", - "salivary gland" + "suction blister cells", + "PBMCs", + "skin biopsy", + "none", + "suction blister fluid", + "cell line", + "stool" ] }, + "individualID": {}, "biospecimenSubtype": { "enum": [ - "PFA-fixed tissue", "nuclei suspension", + "supernatant", + "frozen tissue", "cell suspension", + "cell or tissue lysate", "FFPE tissue", + "PFA-fixed tissue", "flow-sorted cells", "fresh tissue", - "supernatant", - "cell or tissue lysate", - "frozen tissue", "" ] }, "treatmentTimepoint": {}, - "plateID": { - "not": { - "type": "null" - }, - "minLength": 1 + "program": { + "enum": [ + "AMP RA/SLE", + "Community Contribution", + "AMP AIM" + ] }, - "visitID": {}, + "salivaCollectionProcedure": { + "enum": [ + "stimulated", + "unstimulated", + "" + ] + }, + "krennLining": {}, + "krennSynovitisScore": {}, + "krennInflammatory": {}, "anatomicalSite": { "enum": [ - "left wrist joint", - "left 2nd MCP joint", + "right 3rd MCP joint", "right 2nd MTP joint", - "left hip joint", - "unknown", "left ankle joint", "right ankle joint", - "right wrist joint", + "unknown", "left knee joint", + "left wrist joint", + "right 2nd MCP joint", + "right knee joint", + "left hip joint", "other site", - "right hip joint", + "left 2nd MCP joint", "right 1st MTP joint", - "right 3rd MCP joint", - "right knee joint", - "right 2nd MCP joint", - "" - ] - }, - "skinSiteStatus": { - "enum": [ - "healthy control", - "lesional", - "lesional proximal", - "non-lesional", + "right hip joint", + "right wrist joint", "" ] }, - "cellOntologyID": {}, - "cellType": {}, - "krennLining": {}, - "krennSynovitisScore": {}, "krennStroma": {}, "synovialCollectionProcedure": { "enum": [ "arthroplasty", - "biopsy", "synovectomy", "unknown", + "biopsy", "" ] }, - "krennInflammatory": {}, - "salivaCollectionProcedure": { - "enum": [ - "unstimulated", - "stimulated", - "" - ] - }, + "cellType": {}, + "cellOntologyID": {}, "primaryCellSource": { "enum": [ + "uvea", "PBMCs", - "synovial tissue", - "kidney", - "whole blood", "total leukocytes", - "uvea", - "salivary gland", - "urine", + "whole blood", "pannus-derived epidermis", + "urine", + "kidney", + "synovial tissue", "pannus-derived dermis", + "salivary gland", + "" + ] + }, + "skinSiteStatus": { + "enum": [ + "lesional", + "non-lesional", + "healthy control", + "lesional proximal", "" ] }, "userDefinedCellType": {}, - "FACSPopulation": {} + "FACSPopulation": {}, + "visitID": {} }, "required": [ "treatment", "project", "biospecimenID", - "program", "Component", "biospecimenType", - "plateID" + "program" ], "allOf": [ { "if": { "properties": { - "program": { + "biospecimenType": { "enum": [ - "AMP AIM" + "saliva" ] } }, "required": [ - "program" + "biospecimenType" ] }, "then": { "properties": { - "visitID": { - "not": { - "type": "null" - }, - "minLength": 1 + "salivaCollectionProcedure": { + "enum": [ + "stimulated", + "unstimulated" + ] } }, "required": [ - "visitID" + "salivaCollectionProcedure" ] } }, { "if": { "properties": { - "program": { + "biospecimenType": { "enum": [ - "AMP RA/SLE" + "synovial tissue" ] } }, "required": [ - "program" + "biospecimenType" ] }, "then": { "properties": { - "visitID": { - "not": { - "type": "null" - }, - "minLength": 1 - } + "krennLining": {} }, "required": [ - "visitID" + "krennLining" ] } }, @@ -233,7 +221,7 @@ "properties": { "biospecimenType": { "enum": [ - "suction blister cells" + "synovial tissue" ] } }, @@ -243,28 +231,32 @@ }, "then": { "properties": { - "anatomicalSite": { + "krennSynovitisScore": {} + }, + "required": [ + "krennSynovitisScore" + ] + } + }, + { + "if": { + "properties": { + "biospecimenType": { "enum": [ - "left wrist joint", - "left 2nd MCP joint", - "right 2nd MTP joint", - "left hip joint", - "unknown", - "left ankle joint", - "right ankle joint", - "right wrist joint", - "left knee joint", - "other site", - "right hip joint", - "right 1st MTP joint", - "right 3rd MCP joint", - "right knee joint", - "right 2nd MCP joint" + "synovial tissue" ] } }, "required": [ - "anatomicalSite" + "biospecimenType" + ] + }, + "then": { + "properties": { + "krennInflammatory": {} + }, + "required": [ + "krennInflammatory" ] } }, @@ -273,7 +265,7 @@ "properties": { "biospecimenType": { "enum": [ - "skin biopsy" + "synovial tissue" ] } }, @@ -285,21 +277,21 @@ "properties": { "anatomicalSite": { "enum": [ - "left wrist joint", - "left 2nd MCP joint", + "right 3rd MCP joint", "right 2nd MTP joint", - "left hip joint", - "unknown", "left ankle joint", "right ankle joint", - "right wrist joint", + "unknown", "left knee joint", + "left wrist joint", + "right 2nd MCP joint", + "right knee joint", + "left hip joint", "other site", - "right hip joint", + "left 2nd MCP joint", "right 1st MTP joint", - "right 3rd MCP joint", - "right knee joint", - "right 2nd MCP joint" + "right hip joint", + "right wrist joint" ] } }, @@ -313,7 +305,7 @@ "properties": { "biospecimenType": { "enum": [ - "synovial tissue" + "skin swab" ] } }, @@ -325,21 +317,21 @@ "properties": { "anatomicalSite": { "enum": [ - "left wrist joint", - "left 2nd MCP joint", + "right 3rd MCP joint", "right 2nd MTP joint", - "left hip joint", - "unknown", "left ankle joint", "right ankle joint", - "right wrist joint", + "unknown", "left knee joint", + "left wrist joint", + "right 2nd MCP joint", + "right knee joint", + "left hip joint", "other site", - "right hip joint", + "left 2nd MCP joint", "right 1st MTP joint", - "right 3rd MCP joint", - "right knee joint", - "right 2nd MCP joint" + "right hip joint", + "right wrist joint" ] } }, @@ -365,21 +357,21 @@ "properties": { "anatomicalSite": { "enum": [ - "left wrist joint", - "left 2nd MCP joint", + "right 3rd MCP joint", "right 2nd MTP joint", - "left hip joint", - "unknown", "left ankle joint", "right ankle joint", - "right wrist joint", + "unknown", "left knee joint", + "left wrist joint", + "right 2nd MCP joint", + "right knee joint", + "left hip joint", "other site", - "right hip joint", + "left 2nd MCP joint", "right 1st MTP joint", - "right 3rd MCP joint", - "right knee joint", - "right 2nd MCP joint" + "right hip joint", + "right wrist joint" ] } }, @@ -393,7 +385,7 @@ "properties": { "biospecimenType": { "enum": [ - "skin swab" + "suction blister cells" ] } }, @@ -405,21 +397,21 @@ "properties": { "anatomicalSite": { "enum": [ - "left wrist joint", - "left 2nd MCP joint", + "right 3rd MCP joint", "right 2nd MTP joint", - "left hip joint", - "unknown", "left ankle joint", "right ankle joint", - "right wrist joint", + "unknown", "left knee joint", + "left wrist joint", + "right 2nd MCP joint", + "right knee joint", + "left hip joint", "other site", - "right hip joint", + "left 2nd MCP joint", "right 1st MTP joint", - "right 3rd MCP joint", - "right knee joint", - "right 2nd MCP joint" + "right hip joint", + "right wrist joint" ] } }, @@ -433,7 +425,7 @@ "properties": { "biospecimenType": { "enum": [ - "suction blister fluid" + "skin biopsy" ] } }, @@ -445,21 +437,21 @@ "properties": { "anatomicalSite": { "enum": [ - "left wrist joint", - "left 2nd MCP joint", + "right 3rd MCP joint", "right 2nd MTP joint", - "left hip joint", - "unknown", "left ankle joint", "right ankle joint", - "right wrist joint", + "unknown", "left knee joint", + "left wrist joint", + "right 2nd MCP joint", + "right knee joint", + "left hip joint", "other site", - "right hip joint", + "left 2nd MCP joint", "right 1st MTP joint", - "right 3rd MCP joint", - "right knee joint", - "right 2nd MCP joint" + "right hip joint", + "right wrist joint" ] } }, @@ -473,7 +465,7 @@ "properties": { "biospecimenType": { "enum": [ - "suction blister cells" + "suction blister fluid" ] } }, @@ -483,17 +475,28 @@ }, "then": { "properties": { - "skinSiteStatus": { + "anatomicalSite": { "enum": [ - "healthy control", - "lesional", - "lesional proximal", - "non-lesional" + "right 3rd MCP joint", + "right 2nd MTP joint", + "left ankle joint", + "right ankle joint", + "unknown", + "left knee joint", + "left wrist joint", + "right 2nd MCP joint", + "right knee joint", + "left hip joint", + "other site", + "left 2nd MCP joint", + "right 1st MTP joint", + "right hip joint", + "right wrist joint" ] } }, "required": [ - "skinSiteStatus" + "anatomicalSite" ] } }, @@ -502,7 +505,7 @@ "properties": { "biospecimenType": { "enum": [ - "skin biopsy" + "synovial tissue" ] } }, @@ -512,17 +515,10 @@ }, "then": { "properties": { - "skinSiteStatus": { - "enum": [ - "healthy control", - "lesional", - "lesional proximal", - "non-lesional" - ] - } + "krennStroma": {} }, "required": [ - "skinSiteStatus" + "krennStroma" ] } }, @@ -531,7 +527,7 @@ "properties": { "biospecimenType": { "enum": [ - "skin swab" + "synovial tissue" ] } }, @@ -541,17 +537,17 @@ }, "then": { "properties": { - "skinSiteStatus": { + "synovialCollectionProcedure": { "enum": [ - "healthy control", - "lesional", - "lesional proximal", - "non-lesional" + "arthroplasty", + "synovectomy", + "unknown", + "biopsy" ] } }, "required": [ - "skinSiteStatus" + "synovialCollectionProcedure" ] } }, @@ -560,7 +556,7 @@ "properties": { "biospecimenType": { "enum": [ - "suction blister fluid" + "synovial fluid" ] } }, @@ -570,17 +566,17 @@ }, "then": { "properties": { - "skinSiteStatus": { + "synovialCollectionProcedure": { "enum": [ - "healthy control", - "lesional", - "lesional proximal", - "non-lesional" + "arthroplasty", + "synovectomy", + "unknown", + "biopsy" ] } }, "required": [ - "skinSiteStatus" + "synovialCollectionProcedure" ] } }, @@ -589,7 +585,7 @@ "properties": { "biospecimenType": { "enum": [ - "cell line" + "primary cell culture" ] } }, @@ -599,10 +595,10 @@ }, "then": { "properties": { - "cellOntologyID": {} + "cellType": {} }, "required": [ - "cellOntologyID" + "cellType" ] } }, @@ -611,7 +607,7 @@ "properties": { "biospecimenType": { "enum": [ - "primary cell culture" + "cell line" ] } }, @@ -621,10 +617,10 @@ }, "then": { "properties": { - "cellOntologyID": {} + "cellType": {} }, "required": [ - "cellOntologyID" + "cellType" ] } }, @@ -643,10 +639,10 @@ }, "then": { "properties": { - "cellOntologyID": {} + "cellType": {} }, "required": [ - "cellOntologyID" + "cellType" ] } }, @@ -665,10 +661,10 @@ }, "then": { "properties": { - "cellOntologyID": {} + "cellType": {} }, "required": [ - "cellOntologyID" + "cellType" ] } }, @@ -677,7 +673,7 @@ "properties": { "biospecimenType": { "enum": [ - "cell line" + "primary cell culture" ] } }, @@ -687,10 +683,10 @@ }, "then": { "properties": { - "cellType": {} + "cellOntologyID": {} }, "required": [ - "cellType" + "cellOntologyID" ] } }, @@ -699,7 +695,7 @@ "properties": { "biospecimenType": { "enum": [ - "primary cell culture" + "cell line" ] } }, @@ -709,10 +705,10 @@ }, "then": { "properties": { - "cellType": {} + "cellOntologyID": {} }, "required": [ - "cellType" + "cellOntologyID" ] } }, @@ -731,10 +727,10 @@ }, "then": { "properties": { - "cellType": {} + "cellOntologyID": {} }, "required": [ - "cellType" + "cellOntologyID" ] } }, @@ -753,10 +749,10 @@ }, "then": { "properties": { - "cellType": {} + "cellOntologyID": {} }, "required": [ - "cellType" + "cellOntologyID" ] } }, @@ -765,7 +761,7 @@ "properties": { "biospecimenType": { "enum": [ - "synovial tissue" + "primary cell culture" ] } }, @@ -775,32 +771,23 @@ }, "then": { "properties": { - "krennLining": {} - }, - "required": [ - "krennLining" - ] - } - }, - { - "if": { - "properties": { - "biospecimenType": { + "primaryCellSource": { "enum": [ - "synovial tissue" + "uvea", + "PBMCs", + "total leukocytes", + "whole blood", + "pannus-derived epidermis", + "urine", + "kidney", + "synovial tissue", + "pannus-derived dermis", + "salivary gland" ] } }, "required": [ - "biospecimenType" - ] - }, - "then": { - "properties": { - "krennSynovitisScore": {} - }, - "required": [ - "krennSynovitisScore" + "primaryCellSource" ] } }, @@ -809,7 +796,7 @@ "properties": { "biospecimenType": { "enum": [ - "synovial tissue" + "skin swab" ] } }, @@ -819,10 +806,17 @@ }, "then": { "properties": { - "krennStroma": {} + "skinSiteStatus": { + "enum": [ + "lesional", + "non-lesional", + "healthy control", + "lesional proximal" + ] + } }, "required": [ - "krennStroma" + "skinSiteStatus" ] } }, @@ -831,7 +825,7 @@ "properties": { "biospecimenType": { "enum": [ - "synovial tissue" + "suction blister cells" ] } }, @@ -841,17 +835,17 @@ }, "then": { "properties": { - "synovialCollectionProcedure": { + "skinSiteStatus": { "enum": [ - "arthroplasty", - "biopsy", - "synovectomy", - "unknown" + "lesional", + "non-lesional", + "healthy control", + "lesional proximal" ] } }, "required": [ - "synovialCollectionProcedure" + "skinSiteStatus" ] } }, @@ -860,7 +854,7 @@ "properties": { "biospecimenType": { "enum": [ - "synovial fluid" + "skin biopsy" ] } }, @@ -870,17 +864,17 @@ }, "then": { "properties": { - "synovialCollectionProcedure": { + "skinSiteStatus": { "enum": [ - "arthroplasty", - "biopsy", - "synovectomy", - "unknown" + "lesional", + "non-lesional", + "healthy control", + "lesional proximal" ] } }, "required": [ - "synovialCollectionProcedure" + "skinSiteStatus" ] } }, @@ -889,7 +883,7 @@ "properties": { "biospecimenType": { "enum": [ - "synovial tissue" + "suction blister fluid" ] } }, @@ -899,72 +893,61 @@ }, "then": { "properties": { - "krennInflammatory": {} + "skinSiteStatus": { + "enum": [ + "lesional", + "non-lesional", + "healthy control", + "lesional proximal" + ] + } }, "required": [ - "krennInflammatory" + "skinSiteStatus" ] } }, { "if": { "properties": { - "biospecimenType": { + "biospecimenSubtype": { "enum": [ - "saliva" + "cell suspension" ] } }, "required": [ - "biospecimenType" + "biospecimenSubtype" ] }, "then": { "properties": { - "salivaCollectionProcedure": { - "enum": [ - "unstimulated", - "stimulated" - ] - } + "userDefinedCellType": {} }, "required": [ - "salivaCollectionProcedure" + "userDefinedCellType" ] } }, { "if": { "properties": { - "biospecimenType": { + "biospecimenSubtype": { "enum": [ - "primary cell culture" + "flow-sorted cells" ] } }, "required": [ - "biospecimenType" + "biospecimenSubtype" ] }, "then": { "properties": { - "primaryCellSource": { - "enum": [ - "PBMCs", - "synovial tissue", - "kidney", - "whole blood", - "total leukocytes", - "uvea", - "salivary gland", - "urine", - "pannus-derived epidermis", - "pannus-derived dermis" - ] - } + "userDefinedCellType": {} }, "required": [ - "primaryCellSource" + "userDefinedCellType" ] } }, @@ -973,7 +956,7 @@ "properties": { "biospecimenSubtype": { "enum": [ - "cell suspension" + "flow-sorted cells" ] } }, @@ -983,51 +966,61 @@ }, "then": { "properties": { - "userDefinedCellType": {} + "FACSPopulation": { + "not": { + "type": "null" + }, + "minLength": 1 + } }, "required": [ - "userDefinedCellType" + "FACSPopulation" ] } }, { "if": { "properties": { - "biospecimenSubtype": { + "program": { "enum": [ - "flow-sorted cells" + "AMP