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Merged
jmvera255 merged 8 commits into from
May 12, 2026
Merged

2026.04.r1 updates #93

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5869340
revise metadata-related attributes for desired behavior in main conte…
jmvera255 May 12, 2026
859dc67
create new conditional attribute 'demultiplexMethod' to capture detai…
jmvera255 May 12, 2026
65993fe
Merge 859dc67280d7c9d66bfd2f1b238384e2bcbf53a7 into 83dc7739fb91cc9f1…
jmvera255 May 12, 2026
2b3bf77
GitHub Action: commit results of ci-schema-convert workflow
jmvera255 May 12, 2026
beec38c
remove redundancy in metadataType enums
jmvera255 May 12, 2026
32240c4
add 'demultiplexMethod' to spatial context
jmvera255 May 12, 2026
32d9ab4
Merge 32240c437408b870e2b6710fb60201e1790af7e0 into 83dc7739fb91cc9f1…
jmvera255 May 12, 2026
a6053f3
GitHub Action: commit results of ci-schema-convert workflow
jmvera255 May 12, 2026
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3 changes: 2 additions & 1 deletion ark.all_attributes.csv
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"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_list","","","",""
"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 microarray map, tissue multiarray map, user manual","","TRUE","","","","string","","","",""
"metadataType","A label further classifying the content of metadata resource.","assay, biospecimen, cell coordinates, clinical, data dictionary, demographics, 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","","","",""
Expand Down Expand Up @@ -108,3 +108,4 @@
"ImmPortAccession","Accession to corresponding information in ImmPort.","","","FALSE","","","regex search ^SDY error","string","","","","^SDY"
"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","","","","^CL:"
"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","","","","^pmc:PMC[0-9]{8}"
"demultiplexMethod","This attribute indicates the general method that needs to be used to demultiplex multispecimen raw data.","genotypic demux, hashtag oligos, sample barcode, slide array map","","TRUE","","","","string","","","",""
3 changes: 2 additions & 1 deletion model_contexts/biospecimen/ark.biospecimen_model.csv
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"specimenModality","Label assigned to experimental data files indicating whether the data contained corresponds to a single or multiple biospecimens","multispecimen, single specimen, unknown","","TRUE","","","","string","","","",""