RA/SLE" ] } }, "required": [ - "biospecimenSubtype" + "program" ] }, "then": { "properties": { - "userDefinedCellType": {} + "visitID": { + "not": { + "type": "null" + }, + "minLength": 1 + } }, "required": [ - "userDefinedCellType" + "visitID" ] } }, { "if": { "properties": { - "biospecimenSubtype": { + "program": { "enum": [ - "flow-sorted cells" + "AMP AIM" ] } }, "required": [ - "biospecimenSubtype" + "program" ] }, "then": { "properties": { - "FACSPopulation": { + "visitID": { "not": { "type": "null" }, @@ -1035,7 +1028,7 @@ } }, "required": [ - "FACSPopulation" + "visitID" ] } } diff --git a/model_json_schema/ark.OlinkAssayMetadataTemplate.schema.json b/model_json_schema/ark.OlinkAssayMetadataTemplate.schema.json index 93e0034..7727f0f 100644 --- a/model_json_schema/ark.OlinkAssayMetadataTemplate.schema.json +++ b/model_json_schema/ark.OlinkAssayMetadataTemplate.schema.json @@ -4,61 +4,61 @@ "title": "ark", "type": "object", "properties": { - "targetPanelSynID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "plateID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "Component": { - "not": { - "type": "null" - }, - "minLength": 1 - }, "assay": { "enum": [ - "Olink Flex", "Olink Target 48", - "Olink Explore HT", + "Olink Flex", "Olink Focus", + "Olink Explore HT", "Olink Reveal", "Olink Target 96" ] }, - "targetPanel": { + "plateID": { "not": { "type": "null" }, "minLength": 1 }, - "targetPanelSize": {}, "platform": { "type": "array", "items": { "enum": [ - "Illumina NovaSeq 6000", - "Fluidigm BioMark", "Illumina NextSeq 500", + "Illumina NovaSeq 6000", "Olink Signature Q100", + "Fluidigm BioMark", "unknown", "" ] }, "maxItems": 5 + }, + "targetPanelSize": {}, + "targetPanelSynID": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "Component": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "targetPanel": { + "not": { + "type": "null" + }, + "minLength": 1 } }, "required": [ - "targetPanelSynID", + "assay", "plateID", + "targetPanelSynID", "Component", - "assay", "targetPanel" ] } \ No newline at end of file diff --git a/model_json_schema/ark.OlinkFileAnnotationTemplate.schema.json b/model_json_schema/ark.OlinkFileAnnotationTemplate.schema.json index cc43836..3fe37b0 100644 --- a/model_json_schema/ark.OlinkFileAnnotationTemplate.schema.json +++ b/model_json_schema/ark.OlinkFileAnnotationTemplate.schema.json @@ -10,67 +10,67 @@ }, "minLength": 1 }, - "Component": { - "not": { - "type": "null" - }, - "minLength": 1 + "specimenModality": { + "enum": [ + "multispecimen", + "single specimen" + ] }, "resourceType": { "enum": [ "figure", - "code", "metadata", + "code", "experimental data" ] }, + "Component": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "fileFormat": { "enum": [ - "fcs", - "xlsx", - "pdf", - "zip", - "rds", + "fastq", "fam", - "bim", - "h5ad", + "svs", + "bai", + "vcf", + "czi", + "tgz", + "geojson", + "pdf", + "txt", + "tbi", "dose", + "mcd", + "zip", "parquet", - "bed", - "mtx", + "bam", + "h5ad", + "info", + "rec", "xls", + "rds", + "bed", + "csv", "docx", + "mtx", + "fcs", + "h5", "erate", - "info", - "bam", + "xlsx", "tsv", - "txt", - "csv", - "vcf", - "h5", - "rec", - "bai", - "geojson", - "mcd", - "tbi", - "svs", - "czi", - "fastq", - "tgz" - ] - }, - "specimenModality": { - "enum": [ - "single specimen", - "multispecimen" + "bim" ] } }, "required": [ "plateID", - "Component", + "specimenModality", "resourceType", - "fileFormat", - "specimenModality" + "Component", + "fileFormat" ] } \ No newline at end of file diff --git a/model_json_schema/ark.PublicationMetadataTemplate.schema.json b/model_json_schema/ark.PublicationMetadataTemplate.schema.json index 3b205d4..e23d228 100644 --- a/model_json_schema/ark.PublicationMetadataTemplate.schema.json +++ b/model_json_schema/ark.PublicationMetadataTemplate.schema.json @@ -4,17 +4,31 @@ "title": "ark", "type": "object", "properties": { + "program": { + "enum": [ + "AMP RA/SLE", + "AMP AIM", + "Community Contribution" + ] + }, + "associatedDataset": {}, + "title": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "project": { "type": "array", "items": { "enum": [ - "SLE", - "ELLIPSS", - "STAMP", - "LOCKIT", + "RA", "V-CoRT", "AIM for RA", - "RA" + "ELLIPSS", + "LOCKIT", + "SLE", + "STAMP" ] }, "maxItems": 7 @@ -25,58 +39,44 @@ }, "minLength": 1 }, - "DOI": { + "journal": { "not": { "type": "null" }, "minLength": 1 }, - "program": { - "enum": [ - "Community Contribution", - "AMP RA/SLE", - "AMP AIM" - ] - }, "Component": { "not": { "type": "null" }, "minLength": 1 }, - "title": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "associatedDataset": {}, - "PMID": { + "year": { "not": { "type": "null" }, "minLength": 1 }, - "publicationType": { - "enum": [ - "peer-reviewed", - "pre-print", - "correction" - ] - }, - "journal": { + "DOI": { "not": { "type": "null" }, "minLength": 1 }, "PMCID": {}, - "year": { + "PMID": { "not": { "type": "null" }, "minLength": 1 }, + "publicationType": { + "enum": [ + "pre-print", + "correction", + "peer-reviewed" + ] + }, "programPhase": { "type": "array", "items": { @@ -90,16 +90,16 @@ } }, "required": [ + "program", + "title", "project", "publicationDate", - "DOI", - "program", + "journal", "Component", - "title", + "year", + "DOI", "PMID", - "publicationType", - "journal", - "year" + "publicationType" ], "allOf": [ { diff --git a/model_json_schema/ark.ScRNASeqAssayMetadataTemplate.schema.json b/model_json_schema/ark.ScRNASeqAssayMetadataTemplate.schema.json index 23a96d6..b95f558 100644 --- a/model_json_schema/ark.ScRNASeqAssayMetadataTemplate.schema.json +++ b/model_json_schema/ark.ScRNASeqAssayMetadataTemplate.schema.json @@ -4,155 +4,79 @@ "title": "ark", "type": "object", "properties": { - "sampleProcessingBatch": {}, - "platform": { - "type": "array", - "items": { - "enum": [ - "Chromium iX", - "Chromium Next GEM Chip K", - "BD FACSCanto II", - "BD LSRFortessa", - "Chromium Next GEM Chip Q", - "Thermo Fisher Attune NxT", - "Cytek Aurora Evo", - "GEM-X OCM 5' Chip", - "Cytek Aurora", - "BD FACSCanto", - "Hyperion", - "BD FACSymphony S6", - "Chromium X", - "Xenium", - "Helios Mass Cytometer", - "unknown", - "Illumina NextSeq 500", - "none", - "BD FACSMelody", - "Illumina NovaSeq X", - "Chromium Next GEM Chip M", - "Chromium Next GEM Chip G", - "Not Applicable", - "BD FACSDiscover A8", - "Olink Signature Q100", - "Fluidigm BioMark", - "BD FACSLyric Clinical", - "Thermo Fisher Attune Xenith", - "BD FACSAria Fusion cell sorter", - "Illumina HiSeq X Ten", - "Illumina NovaSeq 6000", - "Sony MA900", - "CyTOF XT", - "Chromium Xo", - "Thermo Fisher Attune CytPix", - "Chromium Next GEM Chip H", - "GEM-X Flex Gene Expression Chip", - "Chromium Controller", - "BD FACSDiscover S8", - "BD FACSAria III", - "Chromium GEM-X Single Cell 3' Chip v4", - "Illumina HiSeq 2500", - "Visium CytAssist" - ] - }, - "maxItems": 43 + "specimenModality": { + "enum": [ + "multispecimen", + "single specimen" + ] }, - "dataCollectionBatch": {}, "totalReads": { "not": { "type": "null" }, "minLength": 1 }, - "inputCellCount": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "assay": { + "nucleicAcidSource": { "type": "array", "items": { "enum": [ - "H&E", - "feature barcode sequencing", - "ASAPSeq", - "Olink Flex", - "RNASeq", - "CyTOF", - "CosMX", - "CE-MS", - "WES", - "multiplexed ELISA", - "Xenium", - "SNP array", - "Visium", - "kiloplex", - "snRNASeq", - "CITESeq", - "Olink Focus", - "Olink Target 96", - "scRNASeq", - "imaging mass spectrometry", - "serial IHC", - "Olink Explore HT", - "snATACSeq", - "WGS", - "NULISA", - "imaging mass cytometry", - "LC-MS/MS", - "VDJSeq", - "Olink Reveal", - "SomaScan", - "GenePS SeqFISH", - "scVDJSeq", - "flow cytometry", - "Olink Target 48" + "TCR mRNA", + "surface protein feature barcode", + "CRISPR protospacer feature barcode", + "poly(A) RNA", + "rRNA-depleted RNA", + "multiplexing oligo", + "globin-depleted RNA", + "Tn5-accessible gDNA", + "antigen capture barcode", + "BCR mRNA", + "intracellular protein feature barcode", + "gDNA" ] }, - "maxItems": 34 + "maxItems": 12 }, - "sequencingSaturation": {}, "alignmentReference": { "enum": [ - "modified GRCh38", "vdj_GRCh38_alts_ensembl-4.0.0", - "10x Cell Ranger Human GRCh38 2024-A", "unknown", - "10x Cell Ranger Human GRCh38 2020-A" + "10x Cell Ranger Human GRCh38 2024-A", + "10x Cell Ranger Human GRCh38 2020-A", + "modified GRCh38" ] }, "softwareAndVersion": { "enum": [ - "Cell Ranger v3.1.0", - "Space Ranger 3.1.1", - "Space Ranger 3.1.3", - "Space Ranger 3.0.1", "Cell Ranger v7.1.0", - "Cell Ranger v6.1.1", - "Space Ranger 3.0.0", - "Cell Ranger v6.1.2", - "Cell Ranger v5.0.0", - "Cell Ranger v6.1.0", - "demuxlet", - "Cell Ranger v7.0.0", - "Cell Ranger v7.0.1", - "BD FACSDiva 8.0.1", "Cell Ranger v8.0.0", - "Cell Ranger v5.0.1", - "Cell Ranger v4.0.0", "Space Ranger 3.1.2", - "Cell Ranger v9.0.0", + "Space Ranger 3.0.1", + "Cell Ranger v7.0.1", "Cell Ranger v8.0.1", + "Space Ranger 3.1.3", "Cell Ranger v3.0.0", - "Cell Ranger 9.0.1", - "Cell Ranger v6.0.1", - "Cell Ranger v7.2.0", - "Cell Ranger ATAC v1.1.0", "Cell Ranger v3.0.1", - "Cell Ranger v3.0.2", - "Space Ranger 3.1.0", + "Cell Ranger v4.0.0", + "Cell Ranger v5.0.0", + "Cell Ranger v6.1.0", + "Cell Ranger v5.0.1", "Cell Ranger v6.0.0", + "Space Ranger 3.1.0", + "Cell Ranger v9.0.0", + "Cell Ranger v6.1.2", "Cell Ranger v6.0.2", + "Cell Ranger v3.0.2", + "Cell Ranger v3.1.0", + "Cell Ranger 9.0.1", + "Cell Ranger ATAC v1.1.0", + "Cell Ranger v7.2.0", + "Space Ranger 3.1.1", + "BD FACSDiva 8.0.1", + "Cell Ranger v6.0.1", + "demuxlet", + "Cell Ranger v6.1.1", + "Space Ranger 3.0.0", + "Cell Ranger v7.0.0", "" ] }, @@ -164,124 +88,197 @@ }, "libraryPrepMethod": { "enum": [ - "custom DASH-treatment", - "10x Chromium Next GEM Single Cell ATAC v2", + "10x Chromium Single Cell Human BCR", "10x Chromium Next GEM Single Cell 5' v2", - "10x GEM-X Universal 5? Gene Expression v3", - "Fluidigm C1 HT", - "NEBNext Ultra II Directional RNA Library", "10x Chromium Fixed RNA Human Transcriptome", - "10x Chromium Single Cell Human TCR", + "10x GEM-X Universal 5? Gene Expression v3", + "in-house library prep", + "10x Chromium Next GEM Single Cell 3'", + "Chromium Next GEM Single Cell ATAC v1.1", + "TruSeq Stranded mRNA", + "SMART-Seq Human TCR with UMI", + "Nextera XT DNA", + "custom DASH-treatment", "SMARTer Stranded Total RNA v2", + "QIAseq miRNA Library", + "10x Chromium GEM-X Single Cell 5' v3", + "10x Chromium Single Cell Human TCR", + "SMART-Seq Human BCR with UMI", "Takara Human TCRv2 profiling for Illumina", - "10x Chromium GEM-X Single Cell 3' v4", - "10x Chromium Single Cell Human BCR", + "SMART-Seq v4 Ultra Low Input RNA", "10x Chromium Next GEM Single Cell 3' 3.1", - "Chromium Next GEM Single Cell ATAC v1.1", - "10x Chromium Next GEM Single Cell 3'", + "Takara Human scTCR profiling for Illumina", "NEBNext Human Immune Sequencing Kit", - "10x GEM-X Flex Gene Expression Human", - "in-house library prep", - "10x Chromium GEM-X Single Cell 5' v3", + "Fluidigm C1 HT", "Nextera XT", + "10x GEM-X Flex Gene Expression Human", + "10x Chromium Next GEM Single Cell ATAC v2", + "NEBNext Ultra II Directional RNA Library", "CEL-Seq2", - "TruSeq Stranded mRNA", - "Takara Human scTCR profiling for Illumina", - "SMART-Seq Human TCR with UMI", - "SMART-Seq v4 Ultra Low Input RNA", - "Nextera XT DNA", - "Takara Human TCR profiling for Illumina", - "SMART-Seq Human BCR with UMI", - "QIAseq miRNA Library", "Takara Human BCR profiling for Illumina", + "Takara Human TCR profiling for Illumina", + "10x Chromium GEM-X Single Cell 3' v4", "10x Chromium Next GEM Single Cell 5' v1.1" ] }, + "sampleProcessingBatch": {}, + "dataCollectionBatch": {}, + "platform": { + "type": "array", + "items": { + "enum": [ + "Helios Mass Cytometer", + "Chromium Next GEM Chip K", + "Chromium GEM-X Single Cell 3' Chip v4", + "Visium CytAssist", + "BD FACSymphony S6", + "GEM-X OCM 5' Chip", + "Sony MA900", + "unknown", + "Chromium Controller", + "Chromium Xo", + "Cytek Aurora", + "Chromium Next GEM Chip G", + "Hyperion", + "Illumina HiSeq X Ten", + "Chromium Next GEM Chip Q", + "Cytek Aurora Evo", + "BD FACSDiscover S8", + "Chromium Next GEM Chip M", + "BD FACSDiscover A8", + "GEM-X Flex Gene Expression Chip", + "BD FACSCanto II", + "none", + "Chromium iX", + "Illumina NextSeq 500", + "Illumina NovaSeq X", + "Illumina NovaSeq 6000", + "Not Applicable", + "Thermo Fisher Attune CytPix", + "BD FACSAria Fusion cell sorter", + "BD FACSMelody", + "BD FACSAria III", + "Thermo Fisher Attune NxT", + "Olink Signature Q100", + "Chromium Next GEM Chip H", + "BD FACSCanto", + "Illumina HiSeq 2500", + "CyTOF XT", + "Thermo Fisher Attune Xenith", + "Chromium X", + "BD FACSLyric Clinical", + "Fluidigm BioMark", + "BD LSRFortessa", + "Xenium" + ] + }, + "maxItems": 43 + }, + "inputCellCount": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "percentCellViability": { "not": { "type": "null" }, "minLength": 1 }, - "nucleicAcidSource": { + "assay": { "type": "array", "items": { "enum": [ - "CRISPR protospacer feature barcode", - "TCR mRNA", - "multiplexing oligo", - "gDNA", - "poly(A) RNA", - "antigen capture barcode", - "BCR mRNA", - "globin-depleted RNA", - "Tn5-accessible gDNA", - "rRNA-depleted RNA", - "surface protein feature barcode", - "intracellular protein feature barcode" + "scRNASeq", + "NULISA", + "Olink Reveal", + "VDJSeq", + "WGS", + "Olink Focus", + "Visium", + "GenePS SeqFISH", + "RNASeq", + "Olink Explore HT", + "snRNASeq", + "imaging mass spectrometry", + "SNP array", + "CosMX", + "flow cytometry", + "Olink Target 96", + "H&E", + "SomaScan", + "feature barcode sequencing", + "CITESeq", + "LC-MS/MS", + "CyTOF", + "ASAPSeq", + "WES", + "scVDJSeq", + "serial IHC", + "snATACSeq", + "Olink Flex", + "kiloplex", + "Olink Target 48", + "imaging mass cytometry", + "multiplexed ELISA", + "Xenium", + "CE-MS" ] }, - "maxItems": 12 - }, - "specimenModality": { - "enum": [ - "single specimen", - "multispecimen" - ] + "maxItems": 34 }, + "sequencingSaturation": {}, + "libraryID": {}, + "biospecimenID": {}, "10xProbeSetReference": { "enum": [ - "Visium Human Transcriptome v1", "custom probe set", - "Flex Human Transcriptome Probe Set v1.0.1", "Flex Human Transcriptome Probe Set v1.1.0", "Visium Human Transcriptome v2", + "Visium Human Transcriptome v1", + "Flex Human Transcriptome Probe Set v1.0.1", "" ] - }, - "biospecimenID": {}, - "libraryID": {} + } }, "required": [ - "platform", + "specimenModality", "totalReads", - "inputCellCount", - "assay", + "nucleicAcidSource", "alignmentReference", "Component", "libraryPrepMethod", + "platform", + "inputCellCount", "percentCellViability", - "nucleicAcidSource", - "specimenModality" + "assay" ], "allOf": [ { "if": { "properties": { - "libraryPrepMethod": { + "specimenModality": { "enum": [ - "10x GEM-X Flex Gene Expression Human" + "multispecimen" ] } }, "required": [ - "libraryPrepMethod" + "specimenModality" ] }, "then": { "properties": { - "10xProbeSetReference": { - "enum": [ - "Visium Human Transcriptome v1", - "custom probe set", - "Flex Human Transcriptome Probe Set v1.0.1", - "Flex Human Transcriptome Probe Set v1.1.0", - "Visium Human Transcriptome v2" - ] + "libraryID": { + "not": { + "type": "null" + }, + "minLength": 1 } }, "required": [ - "10xProbeSetReference" + "libraryID" ] } }, @@ -315,27 +312,30 @@ { "if": { "properties": { - "specimenModality": { + "libraryPrepMethod": { "enum": [ - "multispecimen" + "10x GEM-X Flex Gene Expression Human" ] } }, "required": [ - "specimenModality" + "libraryPrepMethod" ] }, "then": { "properties": { - "libraryID": { - "not": { - "type": "null" - }, - "minLength": 1 + "10xProbeSetReference": { + "enum": [ + "custom probe set", + "Flex Human Transcriptome Probe Set v1.1.0", + "Visium Human Transcriptome v2", + "Visium Human Transcriptome v1", + "Flex Human Transcriptome Probe Set v1.0.1" + ] } }, "required": [ - "libraryID" + "10xProbeSetReference" ] } } diff --git a/model_json_schema/ark.ScRNASeqProcessedDataAnnotationTemplate.schema.json b/model_json_schema/ark.ScRNASeqProcessedDataAnnotationTemplate.schema.json index ef8e2f2..c2b1c04 100644 --- a/model_json_schema/ark.ScRNASeqProcessedDataAnnotationTemplate.schema.json +++ b/model_json_schema/ark.ScRNASeqProcessedDataAnnotationTemplate.schema.json @@ -4,32 +4,54 @@ "title": "ark", "type": "object", "properties": { - "fileFormat": { - "enum": [ - "bim", - "bam", - "h5", - "fam", - "tsv", - "tgz", - "txt", - "bed", - "xlsx", - "mtx", - "bai", - "h5ad", - "csv", - "zip", - "xls", - "Rds" - ] + "assay": { + "type": "array", + "items": { + "enum": [ + "CITESeq", + "Olink Focus", + "NULISA", + "Xenium", + "imaging mass spectrometry", + "Olink Target 48", + "snATACSeq", + "CosMX", + "flow cytometry", + "Visium", + "VDJSeq", + "serial IHC", + "multiplexed ELISA", + "WES", + "CyTOF", + "RNASeq", + "Olink Reveal", + "Olink Flex", + "Olink Explore HT", + "SomaScan", + "ASAPSeq", + "SNP array", + "CE-MS", + "GenePS SeqFISH", + "kiloplex", + "scRNASeq", + "LC-MS/MS", + "H&E", + "imaging mass cytometry", + "snRNASeq", + "Olink Target 96", + "WGS", + "scVDJSeq", + "feature barcode sequencing" + ] + }, + "maxItems": 34 }, "dataLevel": { "enum": [ - "4", "1", - "2", "3", + "4", + "2", "5" ] }, @@ -39,86 +61,59 @@ }, "minLength": 1 }, + "cellRangerOutput": { + "enum": [ + "filtered_peak_bc_matrix", + "filtered MEX", + "raw_peak_bc_matrix", + "filtered_feature_bc_matrix", + "raw_feature_bc_matrix", + "Not Applicable", + "raw MEX" + ] + }, "resourceType": { "type": "array", "items": { "enum": [ - "experimental data", - "metadata" + "metadata", + "experimental data" ] }, "maxItems": 2 }, - "specimenModality": { + "fileFormat": { "enum": [ - "single specimen", - "multispecimen" + "bed", + "h5ad", + "zip", + "tsv", + "bam", + "txt", + "h5", + "xlsx", + "Rds", + "fam", + "mtx", + "bim", + "bai", + "tgz", + "csv", + "xls" ] }, - "assay": { - "type": "array", - "items": { - "enum": [ - "WGS", - "scRNASeq", - "scVDJSeq", - "imaging mass cytometry", - "VDJSeq", - "Visium", - "SomaScan", - "kiloplex", - "GenePS SeqFISH", - "SNP array", - "H&E", - "Olink Explore HT", - "CyTOF", - "multiplexed ELISA", - "ASAPSeq", - "CosMX", - "flow cytometry", - "RNASeq", - "snATACSeq", - "CE-MS", - "feature barcode sequencing", - "Olink Target 96", - "Olink Reveal", - "Olink Focus", - "imaging mass spectrometry", - "LC-MS/MS", - "snRNASeq", - "NULISA", - "serial IHC", - "CITESeq", - "Xenium", - "Olink Flex", - "WES", - "Olink Target 48" - ] - }, - "maxItems": 34 - }, - "cellRangerOutput": { + "specimenModality": { "enum": [ - "raw MEX", - "raw_feature_bc_matrix", - "filtered_feature_bc_matrix", - "Not Applicable", - "filtered_peak_bc_matrix", - "raw_peak_bc_matrix", - "filtered MEX" + "single specimen", + "multispecimen" ] }, - "RObjectClass": { + "targetPanelSynID": {}, + "targetPanelSize": {}, + "targetPanel": {}, + "metadataType": { "enum": [ - "sparse matrix", - "Seurat object", - "data.frame", - "vector", - "ROCR prediction.object", - "list", - "matrix", - "SummarizedExperiment", - "Symphony reference", + "single-cell metadata", "" ] }, @@ -126,8 +121,8 @@ "type": "array", "items": { "enum": [ - "gene counts", "differential expression results", + "gene counts", "epigenomic peaks", "barcode counts", "" @@ -135,215 +130,220 @@ }, "maxItems": 4 }, - "metadataType": { + "RObjectClass": { "enum": [ - "single-cell metadata", + "Symphony reference", + "sparse matrix", + "SummarizedExperiment", + "data.frame", + "matrix", + "vector", + "Seurat object", + "list", + "ROCR prediction.object", "" ] }, "individualID": {}, - "biospecimenID": {}, - "targetPanelSize": {}, - "targetPanelSynID": {}, - "targetPanel": {} + "biospecimenID": {} }, "required": [ - "fileFormat", + "assay", "dataLevel", "Component", + "cellRangerOutput", "resourceType", - "specimenModality", - "assay", - "cellRangerOutput" + "fileFormat", + "specimenModality" ], "allOf": [ { "if": { "properties": { - "fileFormat": { + "assay": { "enum": [ - "Rds" + "feature barcode sequencing" ] } }, "required": [ - "fileFormat" + "assay" ] }, "then": { "properties": { - "RObjectClass": { - "enum": [ - "sparse matrix", - "Seurat object", - "data.frame", - "vector", - "ROCR prediction.object", - "list", - "matrix", - "SummarizedExperiment", - "Symphony reference", - "" - ] + "targetPanelSynID": { + "not": { + "type": "null" + }, + "minLength": 1 } }, "required": [ - "RObjectClass" + "targetPanelSynID" ] } }, { "if": { "properties": { - "resourceType": { + "assay": { "enum": [ - "experimental data" + "feature barcode sequencing" ] } }, "required": [ - "resourceType" + "assay" ] }, "then": { "properties": { - "processedDataType": { - "type": "array", - "items": { - "enum": [ - "gene counts", - "differential expression results", - "epigenomic peaks", - "barcode counts", - "" - ] - }, - "maxItems": 4 - } + "targetPanelSize": {} }, "required": [ - "processedDataType" + "targetPanelSize" ] } }, { "if": { "properties": { - "resourceType": { + "assay": { "enum": [ - "metadata" + "feature barcode sequencing" ] } }, "required": [ - "resourceType" + "assay" ] }, "then": { "properties": { - "metadataType": { - "enum": [ - "single-cell metadata" - ] + "targetPanel": { + "not": { + "type": "null" + }, + "minLength": 1 } }, "required": [ - "metadataType" + "targetPanel" ] } }, { "if": { "properties": { - "specimenModality": { + "resourceType": { "enum": [ - "single specimen" + "metadata" ] } }, "required": [ - "specimenModality" + "resourceType" ] }, "then": { "properties": { - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 + "metadataType": { + "enum": [ + "single-cell metadata" + ] } }, "required": [ - "individualID" + "metadataType" ] } }, { "if": { "properties": { - "specimenModality": { + "resourceType": { "enum": [ - "single specimen" + "experimental data" ] } }, "required": [ - "specimenModality" + "resourceType" ] }, "then": { "properties": { - "biospecimenID": { - "not": { - "type": "null" + "processedDataType": { + "type": "array", + "items": { + "enum": [ + "differential expression results", + "gene counts", + "epigenomic peaks", + "barcode counts", + "" + ] }, - "minLength": 1 + "maxItems": 4 } }, "required": [ - "biospecimenID" + "processedDataType" ] } }, { "if": { "properties": { - "assay": { + "fileFormat": { "enum": [ - "feature barcode sequencing" + "Rds" ] } }, "required": [ - "assay" + "fileFormat" ] }, "then": { "properties": { - "targetPanelSize": {} + "RObjectClass": { + "enum": [ + "Symphony reference", + "sparse matrix", + "SummarizedExperiment", + "data.frame", + "matrix", + "vector", + "Seurat object", + "list", + "ROCR prediction.object", + "" + ] + } }, "required": [ - "targetPanelSize" + "RObjectClass" ] } }, { "if": { "properties": { - "assay": { + "specimenModality": { "enum": [ - "feature barcode sequencing" + "single specimen" ] } }, "required": [ - "assay" + "specimenModality" ] }, "then": { "properties": { - "targetPanelSynID": { + "individualID": { "not": { "type": "null" }, @@ -351,26 +351,26 @@ } }, "required": [ - "targetPanelSynID" + "individualID" ] } }, { "if": { "properties": { - "assay": { + "specimenModality": { "enum": [ - "feature barcode sequencing" + "single specimen" ] } }, "required": [ - "assay" + "specimenModality" ] }, "then": { "properties": { - "targetPanel": { + "biospecimenID": { "not": { "type": "null" }, @@ -378,7 +378,7 @@ } }, "required": [ - "targetPanel" + "biospecimenID" ] } } diff --git a/model_json_schema/ark.ScVDJSeqProcessedDataAnnotationTemplate.schema.json b/model_json_schema/ark.ScVDJSeqProcessedDataAnnotationTemplate.schema.json index 8422a38..c8c3aee 100644 --- a/model_json_schema/ark.ScVDJSeqProcessedDataAnnotationTemplate.schema.json +++ b/model_json_schema/ark.ScVDJSeqProcessedDataAnnotationTemplate.schema.json @@ -4,13 +4,23 @@ "title": "ark", "type": "object", "properties": { + "resourceType": { + "type": "array", + "items": { + "enum": [ + "experimental data", + "metadata" + ] + }, + "maxItems": 2 + }, "dataLevel": { "enum": [ - "3", + "4", + "1", "2", "5", - "4", - "1" + "3" ] }, "Component": { @@ -19,191 +29,179 @@ }, "minLength": 1 }, + "specimenModality": { + "enum": [ + "multispecimen", + "single specimen" + ] + }, "fileFormat": { "enum": [ - "txt", - "h5ad", - "tgz", - "fam", - "bam", - "bim", "xls", - "mtx", - "bed", - "csv", "h5", - "xlsx", + "tgz", "Rds", "zip", + "txt", + "bed", "bai", - "tsv" - ] - }, - "specimenModality": { - "enum": [ - "single specimen", - "multispecimen" + "bim", + "h5ad", + "tsv", + "mtx", + "bam", + "csv", + "fam", + "xlsx" ] }, "assay": { "type": "array", "items": { "enum": [ - "Visium", - "RNASeq", - "WES", + "H&E", + "multiplexed ELISA", + "flow cytometry", + "CITESeq", "imaging mass cytometry", - "Olink Target 96", - "SomaScan", - "kiloplex", + "CyTOF", + "scRNASeq", "snRNASeq", + "NULISA", + "Olink Reveal", + "ASAPSeq", + "scVDJSeq", + "Olink Explore HT", + "Visium", + "snATACSeq", + "GenePS SeqFISH", + "CosMX", "VDJSeq", - "multiplexed ELISA", - "H&E", - "CyTOF", + "CE-MS", + "SomaScan", "WGS", - "NULISA", + "RNASeq", + "Olink Target 96", + "WES", "LC-MS/MS", "SNP array", + "kiloplex", "imaging mass spectrometry", - "snATACSeq", + "Xenium", "Olink Flex", - "serial IHC", - "feature barcode sequencing", - "Olink Reveal", - "scRNASeq", "Olink Target 48", - "Olink Explore HT", - "CE-MS", - "Xenium", - "scVDJSeq", - "Olink Focus", - "CosMX", - "flow cytometry", - "GenePS SeqFISH", - "CITESeq", - "ASAPSeq" + "feature barcode sequencing", + "serial IHC", + "Olink Focus" ] }, "maxItems": 34 }, - "resourceType": { + "processedDataType": { "type": "array", "items": { "enum": [ - "metadata", - "experimental data" + "epigenomic peaks", + "gene counts", + "barcode counts", + "differential expression results", + "" ] }, - "maxItems": 2 + "maxItems": 4 }, + "metadataType": { + "enum": [ + "single-cell metadata", + "" + ] + }, + "biospecimenID": {}, + "individualID": {}, "RObjectClass": { "enum": [ - "vector", - "list", "ROCR prediction.object", + "data.frame", + "sparse matrix", + "list", "Seurat object", "Symphony reference", "SummarizedExperiment", + "vector", "matrix", - "sparse matrix", - "data.frame", "" ] }, - "individualID": {}, - "biospecimenID": {}, - "targetPanelSize": {}, "targetPanelSynID": {}, - "targetPanel": {}, - "metadataType": { - "enum": [ - "single-cell metadata", - "" - ] - }, - "processedDataType": { - "type": "array", - "items": { - "enum": [ - "differential expression results", - "gene counts", - "barcode counts", - "epigenomic peaks", - "" - ] - }, - "maxItems": 4 - } + "targetPanelSize": {}, + "targetPanel": {} }, "required": [ + "resourceType", "dataLevel", "Component", - "fileFormat", "specimenModality", - "assay", - "resourceType" + "fileFormat", + "assay" ], "allOf": [ { "if": { "properties": { - "fileFormat": { + "resourceType": { "enum": [ - "Rds" + "experimental data" ] } }, "required": [ - "fileFormat" + "resourceType" ] }, "then": { "properties": { - "RObjectClass": { - "enum": [ - "vector", - "list", - "ROCR prediction.object", - "Seurat object", - "Symphony reference", - "SummarizedExperiment", - "matrix", - "sparse matrix", - "data.frame", - "" - ] + "processedDataType": { + "type": "array", + "items": { + "enum": [ + "epigenomic peaks", + "gene counts", + "barcode counts", + "differential expression results", + "" + ] + }, + "maxItems": 4 } }, "required": [ - "RObjectClass" + "processedDataType" ] } }, { "if": { "properties": { - "specimenModality": { + "resourceType": { "enum": [ - "single specimen" + "metadata" ] } }, "required": [ - "specimenModality" + "resourceType" ] }, "then": { "properties": { - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 + "metadataType": { + "enum": [ + "single-cell metadata" + ] } }, "required": [ - "individualID" + "metadataType" ] } }, @@ -237,49 +235,62 @@ { "if": { "properties": { - "assay": { + "specimenModality": { "enum": [ - "feature barcode sequencing" + "single specimen" ] } }, "required": [ - "assay" + "specimenModality" ] }, "then": { "properties": { - "targetPanelSize": {} + "individualID": { + "not": { + "type": "null" + }, + "minLength": 1 + } }, "required": [ - "targetPanelSize" + "individualID" ] } }, { "if": { "properties": { - "assay": { + "fileFormat": { "enum": [ - "feature barcode sequencing" + "Rds" ] } }, "required": [ - "assay" + "fileFormat" ] }, "then": { "properties": { - "targetPanelSynID": { - "not": { - "type": "null" - }, - "minLength": 1 + "RObjectClass": { + "enum": [ + "ROCR prediction.object", + "data.frame", + "sparse matrix", + "list", + "Seurat object", + "Symphony reference", + "SummarizedExperiment", + "vector", + "matrix", + "" + ] } }, "required": [ - "targetPanelSynID" + "RObjectClass" ] } }, @@ -298,7 +309,7 @@ }, "then": { "properties": { - "targetPanel": { + "targetPanelSynID": { "not": { "type": "null" }, @@ -306,67 +317,56 @@ } }, "required": [ - "targetPanel" + "targetPanelSynID" ] } }, { "if": { "properties": { - "resourceType": { + "assay": { "enum": [ - "metadata" + "feature barcode sequencing" ] } }, "required": [ - "resourceType" + "assay" ] }, "then": { "properties": { - "metadataType": { - "enum": [ - "single-cell metadata" - ] - } + "targetPanelSize": {} }, "required": [ - "metadataType" + "targetPanelSize" ] } }, { "if": { "properties": { - "resourceType": { + "assay": { "enum": [ - "experimental data" + "feature barcode sequencing" ] } }, "required": [ - "resourceType" + "assay" ] }, "then": { "properties": { - "processedDataType": { - "type": "array", - "items": { - "enum": [ - "differential expression results", - "gene counts", - "barcode counts", - "epigenomic peaks", - "" - ] + "targetPanel": { + "not": { + "type": "null" }, - "maxItems": 4 + "minLength": 1 } }, "required": [ - "processedDataType" + "targetPanel" ] } } diff --git a/model_json_schema/ark.SnATAC-seqAssayMetadataTemplate.schema.json b/model_json_schema/ark.SnATAC-seqAssayMetadataTemplate.schema.json index 077a1d3..cca6191 100644 --- a/model_json_schema/ark.SnATAC-seqAssayMetadataTemplate.schema.json +++ b/model_json_schema/ark.SnATAC-seqAssayMetadataTemplate.schema.json @@ -4,62 +4,78 @@ "title": "ark", "type": "object", "properties": { - "percentCellViability": { + "softwareAndVersion": { + "enum": [ + "Cell Ranger v3.0.2", + "BD FACSDiva 8.0.1", + "Cell Ranger v7.0.0", + "Cell Ranger v3.0.0", + "Cell Ranger v6.0.0", + "Cell Ranger v5.0.1", + "Cell Ranger v7.0.1", + "Cell Ranger v7.2.0", + "Space Ranger 3.1.1", + "demuxlet", + "Space Ranger 3.1.2", + "Cell Ranger 9.0.1", + "Cell Ranger v6.0.2", + "Cell Ranger v6.1.1", + "Space Ranger 3.0.1", + "Cell Ranger v4.0.0", + "Space Ranger 3.1.0", + "Space Ranger 3.1.3", + "Cell Ranger v8.0.1", + "Cell Ranger v3.0.1", + "Cell Ranger v5.0.0", + "Cell Ranger v6.1.2", + "Cell Ranger v9.0.0", + "Cell Ranger ATAC v1.1.0", + "Cell Ranger v3.1.0", + "Cell Ranger v7.1.0", + "Cell Ranger v6.0.1", + "Cell Ranger v8.0.0", + "Cell Ranger v6.1.0", + "Space Ranger 3.0.0", + "" + ] + }, + "Component": { "not": { "type": "null" }, "minLength": 1 }, - "platform": { + "nucleicAcidSource": { "type": "array", "items": { "enum": [ - "Visium CytAssist", - "BD FACSLyric Clinical", - "Chromium Next GEM Chip M", - "BD FACSDiscover S8", - "Cytek Aurora", - "Chromium Next GEM Chip H", - "none", - "BD FACSCanto", - "CyTOF XT", - "Helios Mass Cytometer", - "Chromium Next GEM Chip Q", - "Illumina HiSeq X Ten", - "Sony MA900", - "BD FACSAria III", - "unknown", - "Olink Signature Q100", - "Illumina NextSeq 500", - "Chromium iX", - "GEM-X OCM 5' Chip", - "BD FACSymphony S6", - "Fluidigm BioMark", - "Chromium X", - "Chromium GEM-X Single Cell 3' Chip v4", - "Hyperion", - "BD FACSAria Fusion cell sorter", - "BD FACSCanto II", - "BD LSRFortessa", - "Thermo Fisher Attune NxT", - "Chromium Next GEM Chip K", - "Thermo Fisher Attune Xenith", - "Illumina NovaSeq X", - "Illumina NovaSeq 6000", - "Chromium Xo", - "Xenium", - "Illumina HiSeq 2500", - "Chromium Next GEM Chip G", - "Chromium Controller", - "Thermo Fisher Attune CytPix", - "Cytek Aurora Evo", - "BD FACSMelody", - "GEM-X Flex Gene Expression Chip", - "Not Applicable", - "BD FACSDiscover A8" + "multiplexing oligo", + "BCR mRNA", + "TCR mRNA", + "surface protein feature barcode", + "globin-depleted RNA", + "rRNA-depleted RNA", + "intracellular protein feature barcode", + "poly(A) RNA", + "Tn5-accessible gDNA", + "antigen capture barcode", + "gDNA", + "CRISPR protospacer feature barcode" ] }, - "maxItems": 43 + "maxItems": 12 + }, + "totalReads": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "percentCellViability": { + "not": { + "type": "null" + }, + "minLength": 1 }, "specimenModality": { "enum": [ @@ -69,189 +85,173 @@ }, "libraryPrepMethod": { "enum": [ - "in-house library prep", - "TruSeq Stranded mRNA", - "10x GEM-X Universal 5? Gene Expression v3", - "SMART-Seq Human BCR with UMI", - "SMARTer Stranded Total RNA v2", "CEL-Seq2", - "10x Chromium Next GEM Single Cell ATAC v2", + "Takara Human scTCR profiling for Illumina", + "NEBNext Human Immune Sequencing Kit", + "10x Chromium GEM-X Single Cell 3' v4", + "custom DASH-treatment", + "Takara Human BCR profiling for Illumina", + "SMART-Seq Human BCR with UMI", + "NEBNext Ultra II Directional RNA Library", + "SMART-Seq v4 Ultra Low Input RNA", "SMART-Seq Human TCR with UMI", - "10x Chromium Fixed RNA Human Transcriptome", - "10x Chromium Single Cell Human BCR", + "SMARTer Stranded Total RNA v2", "10x Chromium Next GEM Single Cell 3'", - "custom DASH-treatment", + "10x Chromium Fixed RNA Human Transcriptome", + "10x Chromium Next GEM Single Cell 3' 3.1", + "Nextera XT DNA", "10x Chromium GEM-X Single Cell 5' v3", - "NEBNext Ultra II Directional RNA Library", + "10x Chromium Next GEM Single Cell 5' v1.1", "10x GEM-X Flex Gene Expression Human", - "Takara Human BCR profiling for Illumina", - "Nextera XT DNA", - "Takara Human TCRv2 profiling for Illumina", + "10x GEM-X Universal 5? Gene Expression v3", + "Fluidigm C1 HT", "QIAseq miRNA Library", - "Chromium Next GEM Single Cell ATAC v1.1", - "10x Chromium GEM-X Single Cell 3' v4", + "10x Chromium Single Cell Human BCR", "10x Chromium Next GEM Single Cell 5' v2", - "Fluidigm C1 HT", "Takara Human TCR profiling for Illumina", - "Takara Human scTCR profiling for Illumina", - "SMART-Seq v4 Ultra Low Input RNA", - "10x Chromium Next GEM Single Cell 5' v1.1", - "10x Chromium Next GEM Single Cell 3' 3.1", - "NEBNext Human Immune Sequencing Kit", + "TruSeq Stranded mRNA", "Nextera XT", - "10x Chromium Single Cell Human TCR" + "10x Chromium Single Cell Human TCR", + "Chromium Next GEM Single Cell ATAC v1.1", + "10x Chromium Next GEM Single Cell ATAC v2", + "Takara Human TCRv2 profiling for Illumina", + "in-house library prep" ] }, - "totalReads": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "inputCellCount": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "sequencingSaturation": {}, "assay": { "type": "array", "items": { "enum": [ - "LC-MS/MS", - "Olink Focus", - "CE-MS", - "serial IHC", + "feature barcode sequencing", + "SNP array", + "Olink Target 48", + "ASAPSeq", + "flow cytometry", "GenePS SeqFISH", - "snRNASeq", + "serial IHC", "H&E", - "NULISA", - "Olink Target 48", + "CyTOF", + "Visium", + "Olink Target 96", + "VDJSeq", "Olink Reveal", + "CosMX", + "Olink Explore HT", + "Xenium", + "snRNASeq", + "WGS", + "SomaScan", + "snATACSeq", "Olink Flex", - "WES", + "scRNASeq", + "kiloplex", "multiplexed ELISA", "scVDJSeq", - "VDJSeq", - "CyTOF", - "scRNASeq", - "Olink Explore HT", - "snATACSeq", + "CITESeq", + "Olink Focus", + "imaging mass spectrometry", "RNASeq", + "LC-MS/MS", "imaging mass cytometry", - "feature barcode sequencing", - "imaging mass spectrometry", - "kiloplex", - "Visium", - "SomaScan", - "Xenium", - "SNP array", - "CosMX", - "ASAPSeq", - "flow cytometry", - "Olink Target 96", - "CITESeq", - "WGS" + "NULISA", + "CE-MS", + "WES" ] }, "maxItems": 34 }, - "Component": { + "sequencingSaturation": {}, + "sampleProcessingBatch": {}, + "inputCellCount": { "not": { "type": "null" }, "minLength": 1 }, - "sampleProcessingBatch": {}, - "dataCollectionBatch": {}, - "softwareAndVersion": { - "enum": [ - "Cell Ranger v6.0.2", - "Cell Ranger v9.0.0", - "Cell Ranger v6.1.1", - "Space Ranger 3.1.3", - "Cell Ranger v6.1.2", - "Cell Ranger v7.0.0", - "Cell Ranger v3.0.1", - "Cell Ranger v3.1.0", - "Space Ranger 3.0.1", - "Cell Ranger v6.0.1", - "Space Ranger 3.0.0", - "Cell Ranger 9.0.1", - "Cell Ranger v8.0.1", - "Cell Ranger ATAC v1.1.0", - "Cell Ranger v4.0.0", - "Space Ranger 3.1.2", - "Cell Ranger v7.1.0", - "Cell Ranger v6.1.0", - "Cell Ranger v3.0.0", - "Space Ranger 3.1.0", - "Cell Ranger v8.0.0", - "Cell Ranger v5.0.0", - "Space Ranger 3.1.1", - "Cell Ranger v7.0.1", - "demuxlet", - "Cell Ranger v7.2.0", - "Cell Ranger v3.0.2", - "Cell Ranger v5.0.1", - "BD FACSDiva 8.0.1", - "Cell Ranger v6.0.0", - "" - ] - }, - "nucleicAcidSource": { + "platform": { "type": "array", "items": { "enum": [ - "CRISPR protospacer feature barcode", - "poly(A) RNA", - "globin-depleted RNA", - "intracellular protein feature barcode", - "surface protein feature barcode", - "gDNA", - "BCR mRNA", - "antigen capture barcode", - "Tn5-accessible gDNA", - "rRNA-depleted RNA", - "multiplexing oligo", - "TCR mRNA" + "none", + "Chromium Xo", + "BD FACSDiscover A8", + "BD FACSDiscover S8", + "BD LSRFortessa", + "Chromium GEM-X Single Cell 3' Chip v4", + "Chromium Next GEM Chip G", + "GEM-X Flex Gene Expression Chip", + "Cytek Aurora Evo", + "Helios Mass Cytometer", + "Thermo Fisher Attune NxT", + "Fluidigm BioMark", + "Not Applicable", + "CyTOF XT", + "Visium CytAssist", + "Chromium Next GEM Chip M", + "Sony MA900", + "Chromium Next GEM Chip H", + "BD FACSAria III", + "Cytek Aurora", + "BD FACSCanto", + "Thermo Fisher Attune Xenith", + "Xenium", + "unknown", + "BD FACSCanto II", + "BD FACSLyric Clinical", + "Chromium Controller", + "Chromium X", + "BD FACSymphony S6", + "GEM-X OCM 5' Chip", + "Thermo Fisher Attune CytPix", + "Illumina NovaSeq X", + "Olink Signature Q100", + "Illumina NextSeq 500", + "BD FACSMelody", + "Hyperion", + "Chromium Next GEM Chip Q", + "Chromium Next GEM Chip K", + "BD FACSAria Fusion cell sorter", + "Illumina HiSeq X Ten", + "Illumina NovaSeq 6000", + "Illumina HiSeq 2500", + "Chromium iX" ] }, - "maxItems": 12 + "maxItems": 43 }, + "dataCollectionBatch": {}, "alignmentReference": { "enum": [ - "10x Cell Ranger Human GRCh38 2020-A", "unknown", - "vdj_GRCh38_alts_ensembl-4.0.0", "10x Cell Ranger Human GRCh38 2024-A", - "modified GRCh38" + "10x Cell Ranger Human GRCh38 2020-A", + "modified GRCh38", + "vdj_GRCh38_alts_ensembl-4.0.0" ] }, "libraryID": {}, "biospecimenID": {}, "10xProbeSetReference": { "enum": [ - "Visium Human Transcriptome v1", + "Flex Human Transcriptome Probe Set v1.1.0", "Visium Human Transcriptome v2", + "Visium Human Transcriptome v1", "custom probe set", - "Flex Human Transcriptome Probe Set v1.1.0", "Flex Human Transcriptome Probe Set v1.0.1", "" ] } }, "required": [ + "Component", + "nucleicAcidSource", + "totalReads", "percentCellViability", - "platform", "specimenModality", "libraryPrepMethod", - "totalReads", - "inputCellCount", "assay", - "Component", - "nucleicAcidSource", + "inputCellCount", + "platform", "alignmentReference" ], "allOf": [ @@ -326,10 +326,10 @@ "properties": { "10xProbeSetReference": { "enum": [ - "Visium Human Transcriptome v1", + "Flex Human Transcriptome Probe Set v1.1.0", "Visium Human Transcriptome v2", + "Visium Human Transcriptome v1", "custom probe set", - "Flex Human Transcriptome Probe Set v1.1.0", "Flex Human Transcriptome Probe Set v1.0.1" ] } diff --git a/model_json_schema/ark.SnATACSeqProcessedDataAnnotationTemplate.schema.json b/model_json_schema/ark.SnATACSeqProcessedDataAnnotationTemplate.schema.json index ad77cf0..4525fbc 100644 --- a/model_json_schema/ark.SnATACSeqProcessedDataAnnotationTemplate.schema.json +++ b/model_json_schema/ark.SnATACSeqProcessedDataAnnotationTemplate.schema.json @@ -4,129 +4,121 @@ "title": "ark", "type": "object", "properties": { + "Component": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "cellRangerOutput": { "enum": [ - "raw MEX", - "Not Applicable", - "filtered_feature_bc_matrix", + "filtered MEX", "raw_feature_bc_matrix", "raw_peak_bc_matrix", - "filtered MEX", - "filtered_peak_bc_matrix" - ] - }, - "dataLevel": { - "enum": [ - "4", - "2", - "1", - "3", - "5" - ] - }, - "specimenModality": { - "enum": [ - "single specimen", - "multispecimen" + "Not Applicable", + "filtered_peak_bc_matrix", + "raw MEX", + "filtered_feature_bc_matrix" ] }, "fileFormat": { "enum": [ - "bam", - "txt", - "xlsx", - "fam", - "mtx", - "csv", + "tsv", "bai", + "bed", + "csv", + "zip", + "mtx", + "h5ad", "Rds", - "h5", "tgz", + "txt", + "fam", "xls", - "tsv", + "xlsx", "bim", - "zip", - "h5ad", - "bed" + "h5", + "bam" ] }, "resourceType": { "type": "array", "items": { "enum": [ - "metadata", - "experimental data" + "experimental data", + "metadata" ] }, "maxItems": 2 }, + "dataLevel": { + "enum": [ + "5", + "2", + "4", + "1", + "3" + ] + }, "assay": { "type": "array", "items": { "enum": [ - "serial IHC", - "ASAPSeq", - "scRNASeq", - "CE-MS", - "Olink Target 48", - "flow cytometry", - "RNASeq", - "imaging mass spectrometry", - "CITESeq", - "SNP array", - "SomaScan", - "snRNASeq", "Olink Reveal", - "WES", - "H&E", + "GenePS SeqFISH", + "NULISA", + "Olink Target 48", + "kiloplex", "LC-MS/MS", + "snATACSeq", + "WES", + "flow cytometry", + "CE-MS", "Olink Target 96", - "VDJSeq", - "NULISA", + "imaging mass spectrometry", + "ASAPSeq", + "Olink Flex", "Xenium", + "WGS", + "SomaScan", + "scVDJSeq", + "Olink Explore HT", "Olink Focus", - "CyTOF", - "snATACSeq", - "Olink Flex", + "H&E", + "Visium", + "CITESeq", "imaging mass cytometry", + "VDJSeq", "multiplexed ELISA", - "kiloplex", + "SNP array", + "snRNASeq", "CosMX", - "Olink Explore HT", + "scRNASeq", + "RNASeq", "feature barcode sequencing", - "Visium", - "WGS", - "GenePS SeqFISH", - "scVDJSeq" + "serial IHC", + "CyTOF" ] }, "maxItems": 34 }, - "Component": { - "not": { - "type": "null" - }, - "minLength": 1 + "specimenModality": { + "enum": [ + "single specimen", + "multispecimen" + ] }, - "biospecimenID": {}, - "individualID": {}, "RObjectClass": { "enum": [ - "data.frame", - "vector", - "sparse matrix", "Symphony reference", + "SummarizedExperiment", "list", - "matrix", - "Seurat object", "ROCR prediction.object", - "SummarizedExperiment", - "" - ] - }, - "metadataType": { - "enum": [ - "single-cell metadata", + "sparse matrix", + "data.frame", + "Seurat object", + "matrix", + "vector", "" ] }, @@ -134,8 +126,8 @@ "type": "array", "items": { "enum": [ - "differential expression results", "gene counts", + "differential expression results", "barcode counts", "epigenomic peaks", "" @@ -143,166 +135,174 @@ }, "maxItems": 4 }, + "metadataType": { + "enum": [ + "single-cell metadata", + "" + ] + }, "targetPanel": {}, + "targetPanelSynID": {}, "targetPanelSize": {}, - "targetPanelSynID": {} + "individualID": {}, + "biospecimenID": {} }, "required": [ + "Component", "cellRangerOutput", - "dataLevel", - "specimenModality", "fileFormat", "resourceType", + "dataLevel", "assay", - "Component" + "specimenModality" ], "allOf": [ { "if": { "properties": { - "specimenModality": { + "fileFormat": { "enum": [ - "single specimen" + "Rds" ] } }, "required": [ - "specimenModality" + "fileFormat" ] }, "then": { "properties": { - "biospecimenID": { - "not": { - "type": "null" - }, - "minLength": 1 + "RObjectClass": { + "enum": [ + "Symphony reference", + "SummarizedExperiment", + "list", + "ROCR prediction.object", + "sparse matrix", + "data.frame", + "Seurat object", + "matrix", + "vector", + "" + ] } }, "required": [ - "biospecimenID" + "RObjectClass" ] } }, { "if": { "properties": { - "specimenModality": { + "resourceType": { "enum": [ - "single specimen" + "experimental data" ] } }, "required": [ - "specimenModality" + "resourceType" ] }, "then": { "properties": { - "individualID": { - "not": { - "type": "null" + "processedDataType": { + "type": "array", + "items": { + "enum": [ + "gene counts", + "differential expression results", + "barcode counts", + "epigenomic peaks", + "" + ] }, - "minLength": 1 + "maxItems": 4 } }, "required": [ - "individualID" + "processedDataType" ] } }, { "if": { "properties": { - "fileFormat": { + "resourceType": { "enum": [ - "Rds" + "metadata" ] } }, "required": [ - "fileFormat" + "resourceType" ] }, "then": { "properties": { - "RObjectClass": { + "metadataType": { "enum": [ - "data.frame", - "vector", - "sparse matrix", - "Symphony reference", - "list", - "matrix", - "Seurat object", - "ROCR prediction.object", - "SummarizedExperiment", - "" + "single-cell metadata" ] } }, "required": [ - "RObjectClass" + "metadataType" ] } }, { "if": { "properties": { - "resourceType": { + "assay": { "enum": [ - "metadata" + "feature barcode sequencing" ] } }, "required": [ - "resourceType" + "assay" ] }, "then": { "properties": { - "metadataType": { - "enum": [ - "single-cell metadata" - ] + "targetPanel": { + "not": { + "type": "null" + }, + "minLength": 1 } }, "required": [ - "metadataType" + "targetPanel" ] } }, { "if": { "properties": { - "resourceType": { + "assay": { "enum": [ - "experimental data" + "feature barcode sequencing" ] } }, "required": [ - "resourceType" + "assay" ] }, "then": { "properties": { - "processedDataType": { - "type": "array", - "items": { - "enum": [ - "differential expression results", - "gene counts", - "barcode counts", - "epigenomic peaks", - "" - ] + "targetPanelSynID": { + "not": { + "type": "null" }, - "maxItems": 4 + "minLength": 1 } }, "required": [ - "processedDataType" + "targetPanelSynID" ] } }, @@ -321,56 +321,56 @@ }, "then": { "properties": { - "targetPanel": { - "not": { - "type": "null" - }, - "minLength": 1 - } + "targetPanelSize": {} }, "required": [ - "targetPanel" + "targetPanelSize" ] } }, { "if": { "properties": { - "assay": { + "specimenModality": { "enum": [ - "feature barcode sequencing" + "single specimen" ] } }, "required": [ - "assay" + "specimenModality" ] }, "then": { "properties": { - "targetPanelSize": {} + "individualID": { + "not": { + "type": "null" + }, + "minLength": 1 + } }, "required": [ - "targetPanelSize" + "individualID" ] } }, { "if": { "properties": { - "assay": { + "specimenModality": { "enum": [ - "feature barcode sequencing" + "single specimen" ] } }, "required": [ - "assay" + "specimenModality" ] }, "then": { "properties": { - "targetPanelSynID": { + "biospecimenID": { "not": { "type": "null" }, @@ -378,7 +378,7 @@ } }, "required": [ - "targetPanelSynID" + "biospecimenID" ] } } diff --git a/model_json_schema/ark.SnRNASeqAssayMetadataTemplate.schema.json b/model_json_schema/ark.SnRNASeqAssayMetadataTemplate.schema.json index ba3852e..382007e 100644 --- a/model_json_schema/ark.SnRNASeqAssayMetadataTemplate.schema.json +++ b/model_json_schema/ark.SnRNASeqAssayMetadataTemplate.schema.json @@ -4,79 +4,77 @@ "title": "ark", "type": "object", "properties": { - "libraryPrepMethod": { + "sampleProcessingBatch": {}, + "nucleicAcidSource": { + "type": "array", + "items": { + "enum": [ + "TCR mRNA", + "poly(A) RNA", + "BCR mRNA", + "multiplexing oligo", + "surface protein feature barcode", + "Tn5-accessible gDNA", + "antigen capture barcode", + "intracellular protein feature barcode", + "CRISPR protospacer feature barcode", + "rRNA-depleted RNA", + "gDNA", + "globin-depleted RNA" + ] + }, + "maxItems": 12 + }, + "inputCellCount": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "specimenModality": { "enum": [ - "Chromium Next GEM Single Cell ATAC v1.1", - "10x Chromium GEM-X Single Cell 5' v3", - "custom DASH-treatment", - "10x Chromium Next GEM Single Cell 3' 3.1", - "NEBNext Human Immune Sequencing Kit", - "Takara Human TCR profiling for Illumina", - "10x Chromium Next GEM Single Cell 3'", - "10x Chromium Next GEM Single Cell 5' v1.1", - "NEBNext Ultra II Directional RNA Library", - "10x GEM-X Flex Gene Expression Human", - "SMART-Seq Human TCR with UMI", - "in-house library prep", - "CEL-Seq2", - "Takara Human TCRv2 profiling for Illumina", - "10x Chromium Single Cell Human TCR", - "SMARTer Stranded Total RNA v2", - "10x Chromium Next GEM Single Cell 5' v2", - "10x Chromium Next GEM Single Cell ATAC v2", - "10x GEM-X Universal 5? Gene Expression v3", - "Takara Human BCR profiling for Illumina", - "SMART-Seq v4 Ultra Low Input RNA", - "10x Chromium GEM-X Single Cell 3' v4", - "Nextera XT", - "10x Chromium Single Cell Human BCR", - "SMART-Seq Human BCR with UMI", - "Nextera XT DNA", - "TruSeq Stranded mRNA", - "QIAseq miRNA Library", - "10x Chromium Fixed RNA Human Transcriptome", - "Fluidigm C1 HT", - "Takara Human scTCR profiling for Illumina" + "multispecimen", + "single specimen" ] }, "assay": { "type": "array", "items": { "enum": [ - "CE-MS", + "Visium", + "snATACSeq", + "Olink Target 48", + "Olink Reveal", + "snRNASeq", "Olink Target 96", - "Olink Focus", - "imaging mass cytometry", - "WGS", - "multiplexed ELISA", - "Olink Flex", + "WES", "feature barcode sequencing", - "CITESeq", - "Olink Target 48", - "snATACSeq", - "Visium", "VDJSeq", "CosMX", - "kiloplex", - "Olink Explore HT", - "snRNASeq", + "serial IHC", "GenePS SeqFISH", - "scRNASeq", - "SomaScan", + "imaging mass cytometry", "Xenium", - "NULISA", + "WGS", + "CITESeq", "RNASeq", - "imaging mass spectrometry", - "LC-MS/MS", - "WES", - "H&E", "SNP array", - "CyTOF", - "Olink Reveal", + "Olink Flex", "ASAPSeq", + "Olink Explore HT", + "LC-MS/MS", + "H&E", + "Olink Focus", + "flow cytometry", + "multiplexed ELISA", + "scRNASeq", + "CE-MS", + "SomaScan", + "kiloplex", + "imaging mass spectrometry", "scVDJSeq", - "serial IHC", - "flow cytometry" + "CyTOF", + "NULISA" ] }, "maxItems": 34 @@ -94,194 +92,193 @@ }, "minLength": 1 }, - "percentCellViability": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "nucleicAcidSource": { + "platform": { "type": "array", "items": { "enum": [ - "TCR mRNA", - "poly(A) RNA", - "rRNA-depleted RNA", - "intracellular protein feature barcode", - "gDNA", - "multiplexing oligo", - "Tn5-accessible gDNA", - "globin-depleted RNA", - "BCR mRNA", - "antigen capture barcode", - "CRISPR protospacer feature barcode", - "surface protein feature barcode" + "Illumina NovaSeq 6000", + "Olink Signature Q100", + "BD FACSDiscover A8", + "Hyperion", + "BD FACSMelody", + "Chromium Next GEM Chip G", + "Cytek Aurora", + "Not Applicable", + "Chromium X", + "Chromium Xo", + "BD FACSAria III", + "Thermo Fisher Attune CytPix", + "Chromium Next GEM Chip K", + "Chromium Controller", + "BD FACSLyric Clinical", + "Illumina NextSeq 500", + "BD FACSymphony S6", + "GEM-X Flex Gene Expression Chip", + "Xenium", + "Chromium Next GEM Chip H", + "Chromium GEM-X Single Cell 3' Chip v4", + "unknown", + "BD FACSDiscover S8", + "Chromium iX", + "Sony MA900", + "Helios Mass Cytometer", + "BD FACSCanto II", + "Cytek Aurora Evo", + "BD FACSAria Fusion cell sorter", + "BD LSRFortessa", + "GEM-X OCM 5' Chip", + "Visium CytAssist", + "Chromium Next GEM Chip Q", + "Illumina HiSeq 2500", + "BD FACSCanto", + "Illumina NovaSeq X", + "Chromium Next GEM Chip M", + "none", + "Illumina HiSeq X Ten", + "Thermo Fisher Attune NxT", + "Thermo Fisher Attune Xenith", + "Fluidigm BioMark", + "CyTOF XT" ] }, - "maxItems": 12 - }, - "specimenModality": { - "enum": [ - "multispecimen", - "single specimen" - ] - }, - "alignmentReference": { - "enum": [ - "modified GRCh38", - "vdj_GRCh38_alts_ensembl-4.0.0", - "unknown", - "10x Cell Ranger Human GRCh38 2020-A", - "10x Cell Ranger Human GRCh38 2024-A" - ] - }, - "sampleProcessingBatch": {}, - "inputCellCount": { - "not": { - "type": "null" - }, - "minLength": 1 + "maxItems": 43 }, - "sequencingSaturation": {}, "softwareAndVersion": { "enum": [ - "Cell Ranger v7.1.0", - "Cell Ranger v7.0.0", - "Cell Ranger v6.1.2", - "demuxlet", - "Cell Ranger v7.0.1", - "Cell Ranger v8.0.1", - "Space Ranger 3.1.1", "Space Ranger 3.0.0", - "Cell Ranger v7.2.0", - "Cell Ranger v8.0.0", - "Cell Ranger v6.0.2", "BD FACSDiva 8.0.1", - "Cell Ranger v6.0.0", - "Cell Ranger v5.0.1", + "Cell Ranger ATAC v1.1.0", + "Cell Ranger v3.0.1", + "Space Ranger 3.1.1", + "Cell Ranger v4.0.0", "Space Ranger 3.1.0", + "Cell Ranger v5.0.1", "Cell Ranger v6.1.0", - "Cell Ranger v3.0.2", - "Space Ranger 3.1.3", "Cell Ranger v3.1.0", - "Cell Ranger 9.0.1", - "Cell Ranger v6.1.1", - "Cell Ranger v4.0.0", "Cell Ranger v6.0.1", - "Cell Ranger v3.0.0", + "Cell Ranger 9.0.1", + "Space Ranger 3.1.3", + "Cell Ranger v7.2.0", "Cell Ranger v5.0.0", - "Cell Ranger v3.0.1", + "Cell Ranger v3.0.2", + "Cell Ranger v8.0.1", + "Cell Ranger v8.0.0", + "Cell Ranger v6.1.2", + "Cell Ranger v6.0.2", "Cell Ranger v9.0.0", - "Cell Ranger ATAC v1.1.0", + "Cell Ranger v6.1.1", "Space Ranger 3.0.1", "Space Ranger 3.1.2", + "Cell Ranger v7.1.0", + "Cell Ranger v7.0.1", + "Cell Ranger v3.0.0", + "Cell Ranger v7.0.0", + "demuxlet", + "Cell Ranger v6.0.0", "" ] }, - "platform": { - "type": "array", - "items": { - "enum": [ - "BD FACSDiscover A8", - "Chromium Controller", - "Thermo Fisher Attune CytPix", - "BD FACSAria III", - "Chromium Next GEM Chip K", - "Chromium X", - "Visium CytAssist", - "Illumina NovaSeq 6000", - "GEM-X OCM 5' Chip", - "Hyperion", - "BD FACSymphony S6", - "BD FACSCanto", - "Fluidigm BioMark", - "Chromium iX", - "Thermo Fisher Attune Xenith", - "Chromium Next GEM Chip G", - "BD FACSMelody", - "BD FACSLyric Clinical", - "none", - "BD FACSCanto II", - "Illumina HiSeq X Ten", - "Chromium Next GEM Chip Q", - "Illumina NextSeq 500", - "BD FACSAria Fusion cell sorter", - "Illumina NovaSeq X", - "Thermo Fisher Attune NxT", - "Illumina HiSeq 2500", - "Chromium Xo", - "Chromium GEM-X Single Cell 3' Chip v4", - "Xenium", - "Sony MA900", - "unknown", - "Helios Mass Cytometer", - "GEM-X Flex Gene Expression Chip", - "Chromium Next GEM Chip M", - "Cytek Aurora", - "CyTOF XT", - "BD FACSDiscover S8", - "Not Applicable", - "BD LSRFortessa", - "Olink Signature Q100", - "Chromium Next GEM Chip H", - "Cytek Aurora Evo" - ] + "alignmentReference": { + "enum": [ + "unknown", + "10x Cell Ranger Human GRCh38 2024-A", + "modified GRCh38", + "10x Cell Ranger Human GRCh38 2020-A", + "vdj_GRCh38_alts_ensembl-4.0.0" + ] + }, + "sequencingSaturation": {}, + "percentCellViability": { + "not": { + "type": "null" }, - "maxItems": 43 + "minLength": 1 }, + "libraryPrepMethod": { + "enum": [ + "10x Chromium GEM-X Single Cell 3' v4", + "CEL-Seq2", + "Takara Human TCRv2 profiling for Illumina", + "NEBNext Ultra II Directional RNA Library", + "Takara Human BCR profiling for Illumina", + "10x Chromium Next GEM Single Cell ATAC v2", + "10x Chromium GEM-X Single Cell 5' v3", + "Nextera XT", + "10x GEM-X Universal 5? Gene Expression v3", + "Takara Human scTCR profiling for Illumina", + "Chromium Next GEM Single Cell ATAC v1.1", + "custom DASH-treatment", + "SMART-Seq v4 Ultra Low Input RNA", + "Takara Human TCR profiling for Illumina", + "SMART-Seq Human TCR with UMI", + "SMARTer Stranded Total RNA v2", + "10x Chromium Next GEM Single Cell 3'", + "SMART-Seq Human BCR with UMI", + "10x Chromium Next GEM Single Cell 5' v1.1", + "NEBNext Human Immune Sequencing Kit", + "TruSeq Stranded mRNA", + "Fluidigm C1 HT", + "10x Chromium Next GEM Single Cell 3' 3.1", + "10x GEM-X Flex Gene Expression Human", + "10x Chromium Single Cell Human BCR", + "10x Chromium Single Cell Human TCR", + "10x Chromium Fixed RNA Human Transcriptome", + "Nextera XT DNA", + "QIAseq miRNA Library", + "in-house library prep", + "10x Chromium Next GEM Single Cell 5' v2" + ] + }, + "libraryID": {}, + "biospecimenID": {}, "10xProbeSetReference": { "enum": [ - "Flex Human Transcriptome Probe Set v1.1.0", - "Flex Human Transcriptome Probe Set v1.0.1", "Visium Human Transcriptome v2", - "Visium Human Transcriptome v1", "custom probe set", + "Flex Human Transcriptome Probe Set v1.0.1", + "Visium Human Transcriptome v1", + "Flex Human Transcriptome Probe Set v1.1.0", "" ] - }, - "libraryID": {}, - "biospecimenID": {} + } }, "required": [ - "libraryPrepMethod", + "nucleicAcidSource", + "inputCellCount", + "specimenModality", "assay", "totalReads", "Component", - "percentCellViability", - "nucleicAcidSource", - "specimenModality", + "platform", "alignmentReference", - "inputCellCount", - "platform" + "percentCellViability", + "libraryPrepMethod" ], "allOf": [ { "if": { "properties": { - "libraryPrepMethod": { + "specimenModality": { "enum": [ - "10x GEM-X Flex Gene Expression Human" + "multispecimen" ] } }, "required": [ - "libraryPrepMethod" + "specimenModality" ] }, "then": { "properties": { - "10xProbeSetReference": { - "enum": [ - "Flex Human Transcriptome Probe Set v1.1.0", - "Flex Human Transcriptome Probe Set v1.0.1", - "Visium Human Transcriptome v2", - "Visium Human Transcriptome v1", - "custom probe set" - ] + "libraryID": { + "not": { + "type": "null" + }, + "minLength": 1 } }, "required": [ - "10xProbeSetReference" + "libraryID" ] } }, @@ -290,7 +287,7 @@ "properties": { "specimenModality": { "enum": [ - "multispecimen" + "single specimen" ] } }, @@ -300,7 +297,7 @@ }, "then": { "properties": { - "libraryID": { + "biospecimenID": { "not": { "type": "null" }, @@ -308,34 +305,37 @@ } }, "required": [ - "libraryID" + "biospecimenID" ] } }, { "if": { "properties": { - "specimenModality": { + "libraryPrepMethod": { "enum": [ - "single specimen" + "10x GEM-X Flex Gene Expression Human" ] } }, "required": [ - "specimenModality" + "libraryPrepMethod" ] }, "then": { "properties": { - "biospecimenID": { - "not": { - "type": "null" - }, - "minLength": 1 + "10xProbeSetReference": { + "enum": [ + "Visium Human Transcriptome v2", + "custom probe set", + "Flex Human Transcriptome Probe Set v1.0.1", + "Visium Human Transcriptome v1", + "Flex Human Transcriptome Probe Set v1.1.0" + ] } }, "required": [ - "biospecimenID" + "10xProbeSetReference" ] } } diff --git a/model_json_schema/ark.SnRNASeqProcessedDataAnnotationTemplate.schema.json b/model_json_schema/ark.SnRNASeqProcessedDataAnnotationTemplate.schema.json index 3a3f2e4..17694c7 100644 --- a/model_json_schema/ark.SnRNASeqProcessedDataAnnotationTemplate.schema.json +++ b/model_json_schema/ark.SnRNASeqProcessedDataAnnotationTemplate.schema.json @@ -6,13 +6,28 @@ "properties": { "cellRangerOutput": { "enum": [ - "filtered MEX", - "raw_peak_bc_matrix", - "raw MEX", - "Not Applicable", + "filtered_peak_bc_matrix", "raw_feature_bc_matrix", + "raw_peak_bc_matrix", + "filtered MEX", "filtered_feature_bc_matrix", - "filtered_peak_bc_matrix" + "raw MEX", + "Not Applicable" + ] + }, + "Component": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "dataLevel": { + "enum": [ + "4", + "5", + "3", + "1", + "2" ] }, "specimenModality": { @@ -21,140 +36,125 @@ "single specimen" ] }, - "Component": { - "not": { - "type": "null" + "resourceType": { + "type": "array", + "items": { + "enum": [ + "metadata", + "experimental data" + ] }, - "minLength": 1 + "maxItems": 2 }, "fileFormat": { "enum": [ - "csv", - "mtx", - "h5ad", "tsv", - "bai", - "txt", + "csv", + "bam", "xlsx", - "fam", + "zip", + "mtx", + "bed", + "tgz", "bim", + "h5", + "h5ad", "Rds", - "tgz", - "zip", - "bam", + "fam", "xls", - "bed", - "h5" + "txt", + "bai" ] }, "assay": { "type": "array", "items": { "enum": [ - "ASAPSeq", - "VDJSeq", - "Olink Explore HT", - "Olink Target 48", - "kiloplex", - "WES", - "H&E", - "CyTOF", - "LC-MS/MS", - "scVDJSeq", - "Visium", - "feature barcode sequencing", - "serial IHC", "GenePS SeqFISH", - "SomaScan", - "imaging mass cytometry", - "CosMX", "Olink Reveal", - "WGS", - "RNASeq", "flow cytometry", + "snRNASeq", + "Olink Target 48", + "Olink Explore HT", "Xenium", + "scRNASeq", + "CosMX", + "multiplexed ELISA", + "kiloplex", + "scVDJSeq", + "snATACSeq", + "WES", "CE-MS", - "NULISA", - "snRNASeq", + "VDJSeq", + "SomaScan", + "Olink Focus", "CITESeq", + "NULISA", "Olink Flex", + "Visium", + "WGS", + "imaging mass cytometry", + "CyTOF", "SNP array", - "snATACSeq", - "Olink Focus", - "Olink Target 96", - "multiplexed ELISA", + "serial IHC", + "feature barcode sequencing", + "LC-MS/MS", "imaging mass spectrometry", - "scRNASeq" + "Olink Target 96", + "ASAPSeq", + "RNASeq", + "H&E" ] }, "maxItems": 34 }, - "dataLevel": { + "biospecimenID": {}, + "individualID": {}, + "metadataType": { "enum": [ - "5", - "4", - "1", - "2", - "3" + "single-cell metadata", + "" ] }, - "resourceType": { + "processedDataType": { "type": "array", "items": { "enum": [ - "metadata", - "experimental data" + "epigenomic peaks", + "differential expression results", + "barcode counts", + "gene counts", + "" ] }, - "maxItems": 2 + "maxItems": 4 }, - "biospecimenID": {}, - "individualID": {}, "RObjectClass": { "enum": [ - "SummarizedExperiment", "matrix", "ROCR prediction.object", "Symphony reference", "Seurat object", - "sparse matrix", "vector", + "SummarizedExperiment", "list", "data.frame", + "sparse matrix", "" ] }, - "targetPanelSynID": {}, "targetPanelSize": {}, "targetPanel": {}, - "metadataType": { - "enum": [ - "single-cell metadata", - "" - ] - }, - "processedDataType": { - "type": "array", - "items": { - "enum": [ - "differential expression results", - "gene counts", - "epigenomic peaks", - "barcode counts", - "" - ] - }, - "maxItems": 4 - } + "targetPanelSynID": {} }, "required": [ "cellRangerOutput", - "specimenModality", "Component", - "fileFormat", - "assay", "dataLevel", - "resourceType" + "specimenModality", + "resourceType", + "fileFormat", + "assay" ], "allOf": [ { @@ -214,84 +214,95 @@ { "if": { "properties": { - "fileFormat": { + "resourceType": { "enum": [ - "Rds" + "metadata" ] } }, "required": [ - "fileFormat" + "resourceType" ] }, "then": { "properties": { - "RObjectClass": { + "metadataType": { "enum": [ - "SummarizedExperiment", - "matrix", - "ROCR prediction.object", - "Symphony reference", - "Seurat object", - "sparse matrix", - "vector", - "list", - "data.frame", - "" + "single-cell metadata" ] } }, "required": [ - "RObjectClass" + "metadataType" ] } }, { "if": { "properties": { - "assay": { + "resourceType": { "enum": [ - "feature barcode sequencing" + "experimental data" ] } }, "required": [ - "assay" + "resourceType" ] }, "then": { "properties": { - "targetPanelSynID": { - "not": { - "type": "null" + "processedDataType": { + "type": "array", + "items": { + "enum": [ + "epigenomic peaks", + "differential expression results", + "barcode counts", + "gene counts", + "" + ] }, - "minLength": 1 + "maxItems": 4 } }, "required": [ - "targetPanelSynID" + "processedDataType" ] } }, { "if": { "properties": { - "assay": { + "fileFormat": { "enum": [ - "feature barcode sequencing" + "Rds" ] } }, "required": [ - "assay" + "fileFormat" ] }, "then": { "properties": { - "targetPanelSize": {} + "RObjectClass": { + "enum": [ + "matrix", + "ROCR prediction.object", + "Symphony reference", + "Seurat object", + "vector", + "SummarizedExperiment", + "list", + "data.frame", + "sparse matrix", + "" + ] + } }, "required": [ - "targetPanelSize" + "RObjectClass" ] } }, @@ -310,75 +321,64 @@ }, "then": { "properties": { - "targetPanel": { - "not": { - "type": "null" - }, - "minLength": 1 - } + "targetPanelSize": {} }, "required": [ - "targetPanel" + "targetPanelSize" ] } }, { "if": { "properties": { - "resourceType": { + "assay": { "enum": [ - "metadata" + "feature barcode sequencing" ] } }, "required": [ - "resourceType" + "assay" ] }, "then": { "properties": { - "metadataType": { - "enum": [ - "single-cell metadata" - ] + "targetPanel": { + "not": { + "type": "null" + }, + "minLength": 1 } }, "required": [ - "metadataType" + "targetPanel" ] } }, { "if": { "properties": { - "resourceType": { + "assay": { "enum": [ - "experimental data" + "feature barcode sequencing" ] } }, "required": [ - "resourceType" + "assay" ] }, "then": { "properties": { - "processedDataType": { - "type": "array", - "items": { - "enum": [ - "differential expression results", - "gene counts", - "epigenomic peaks", - "barcode counts", - "" - ] + "targetPanelSynID": { + "not": { + "type": "null" }, - "maxItems": 4 + "minLength": 1 } }, "required": [ - "processedDataType" + "targetPanelSynID" ] } } diff --git a/model_json_schema/ark.SpatialAssayMetadataTemplate.schema.json b/model_json_schema/ark.SpatialImagingAssayMetadataTemplate.schema.json similarity index 76% rename from model_json_schema/ark.SpatialAssayMetadataTemplate.schema.json rename to model_json_schema/ark.SpatialImagingAssayMetadataTemplate.schema.json index fa1115f..b4ae43e 100644 --- a/model_json_schema/ark.SpatialAssayMetadataTemplate.schema.json +++ b/model_json_schema/ark.SpatialImagingAssayMetadataTemplate.schema.json @@ -4,83 +4,55 @@ "title": "ark", "type": "object", "properties": { + "targetPanel": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "targetPanelSynID": { "not": { "type": "null" }, "minLength": 1 }, + "assay": { + "enum": [ + "GenePS SeqFISH", + "serial IHC", + "Xenium", + "CosMX", + "Visium", + "H&E", + "imaging mass cytometry" + ] + }, "specimenModality": { "enum": [ "single specimen", "multispecimen" ] }, + "dataCollectionBatch": {}, "targetPanelSize": {}, + "sampleProcessingBatch": {}, "Component": { "not": { "type": "null" }, "minLength": 1 }, - "targetPanel": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "sampleProcessingBatch": {}, - "assay": { - "enum": [ - "Xenium", - "CosMX", - "imaging mass cytometry", - "H&E", - "serial IHC", - "Visium", - "GenePS SeqFISH", - "" - ] - }, - "dataCollectionBatch": {}, - "individualID": {}, "biospecimenID": {}, "slideID": {} }, "required": [ + "targetPanel", "targetPanelSynID", + "assay", "specimenModality", - "Component", - "targetPanel" + "Component" ], "allOf": [ - { - "if": { - "properties": { - "specimenModality": { - "enum": [ - "single specimen" - ] - } - }, - "required": [ - "specimenModality" - ] - }, - "then": { - "properties": { - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 - } - }, - "required": [ - "individualID" - ] - } - }, { "if": { "properties": { diff --git a/model_json_schema/ark.SpatialImagingFileAnnotationTemplate.schema.json b/model_json_schema/ark.SpatialImagingFileAnnotationTemplate.schema.json index 53e3a93..77e03dc 100644 --- a/model_json_schema/ark.SpatialImagingFileAnnotationTemplate.schema.json +++ b/model_json_schema/ark.SpatialImagingFileAnnotationTemplate.schema.json @@ -10,294 +10,266 @@ }, "minLength": 1 }, + "specimenModality": { + "enum": [ + "multispecimen", + "single specimen" + ] + }, "resourceType": { "type": "array", "items": { "enum": [ - "experimental data", - "metadata" + "metadata", + "experimental data" ] }, "maxItems": 2 }, + "assay": { + "enum": [ + "serial IHC", + "CosMX", + "Xenium", + "GenePS SeqFISH", + "imaging mass cytometry", + "H&E", + "Visium" + ] + }, "fileFormat": { "enum": [ - "bed", - "xls", - "erate", - "bai", - "h5ad", - "docx", - "mcd", - "rec", - "tbi", - "fastq", "rds", - "csv", - "vcf", - "tsv", "svs", - "fcs", - "txt", - "xlsx", + "pdf", + "h5ad", + "tgz", + "dose", + "fam", + "h5", "info", + "fcs", + "erate", + "tbi", + "zip", + "mcd", + "bai", + "bim", + "geojson", "bam", - "pdf", + "tsv", + "xlsx", + "vcf", + "csv", + "rec", + "bed", "czi", "mtx", - "bim", - "fam", + "docx", "parquet", - "zip", - "h5", - "dose", - "geojson", - "tgz" + "xls", + "fastq", + "txt" ] }, - "assay": { + "slideID": {}, + "biospecimenID": {}, + "metadataType": { "enum": [ - "serial IHC", - "H&E", - "imaging mass cytometry", - "CosMX", - "Xenium", - "GenePS SeqFISH", - "Visium", + "other", + "cell coordinates", + "target panel", + "single-cell metadata", + "tissue microarray map", "" ] }, - "specimenModality": { - "enum": [ - "multispecimen", - "single specimen" - ] - }, "processedDataType": { "type": "array", "items": { "enum": [ "barcode counts", "differential expression results", - "gene counts", "epigenomic peaks", + "gene counts", "" ] }, "maxItems": 4 }, - "metadataType": { - "enum": [ - "other", - "tissue multiarray map", - "single-cell metadata", - "target panel", - "cell coordinates", - "" - ] - }, "RObjectClass": { "enum": [ - "Seurat object", - "ROCR prediction.object", "Symphony reference", - "matrix", "sparse matrix", "SummarizedExperiment", + "list", + "Seurat object", + "matrix", "vector", "data.frame", - "list", + "ROCR prediction.object", "" ] - }, - "slideID": {}, - "individualID": {}, - "biospecimenID": {} + } }, "required": [ "Component", + "specimenModality", "resourceType", - "fileFormat", - "specimenModality" + "assay", + "fileFormat" ], "allOf": [ { "if": { "properties": { - "resourceType": { + "specimenModality": { "enum": [ - "experimental data" + "multispecimen" ] } }, "required": [ - "resourceType" + "specimenModality" ] }, "then": { "properties": { - "processedDataType": { - "type": "array", - "items": { - "enum": [ - "barcode counts", - "differential expression results", - "gene counts", - "epigenomic peaks", - "" - ] + "slideID": { + "not": { + "type": "null" }, - "maxItems": 4 + "minLength": 1 } }, "required": [ - "processedDataType" + "slideID" ] } }, { "if": { "properties": { - "resourceType": { + "specimenModality": { "enum": [ - "metadata" + "single specimen" ] } }, "required": [ - "resourceType" + "specimenModality" ] }, "then": { "properties": { - "metadataType": { - "enum": [ - "other", - "tissue multiarray map", - "single-cell metadata", - "target panel", - "cell coordinates" - ] + "biospecimenID": { + "not": { + "type": "null" + }, + "minLength": 1 } }, "required": [ - "metadataType" + "biospecimenID" ] } }, { "if": { "properties": { - "fileFormat": { + "resourceType": { "enum": [ - "rds" + "metadata" ] } }, "required": [ - "fileFormat" + "resourceType" ] }, "then": { "properties": { - "RObjectClass": { + "metadataType": { "enum": [ - "Seurat object", - "ROCR prediction.object", - "Symphony reference", - "matrix", - "sparse matrix", - "SummarizedExperiment", - "vector", - "data.frame", - "list", - "" + "other", + "cell coordinates", + "target panel", + "single-cell metadata", + "tissue microarray map" ] } }, "required": [ - "RObjectClass" + "metadataType" ] } }, { "if": { "properties": { - "specimenModality": { + "resourceType": { "enum": [ - "multispecimen" + "experimental data" ] } }, "required": [ - "specimenModality" + "resourceType" ] }, "then": { "properties": { - "slideID": { - "not": { - "type": "null" + "processedDataType": { + "type": "array", + "items": { + "enum": [ + "barcode counts", + "differential expression results", + "epigenomic peaks", + "gene counts", + "" + ] }, - "minLength": 1 + "maxItems": 4 } }, "required": [ - "slideID" + "processedDataType" ] } }, { "if": { "properties": { - "specimenModality": { + "fileFormat": { "enum": [ - "single specimen" + "rds" ] } }, "required": [ - "specimenModality" + "fileFormat" ] }, "then": { "properties": { - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 - } - }, - "required": [ - "individualID" - ] - } - }, - { - "if": { - "properties": { - "specimenModality": { + "RObjectClass": { "enum": [ - "single specimen" + "Symphony reference", + "sparse matrix", + "SummarizedExperiment", + "list", + "Seurat object", + "matrix", + "vector", + "data.frame", + "ROCR prediction.object", + "" ] } }, "required": [ - "specimenModality" - ] - }, - "then": { - "properties": { - "biospecimenID": { - "not": { - "type": "null" - }, - "minLength": 1 - } - }, - "required": [ - "biospecimenID" + "RObjectClass" ] } } diff --git a/model_templates/ark.BDMFCSFileAnnotations.csv b/model_templates/ark.BDMFCSFileAnnotations.csv index 7a601eb..d951309 100644 --- a/model_templates/ark.BDMFCSFileAnnotations.csv +++ b/model_templates/ark.BDMFCSFileAnnotations.csv @@ -1 +1 @@ -parentBiospecimenID,Component,specimenModality,project,biospecimenType,resourceType,sampleProcessingBatch,assay,dataType,eventCount,program,diagnosis,biospecimenSubtype,dataCollectionBatch,dataSubtype,fileFormat,species,platform,individualID,biospecimenID,visitID +dataSubtype,project,fileFormat,sampleProcessingBatch,resourceType,parentBiospecimenID,program,biospecimenType,Component,biospecimenSubtype,dataType,diagnosis,platform,specimenModality,dataCollectionBatch,species,assay,eventCount,visitID,individualID,biospecimenID diff --git a/model_templates/ark.BDMFCSFileAnnotations.xlsx b/model_templates/ark.BDMFCSFileAnnotations.xlsx index ee1b3da..210d271 100644 Binary files a/model_templates/ark.BDMFCSFileAnnotations.xlsx and b/model_templates/ark.BDMFCSFileAnnotations.xlsx differ diff --git a/model_templates/ark.BDMFastqFileAnnotations.csv b/model_templates/ark.BDMFastqFileAnnotations.csv index 1aaf245..d1d5d2a 100644 --- a/model_templates/ark.BDMFastqFileAnnotations.csv +++ b/model_templates/ark.BDMFastqFileAnnotations.csv @@ -1 +1 @@ -fileFormat,specimenModality,parentBiospecimenID,libraryPrepMethod,nucleicAcidSource,project,biospecimenSubtype,assay,dataType,readLength,biospecimenType,platform,diagnosis,dataSubtype,resourceType,program,species,Component,libraryID,individualID,biospecimenID,targetPanelSize,targetPanelSynID,targetPanel,visitID +dataType,resourceType,project,libraryPrepMethod,Component,biospecimenType,nucleicAcidSource,fileFormat,program,species,platform,diagnosis,assay,specimenModality,biospecimenSubtype,readLength,dataSubtype,parentBiospecimenID,visitID,targetPanelSize,targetPanel,targetPanelSynID,biospecimenID,individualID,libraryID diff --git a/model_templates/ark.BDMFastqFileAnnotations.xlsx b/model_templates/ark.BDMFastqFileAnnotations.xlsx index fd6e9de..721ba22 100644 Binary files a/model_templates/ark.BDMFastqFileAnnotations.xlsx and b/model_templates/ark.BDMFastqFileAnnotations.xlsx differ diff --git a/model_templates/ark.BDMMetadataFileAnnotations.csv b/model_templates/ark.BDMMetadataFileAnnotations.csv index 8e97b84..89fd099 100644 --- a/model_templates/ark.BDMMetadataFileAnnotations.csv +++ b/model_templates/ark.BDMMetadataFileAnnotations.csv @@ -1 +1 @@ -fileFormat,resourceType,Component,species,project,program,dataType,metadataType,metadataStandards,programPhase,assay +Component,resourceType,species,dataType,project,fileFormat,program,metadataStandards,metadataType,programPhase,assay diff --git a/model_templates/ark.BDMMetadataFileAnnotations.xlsx b/model_templates/ark.BDMMetadataFileAnnotations.xlsx index 5aa2b35..f6a23d6 100644 Binary files a/model_templates/ark.BDMMetadataFileAnnotations.xlsx and b/model_templates/ark.BDMMetadataFileAnnotations.xlsx differ diff --git a/model_templates/ark.BDMOlinkFileAnnotations.csv b/model_templates/ark.BDMOlinkFileAnnotations.csv index 50272dc..634db69 100644 --- a/model_templates/ark.BDMOlinkFileAnnotations.csv +++ b/model_templates/ark.BDMOlinkFileAnnotations.csv @@ -1 +1 @@ -Component,fileFormat,dataType,visitID,program,targetPanelSynID,plateID,project,resourceType,platform,dataSubtype,targetPanelSize,species,biospecimenType,specimenModality,targetPanel,diagnosis,programPhase +platform,targetPanelSize,visitID,fileFormat,targetPanelSynID,dataType,specimenModality,project,diagnosis,species,plateID,program,Component,biospecimenType,resourceType,dataSubtype,targetPanel,programPhase diff --git a/model_templates/ark.BDMOlinkFileAnnotations.xlsx b/model_templates/ark.BDMOlinkFileAnnotations.xlsx index a379680..10e31b9 100644 Binary files a/model_templates/ark.BDMOlinkFileAnnotations.xlsx and b/model_templates/ark.BDMOlinkFileAnnotations.xlsx differ diff --git a/model_templates/ark.BDMSpatialImagingFileAnnotations.csv b/model_templates/ark.BDMSpatialImagingFileAnnotations.csv index fa4e3c5..0b356dd 100644 --- a/model_templates/ark.BDMSpatialImagingFileAnnotations.csv +++ b/model_templates/ark.BDMSpatialImagingFileAnnotations.csv @@ -1 +1 @@ -assay,fileFormat,targetPanelSynID,specimenModality,visitID,targetPanelSize,dataType,resourceType,biospecimenSubtype,species,Component,diagnosis,dataSubtype,biospecimenType,parentBiospecimenID,targetPanel,project,program,RObjectClass,slideID,individualID,biospecimenID,metadataType,processedDataType +resourceType,targetPanel,targetPanelSynID,visitID,specimenModality,targetPanelSize,project,diagnosis,program,fileFormat,Component,dataSubtype,dataType,species,biospecimenType,parentBiospecimenID,assay,biospecimenSubtype,metadataType,processedDataType,biospecimenID,slideID,RObjectClass diff --git a/model_templates/ark.BDMSpatialImagingFileAnnotations.xlsx b/model_templates/ark.BDMSpatialImagingFileAnnotations.xlsx index b1e699e..cc26724 100644 Binary files a/model_templates/ark.BDMSpatialImagingFileAnnotations.xlsx and b/model_templates/ark.BDMSpatialImagingFileAnnotations.xlsx differ diff --git a/model_templates/ark.BDMscRNASeqProcessedDataAnnotations.csv b/model_templates/ark.BDMscRNASeqProcessedDataAnnotations.csv index cf6b9d9..4e46e6e 100644 --- a/model_templates/ark.BDMscRNASeqProcessedDataAnnotations.csv +++ b/model_templates/ark.BDMscRNASeqProcessedDataAnnotations.csv @@ -1 +1 @@ -fileFormat,diagnosis,dataType,cellRangerOutput,assay,parentBiospecimenID,project,biospecimenType,libraryPrepMethod,softwareAndVersion,Component,dataSubtype,biospecimenSubtype,species,nucleicAcidSource,program,visitID,dataLevel,specimenModality,resourceType,alignmentReference,RObjectClass,targetPanelSynID,targetPanel,targetPanelSize,biospecimenID,individualID,metadataType,processedDataType +parentBiospecimenID,visitID,project,resourceType,diagnosis,softwareAndVersion,dataType,nucleicAcidSource,fileFormat,alignmentReference,assay,libraryPrepMethod,biospecimenSubtype,dataSubtype,Component,program,biospecimenType,cellRangerOutput,specimenModality,dataLevel,species,metadataType,processedDataType,RObjectClass,targetPanel,targetPanelSize,targetPanelSynID,individualID,biospecimenID diff --git a/model_templates/ark.BDMscRNASeqProcessedDataAnnotations.xlsx b/model_templates/ark.BDMscRNASeqProcessedDataAnnotations.xlsx index b11aeaa..4b1ce05 100644 Binary files a/model_templates/ark.BDMscRNASeqProcessedDataAnnotations.xlsx and b/model_templates/ark.BDMscRNASeqProcessedDataAnnotations.xlsx differ diff --git a/model_templates/ark.BDMscVDJSeqProcessedDataAnnotations.csv b/model_templates/ark.BDMscVDJSeqProcessedDataAnnotations.csv index 106ae77..7594753 100644 --- a/model_templates/ark.BDMscVDJSeqProcessedDataAnnotations.csv +++ b/model_templates/ark.BDMscVDJSeqProcessedDataAnnotations.csv @@ -1 +1 @@ -fileFormat,project,visitID,diagnosis,resourceType,parentBiospecimenID,Component,libraryPrepMethod,biospecimenType,dataLevel,nucleicAcidSource,softwareAndVersion,dataSubtype,species,assay,dataType,biospecimenSubtype,alignmentReference,specimenModality,program,RObjectClass,processedDataType,metadataType,targetPanelSynID,targetPanelSize,targetPanel,individualID,biospecimenID +parentBiospecimenID,specimenModality,biospecimenType,softwareAndVersion,dataSubtype,visitID,alignmentReference,program,nucleicAcidSource,biospecimenSubtype,species,Component,dataLevel,project,resourceType,assay,diagnosis,libraryPrepMethod,dataType,fileFormat,individualID,biospecimenID,metadataType,processedDataType,targetPanelSynID,targetPanelSize,targetPanel,RObjectClass diff --git a/model_templates/ark.BDMscVDJSeqProcessedDataAnnotations.xlsx b/model_templates/ark.BDMscVDJSeqProcessedDataAnnotations.xlsx index 41f628c..81a9dc0 100644 Binary files a/model_templates/ark.BDMscVDJSeqProcessedDataAnnotations.xlsx and b/model_templates/ark.BDMscVDJSeqProcessedDataAnnotations.xlsx differ diff --git a/model_templates/ark.BDMsnATACSeqProcessedDataAnnotations.csv b/model_templates/ark.BDMsnATACSeqProcessedDataAnnotations.csv index b66d05c..63e2000 100644 --- a/model_templates/ark.BDMsnATACSeqProcessedDataAnnotations.csv +++ b/model_templates/ark.BDMsnATACSeqProcessedDataAnnotations.csv @@ -1 +1 @@ -biospecimenType,specimenModality,dataSubtype,fileFormat,resourceType,softwareAndVersion,dataLevel,species,alignmentReference,libraryPrepMethod,diagnosis,parentBiospecimenID,assay,nucleicAcidSource,visitID,cellRangerOutput,project,Component,dataType,biospecimenSubtype,program,individualID,biospecimenID,RObjectClass,processedDataType,metadataType,targetPanelSize,targetPanel,targetPanelSynID +dataSubtype,assay,diagnosis,specimenModality,project,dataType,program,softwareAndVersion,resourceType,alignmentReference,Component,biospecimenSubtype,libraryPrepMethod,biospecimenType,fileFormat,parentBiospecimenID,nucleicAcidSource,visitID,species,cellRangerOutput,dataLevel,targetPanelSize,targetPanelSynID,targetPanel,biospecimenID,individualID,processedDataType,metadataType,RObjectClass diff --git a/model_templates/ark.BDMsnATACSeqProcessedDataAnnotations.xlsx b/model_templates/ark.BDMsnATACSeqProcessedDataAnnotations.xlsx index fc8f709..06545e3 100644 Binary files a/model_templates/ark.BDMsnATACSeqProcessedDataAnnotations.xlsx and b/model_templates/ark.BDMsnATACSeqProcessedDataAnnotations.xlsx differ diff --git a/model_templates/ark.BDMsnRNASeqProcessedDataAnnotations.csv b/model_templates/ark.BDMsnRNASeqProcessedDataAnnotations.csv index d167cb7..fc39a13 100644 --- a/model_templates/ark.BDMsnRNASeqProcessedDataAnnotations.csv +++ b/model_templates/ark.BDMsnRNASeqProcessedDataAnnotations.csv @@ -1 +1 @@ -dataLevel,program,assay,diagnosis,visitID,fileFormat,Component,parentBiospecimenID,nucleicAcidSource,biospecimenType,dataType,alignmentReference,project,libraryPrepMethod,dataSubtype,softwareAndVersion,biospecimenSubtype,species,resourceType,specimenModality,cellRangerOutput,targetPanelSize,targetPanel,targetPanelSynID,RObjectClass,metadataType,processedDataType,individualID,biospecimenID +dataLevel,fileFormat,visitID,parentBiospecimenID,assay,species,Component,nucleicAcidSource,dataSubtype,dataType,project,biospecimenType,diagnosis,biospecimenSubtype,softwareAndVersion,libraryPrepMethod,program,cellRangerOutput,alignmentReference,specimenModality,resourceType,RObjectClass,targetPanelSize,targetPanelSynID,targetPanel,biospecimenID,individualID,processedDataType,metadataType diff --git a/model_templates/ark.BDMsnRNASeqProcessedDataAnnotations.xlsx b/model_templates/ark.BDMsnRNASeqProcessedDataAnnotations.xlsx index df47cd1..2ea1f4e 100644 Binary files a/model_templates/ark.BDMsnRNASeqProcessedDataAnnotations.xlsx and b/model_templates/ark.BDMsnRNASeqProcessedDataAnnotations.xlsx differ diff --git a/model_templates/ark.BiospecimenMetadataTemplate.csv b/model_templates/ark.BiospecimenMetadataTemplate.csv index 1761cc4..8f17c51 100644 --- a/model_templates/ark.BiospecimenMetadataTemplate.csv +++ b/model_templates/ark.BiospecimenMetadataTemplate.csv @@ -1 +1 @@ -biospecimenSubtype,biospecimenID,project,parentBiospecimenID,biospecimenType,notes,Component,altSampleID,program,individualID,plateID,cellType,cellOntologyID,userDefinedCellType,FACSPopulation,synovialCollectionProcedure,anatomicalSite,skinSiteStatus,salivaCollectionProcedure,krennStroma,krennSynovitisScore,krennLining,krennInflammatory,primaryCellSource,visitID +biospecimenID,altSampleID,biospecimenSubtype,individualID,project,notes,biospecimenType,Component,program,parentBiospecimenID,cellType,userDefinedCellType,cellOntologyID,FACSPopulation,primaryCellSource,krennStroma,krennSynovitisScore,anatomicalSite,krennLining,krennInflammatory,synovialCollectionProcedure,skinSiteStatus,salivaCollectionProcedure,visitID diff --git a/model_templates/ark.BiospecimenMetadataTemplate.xlsx b/model_templates/ark.BiospecimenMetadataTemplate.xlsx index 8d361df..f0d82f3 100644 Binary files a/model_templates/ark.BiospecimenMetadataTemplate.xlsx and b/model_templates/ark.BiospecimenMetadataTemplate.xlsx differ diff --git a/model_templates/ark.BulkATAC-seqAssayMetadataTemplate.csv b/model_templates/ark.BulkATAC-seqAssayMetadataTemplate.csv index 7dc160e..37eb055 100644 --- a/model_templates/ark.BulkATAC-seqAssayMetadataTemplate.csv +++ b/model_templates/ark.BulkATAC-seqAssayMetadataTemplate.csv @@ -1 +1 @@ -alignmentReference,softwareAndVersion,specimenModality,nucleicAcidSource,platform,Component,totalReads,assay,sampleProcessingBatch,dataCollectionBatch,libraryPrepMethod,libraryID,biospecimenID,10xProbeSetReference +libraryPrepMethod,softwareAndVersion,totalReads,assay,platform,alignmentReference,dataCollectionBatch,Component,specimenModality,nucleicAcidSource,sampleProcessingBatch,10xProbeSetReference,libraryID,biospecimenID diff --git a/model_templates/ark.BulkATAC-seqAssayMetadataTemplate.xlsx b/model_templates/ark.BulkATAC-seqAssayMetadataTemplate.xlsx index c4bc98b..64ff0d5 100644 Binary files a/model_templates/ark.BulkATAC-seqAssayMetadataTemplate.xlsx and b/model_templates/ark.BulkATAC-seqAssayMetadataTemplate.xlsx differ diff --git a/model_templates/ark.BulkRNA-seqAssayMetadataTemplate.csv b/model_templates/ark.BulkRNA-seqAssayMetadataTemplate.csv index 1db47c5..561c8bb 100644 --- a/model_templates/ark.BulkRNA-seqAssayMetadataTemplate.csv +++ b/model_templates/ark.BulkRNA-seqAssayMetadataTemplate.csv @@ -1 +1 @@ -libraryPrepMethod,Component,softwareAndVersion,dataCollectionBatch,nucleicAcidSource,totalReads,assay,sampleProcessingBatch,alignmentReference,specimenModality,platform,10xProbeSetReference,biospecimenID,libraryID +totalReads,assay,alignmentReference,Component,nucleicAcidSource,specimenModality,libraryPrepMethod,dataCollectionBatch,sampleProcessingBatch,softwareAndVersion,platform,biospecimenID,libraryID,10xProbeSetReference diff --git a/model_templates/ark.BulkRNA-seqAssayMetadataTemplate.xlsx b/model_templates/ark.BulkRNA-seqAssayMetadataTemplate.xlsx index df7ae9b..20c0e5d 100644 Binary files a/model_templates/ark.BulkRNA-seqAssayMetadataTemplate.xlsx and b/model_templates/ark.BulkRNA-seqAssayMetadataTemplate.xlsx differ diff --git a/model_templates/ark.ClinicalMetadataTemplate.csv b/model_templates/ark.ClinicalMetadataTemplate.csv index dd25c2f..c3dde7d 100644 --- a/model_templates/ark.ClinicalMetadataTemplate.csv +++ b/model_templates/ark.ClinicalMetadataTemplate.csv @@ -1 +1 @@ -diagnosis,heightUnits,individualID,program,species,age,weight,weightUnits,project,ageUnits,sex,race,Component,ethnicity,comorbidities,height,CDASI,PASI,vitiligoType,VASI,VETI,VIDA,visitID,diabetesType +individualID,heightUnits,height,weightUnits,age,comorbidities,diagnosis,project,species,Component,ageUnits,weight,sex,program,ethnicity,race,PASI,diabetesType,CDASI,VASI,VIDA,VETI,vitiligoType,visitID diff --git a/model_templates/ark.ClinicalMetadataTemplate.xlsx b/model_templates/ark.ClinicalMetadataTemplate.xlsx index 045b662..c3d449c 100644 Binary files a/model_templates/ark.ClinicalMetadataTemplate.xlsx and b/model_templates/ark.ClinicalMetadataTemplate.xlsx differ diff --git a/model_templates/ark.CyTOFAssayMetadataTemplate.csv b/model_templates/ark.CyTOFAssayMetadataTemplate.csv index 9b3edf0..3d629e2 100644 --- a/model_templates/ark.CyTOFAssayMetadataTemplate.csv +++ b/model_templates/ark.CyTOFAssayMetadataTemplate.csv @@ -1 +1 @@ -platform,targetPanelSize,softwareAndVersion,assay,Component,sampleProcessingBatch,biospecimenID,targetPanelSynID,dataCollectionBatch,targetPanel +targetPanelSynID,targetPanel,platform,dataCollectionBatch,assay,Component,softwareAndVersion,biospecimenID,targetPanelSize,sampleProcessingBatch diff --git a/model_templates/ark.CyTOFAssayMetadataTemplate.xlsx b/model_templates/ark.CyTOFAssayMetadataTemplate.xlsx index 6fcc8c2..2874f6c 100644 Binary files a/model_templates/ark.CyTOFAssayMetadataTemplate.xlsx and b/model_templates/ark.CyTOFAssayMetadataTemplate.xlsx differ diff --git a/model_templates/ark.DatasetAnnotationTemplate.csv b/model_templates/ark.DatasetAnnotationTemplate.csv index c3edfb3..5131cf0 100644 --- a/model_templates/ark.DatasetAnnotationTemplate.csv +++ b/model_templates/ark.DatasetAnnotationTemplate.csv @@ -1 +1 @@ -associatedCodeURL,datasetType,ImmPortAccession,project,biospecimenSubtype,publicationSynID,dbGapAccession,species,acknowledgmentStatement,biospecimenType,assay,program,datasetDescription,associatedDataset,Component,diagnosis,datasetStatus,dataType,dataSubtype,ARKRelease,programPhase +Component,datasetType,diagnosis,datasetStatus,biospecimenType,assay,datasetDescription,acknowledgmentStatement,biospecimenSubtype,dbGapAccession,species,associatedCodeURL,dataType,publicationSynID,project,program,associatedDataset,ARKRelease,ImmPortAccession,dataSubtype,programPhase diff --git a/model_templates/ark.DatasetAnnotationTemplate.xlsx b/model_templates/ark.DatasetAnnotationTemplate.xlsx index d95d277..73ed66c 100644 Binary files a/model_templates/ark.DatasetAnnotationTemplate.xlsx and b/model_templates/ark.DatasetAnnotationTemplate.xlsx differ diff --git a/model_templates/ark.FCSFileAnnotationTemplate.csv b/model_templates/ark.FCSFileAnnotationTemplate.csv index cd58a28..ee3e566 100644 --- a/model_templates/ark.FCSFileAnnotationTemplate.csv +++ b/model_templates/ark.FCSFileAnnotationTemplate.csv @@ -1 +1 @@ -specimenModality,eventCount,fileFormat,Component,assay,dataCollectionBatch,sampleProcessingBatch,individualID,biospecimenID +specimenModality,assay,Component,fileFormat,eventCount,biospecimenID,individualID,sampleProcessingBatch,dataCollectionBatch diff --git a/model_templates/ark.FCSFileAnnotationTemplate.xlsx b/model_templates/ark.FCSFileAnnotationTemplate.xlsx index 6b1231a..2800cc1 100644 Binary files a/model_templates/ark.FCSFileAnnotationTemplate.xlsx and b/model_templates/ark.FCSFileAnnotationTemplate.xlsx differ diff --git a/model_templates/ark.FastqFileAnnotationTemplate.csv b/model_templates/ark.FastqFileAnnotationTemplate.csv index 1bd4ac8..7432d1a 100644 --- a/model_templates/ark.FastqFileAnnotationTemplate.csv +++ b/model_templates/ark.FastqFileAnnotationTemplate.csv @@ -1 +1 @@ -Component,assay,specimenModality,fileFormat,readLength,targetPanelSynID,targetPanelSize,targetPanel,biospecimenID,individualID,libraryID +readLength,assay,fileFormat,Component,specimenModality,targetPanel,targetPanelSynID,targetPanelSize,biospecimenID,individualID,libraryID diff --git a/model_templates/ark.FastqFileAnnotationTemplate.xlsx b/model_templates/ark.FastqFileAnnotationTemplate.xlsx index a1e1db6..8561f64 100644 Binary files a/model_templates/ark.FastqFileAnnotationTemplate.xlsx and b/model_templates/ark.FastqFileAnnotationTemplate.xlsx differ diff --git a/model_templates/ark.InVitroBiospecimenMetadataTemplate.csv b/model_templates/ark.InVitroBiospecimenMetadataTemplate.csv index 5d5c450..f3df7ec 100644 --- a/model_templates/ark.InVitroBiospecimenMetadataTemplate.csv +++ b/model_templates/ark.InVitroBiospecimenMetadataTemplate.csv @@ -1 +1 @@ -individualID,treatment,altSampleID,project,notes,biospecimenID,program,Component,parentBiospecimenID,biospecimenType,biospecimenSubtype,treatmentTimepoint,plateID,visitID,anatomicalSite,skinSiteStatus,cellOntologyID,cellType,krennLining,krennSynovitisScore,krennStroma,synovialCollectionProcedure,krennInflammatory,salivaCollectionProcedure,primaryCellSource,userDefinedCellType,FACSPopulation +treatment,project,biospecimenID,notes,parentBiospecimenID,altSampleID,Component,biospecimenType,individualID,biospecimenSubtype,treatmentTimepoint,program,salivaCollectionProcedure,krennLining,krennSynovitisScore,krennInflammatory,anatomicalSite,krennStroma,synovialCollectionProcedure,cellType,cellOntologyID,primaryCellSource,skinSiteStatus,userDefinedCellType,FACSPopulation,visitID diff --git a/model_templates/ark.InVitroBiospecimenMetadataTemplate.xlsx b/model_templates/ark.InVitroBiospecimenMetadataTemplate.xlsx index e3d189f..d72839b 100644 Binary files a/model_templates/ark.InVitroBiospecimenMetadataTemplate.xlsx and b/model_templates/ark.InVitroBiospecimenMetadataTemplate.xlsx differ diff --git a/model_templates/ark.OlinkAssayMetadataTemplate.csv b/model_templates/ark.OlinkAssayMetadataTemplate.csv index 82b9568..bbc35e1 100644 --- a/model_templates/ark.OlinkAssayMetadataTemplate.csv +++ b/model_templates/ark.OlinkAssayMetadataTemplate.csv @@ -1 +1 @@ -targetPanelSynID,plateID,Component,assay,targetPanel,targetPanelSize,platform +assay,plateID,platform,targetPanelSize,targetPanelSynID,Component,targetPanel diff --git a/model_templates/ark.OlinkAssayMetadataTemplate.xlsx b/model_templates/ark.OlinkAssayMetadataTemplate.xlsx index 300aae0..bf2a269 100644 Binary files a/model_templates/ark.OlinkAssayMetadataTemplate.xlsx and b/model_templates/ark.OlinkAssayMetadataTemplate.xlsx differ diff --git a/model_templates/ark.OlinkFileAnnotationTemplate.csv b/model_templates/ark.OlinkFileAnnotationTemplate.csv index e569804..13d4e68 100644 --- a/model_templates/ark.OlinkFileAnnotationTemplate.csv +++ b/model_templates/ark.OlinkFileAnnotationTemplate.csv @@ -1 +1 @@ -plateID,Component,resourceType,fileFormat,specimenModality +plateID,specimenModality,resourceType,Component,fileFormat diff --git a/model_templates/ark.OlinkFileAnnotationTemplate.xlsx b/model_templates/ark.OlinkFileAnnotationTemplate.xlsx index ee8946b..3dcda53 100644 Binary files a/model_templates/ark.OlinkFileAnnotationTemplate.xlsx and b/model_templates/ark.OlinkFileAnnotationTemplate.xlsx differ diff --git a/model_templates/ark.PublicationMetadataTemplate.csv b/model_templates/ark.PublicationMetadataTemplate.csv index d7c0a52..def1dea 100644 --- a/model_templates/ark.PublicationMetadataTemplate.csv +++ b/model_templates/ark.PublicationMetadataTemplate.csv @@ -1 +1 @@ -project,publicationDate,DOI,program,Component,title,associatedDataset,PMID,publicationType,journal,PMCID,year,programPhase +program,associatedDataset,title,project,publicationDate,journal,Component,year,DOI,PMCID,PMID,publicationType,programPhase diff --git a/model_templates/ark.PublicationMetadataTemplate.xlsx b/model_templates/ark.PublicationMetadataTemplate.xlsx index b510014..5dfc9f8 100644 Binary files a/model_templates/ark.PublicationMetadataTemplate.xlsx and b/model_templates/ark.PublicationMetadataTemplate.xlsx differ diff --git a/model_templates/ark.ScRNASeqAssayMetadataTemplate.csv b/model_templates/ark.ScRNASeqAssayMetadataTemplate.csv index a38574a..0f93b4c 100644 --- a/model_templates/ark.ScRNASeqAssayMetadataTemplate.csv +++ b/model_templates/ark.ScRNASeqAssayMetadataTemplate.csv @@ -1 +1 @@ -sampleProcessingBatch,platform,dataCollectionBatch,totalReads,inputCellCount,assay,sequencingSaturation,alignmentReference,softwareAndVersion,Component,libraryPrepMethod,percentCellViability,nucleicAcidSource,specimenModality,10xProbeSetReference,biospecimenID,libraryID +specimenModality,totalReads,nucleicAcidSource,alignmentReference,softwareAndVersion,Component,libraryPrepMethod,sampleProcessingBatch,dataCollectionBatch,platform,inputCellCount,percentCellViability,assay,sequencingSaturation,libraryID,biospecimenID,10xProbeSetReference diff --git a/model_templates/ark.ScRNASeqAssayMetadataTemplate.xlsx b/model_templates/ark.ScRNASeqAssayMetadataTemplate.xlsx index d4aa9a1..3fcc148 100644 Binary files a/model_templates/ark.ScRNASeqAssayMetadataTemplate.xlsx and b/model_templates/ark.ScRNASeqAssayMetadataTemplate.xlsx differ diff --git a/model_templates/ark.ScRNASeqProcessedDataAnnotationTemplate.csv b/model_templates/ark.ScRNASeqProcessedDataAnnotationTemplate.csv index 48330a4..baabe47 100644 --- a/model_templates/ark.ScRNASeqProcessedDataAnnotationTemplate.csv +++ b/model_templates/ark.ScRNASeqProcessedDataAnnotationTemplate.csv @@ -1 +1 @@ -fileFormat,dataLevel,Component,resourceType,specimenModality,assay,cellRangerOutput,RObjectClass,processedDataType,metadataType,individualID,biospecimenID,targetPanelSize,targetPanelSynID,targetPanel +assay,dataLevel,Component,cellRangerOutput,resourceType,fileFormat,specimenModality,targetPanelSynID,targetPanelSize,targetPanel,metadataType,processedDataType,RObjectClass,individualID,biospecimenID diff --git a/model_templates/ark.ScRNASeqProcessedDataAnnotationTemplate.xlsx b/model_templates/ark.ScRNASeqProcessedDataAnnotationTemplate.xlsx index 8f4c004..3a8a084 100644 Binary files a/model_templates/ark.ScRNASeqProcessedDataAnnotationTemplate.xlsx and b/model_templates/ark.ScRNASeqProcessedDataAnnotationTemplate.xlsx differ diff --git a/model_templates/ark.ScVDJSeqProcessedDataAnnotationTemplate.csv b/model_templates/ark.ScVDJSeqProcessedDataAnnotationTemplate.csv index 552a611..26a6682 100644 --- a/model_templates/ark.ScVDJSeqProcessedDataAnnotationTemplate.csv +++ b/model_templates/ark.ScVDJSeqProcessedDataAnnotationTemplate.csv @@ -1 +1 @@ -dataLevel,Component,fileFormat,specimenModality,assay,resourceType,RObjectClass,individualID,biospecimenID,targetPanelSize,targetPanelSynID,targetPanel,metadataType,processedDataType +resourceType,dataLevel,Component,specimenModality,fileFormat,assay,processedDataType,metadataType,biospecimenID,individualID,RObjectClass,targetPanelSynID,targetPanelSize,targetPanel diff --git a/model_templates/ark.ScVDJSeqProcessedDataAnnotationTemplate.xlsx b/model_templates/ark.ScVDJSeqProcessedDataAnnotationTemplate.xlsx index c849a6f..09ae495 100644 Binary files a/model_templates/ark.ScVDJSeqProcessedDataAnnotationTemplate.xlsx and b/model_templates/ark.ScVDJSeqProcessedDataAnnotationTemplate.xlsx differ diff --git a/model_templates/ark.SnATAC-seqAssayMetadataTemplate.csv b/model_templates/ark.SnATAC-seqAssayMetadataTemplate.csv index ead262b..2f92da3 100644 --- a/model_templates/ark.SnATAC-seqAssayMetadataTemplate.csv +++ b/model_templates/ark.SnATAC-seqAssayMetadataTemplate.csv @@ -1 +1 @@ -percentCellViability,platform,specimenModality,libraryPrepMethod,totalReads,inputCellCount,sequencingSaturation,assay,Component,sampleProcessingBatch,dataCollectionBatch,softwareAndVersion,nucleicAcidSource,alignmentReference,libraryID,biospecimenID,10xProbeSetReference +softwareAndVersion,Component,nucleicAcidSource,totalReads,percentCellViability,specimenModality,libraryPrepMethod,assay,sequencingSaturation,sampleProcessingBatch,inputCellCount,platform,dataCollectionBatch,alignmentReference,libraryID,biospecimenID,10xProbeSetReference diff --git a/model_templates/ark.SnATAC-seqAssayMetadataTemplate.xlsx b/model_templates/ark.SnATAC-seqAssayMetadataTemplate.xlsx index d3ff562..b7593d6 100644 Binary files a/model_templates/ark.SnATAC-seqAssayMetadataTemplate.xlsx and b/model_templates/ark.SnATAC-seqAssayMetadataTemplate.xlsx differ diff --git a/model_templates/ark.SnATACSeqProcessedDataAnnotationTemplate.csv b/model_templates/ark.SnATACSeqProcessedDataAnnotationTemplate.csv index 670a3b5..8bc691a 100644 --- a/model_templates/ark.SnATACSeqProcessedDataAnnotationTemplate.csv +++ b/model_templates/ark.SnATACSeqProcessedDataAnnotationTemplate.csv @@ -1 +1 @@ -cellRangerOutput,dataLevel,specimenModality,fileFormat,resourceType,assay,Component,biospecimenID,individualID,RObjectClass,metadataType,processedDataType,targetPanel,targetPanelSize,targetPanelSynID +Component,cellRangerOutput,fileFormat,resourceType,dataLevel,assay,specimenModality,RObjectClass,processedDataType,metadataType,targetPanel,targetPanelSynID,targetPanelSize,individualID,biospecimenID diff --git a/model_templates/ark.SnATACSeqProcessedDataAnnotationTemplate.xlsx b/model_templates/ark.SnATACSeqProcessedDataAnnotationTemplate.xlsx index 0dc61ba..8805370 100644 Binary files a/model_templates/ark.SnATACSeqProcessedDataAnnotationTemplate.xlsx and b/model_templates/ark.SnATACSeqProcessedDataAnnotationTemplate.xlsx differ diff --git a/model_templates/ark.SnRNASeqAssayMetadataTemplate.csv b/model_templates/ark.SnRNASeqAssayMetadataTemplate.csv index 811a3bb..45c623b 100644 --- a/model_templates/ark.SnRNASeqAssayMetadataTemplate.csv +++ b/model_templates/ark.SnRNASeqAssayMetadataTemplate.csv @@ -1 +1 @@ -libraryPrepMethod,assay,totalReads,dataCollectionBatch,Component,percentCellViability,nucleicAcidSource,specimenModality,alignmentReference,sampleProcessingBatch,inputCellCount,sequencingSaturation,softwareAndVersion,platform,10xProbeSetReference,libraryID,biospecimenID +sampleProcessingBatch,nucleicAcidSource,inputCellCount,specimenModality,assay,totalReads,dataCollectionBatch,Component,platform,softwareAndVersion,alignmentReference,sequencingSaturation,percentCellViability,libraryPrepMethod,libraryID,biospecimenID,10xProbeSetReference diff --git a/model_templates/ark.SnRNASeqAssayMetadataTemplate.xlsx b/model_templates/ark.SnRNASeqAssayMetadataTemplate.xlsx index 88c38e5..34754d4 100644 Binary files a/model_templates/ark.SnRNASeqAssayMetadataTemplate.xlsx and b/model_templates/ark.SnRNASeqAssayMetadataTemplate.xlsx differ diff --git a/model_templates/ark.SnRNASeqProcessedDataAnnotationTemplate.csv b/model_templates/ark.SnRNASeqProcessedDataAnnotationTemplate.csv index c1dd44e..59d9501 100644 --- a/model_templates/ark.SnRNASeqProcessedDataAnnotationTemplate.csv +++ b/model_templates/ark.SnRNASeqProcessedDataAnnotationTemplate.csv @@ -1 +1 @@ -cellRangerOutput,specimenModality,Component,fileFormat,assay,dataLevel,resourceType,biospecimenID,individualID,RObjectClass,targetPanelSynID,targetPanelSize,targetPanel,metadataType,processedDataType +cellRangerOutput,Component,dataLevel,specimenModality,resourceType,fileFormat,assay,biospecimenID,individualID,metadataType,processedDataType,RObjectClass,targetPanelSize,targetPanel,targetPanelSynID diff --git a/model_templates/ark.SnRNASeqProcessedDataAnnotationTemplate.xlsx b/model_templates/ark.SnRNASeqProcessedDataAnnotationTemplate.xlsx index fcd9157..78d076a 100644 Binary files a/model_templates/ark.SnRNASeqProcessedDataAnnotationTemplate.xlsx and b/model_templates/ark.SnRNASeqProcessedDataAnnotationTemplate.xlsx differ diff --git a/model_templates/ark.SpatialAssayMetadataTemplate.csv b/model_templates/ark.SpatialAssayMetadataTemplate.csv deleted file mode 100644 index 230677e..0000000 --- a/model_templates/ark.SpatialAssayMetadataTemplate.csv +++ /dev/null @@ -1 +0,0 @@ -targetPanelSynID,specimenModality,targetPanelSize,Component,targetPanel,sampleProcessingBatch,assay,dataCollectionBatch,individualID,biospecimenID,slideID diff --git a/model_templates/ark.SpatialAssayMetadataTemplate.xlsx b/model_templates/ark.SpatialAssayMetadataTemplate.xlsx deleted file mode 100644 index c95fa62..0000000 Binary files a/model_templates/ark.SpatialAssayMetadataTemplate.xlsx and /dev/null differ diff --git a/model_templates/ark.SpatialImagingAssayMetadataTemplate.csv b/model_templates/ark.SpatialImagingAssayMetadataTemplate.csv new file mode 100644 index 0000000..9ea2f69 --- /dev/null +++ b/model_templates/ark.SpatialImagingAssayMetadataTemplate.csv @@ -0,0 +1 @@ +targetPanel,targetPanelSynID,assay,specimenModality,dataCollectionBatch,targetPanelSize,sampleProcessingBatch,Component,biospecimenID,slideID diff --git a/model_templates/ark.SpatialImagingAssayMetadataTemplate.xlsx b/model_templates/ark.SpatialImagingAssayMetadataTemplate.xlsx new file mode 100644 index 0000000..0b2f7f7 Binary files /dev/null and b/model_templates/ark.SpatialImagingAssayMetadataTemplate.xlsx differ diff --git a/model_templates/ark.SpatialImagingFileAnnotationTemplate.csv b/model_templates/ark.SpatialImagingFileAnnotationTemplate.csv index eaf1ccf..f73e4d9 100644 --- a/model_templates/ark.SpatialImagingFileAnnotationTemplate.csv +++ b/model_templates/ark.SpatialImagingFileAnnotationTemplate.csv @@ -1 +1 @@ -Component,resourceType,fileFormat,assay,specimenModality,processedDataType,metadataType,RObjectClass,slideID,individualID,biospecimenID +Component,specimenModality,resourceType,assay,fileFormat,slideID,biospecimenID,metadataType,processedDataType,RObjectClass diff --git a/model_templates/ark.SpatialImagingFileAnnotationTemplate.xlsx b/model_templates/ark.SpatialImagingFileAnnotationTemplate.xlsx index bd40f1c..85a028d 100644 Binary files a/model_templates/ark.SpatialImagingFileAnnotationTemplate.xlsx and b/model_templates/ark.SpatialImagingFileAnnotationTemplate.xlsx differ diff --git a/templates_by_context.txt b/templates_by_context.txt index cdd7fe4..03bd2b9 100644 --- a/templates_by_context.txt +++ b/templates_by_context.txt @@ -26,5 +26,5 @@ ScVDJSeqProcessedDataAnnotationTemplate singlecell SnATACSeqProcessedDataAnnotationTemplate singlecell SnRNASeqProcessedDataAnnotationTemplate singlecell BDMSpatialImagingFileAnnotations spatial -SpatialAssayMetadataTemplate spatial +SpatialImagingAssayMetadataTemplate spatial SpatialImagingFileAnnotationTemplate spatial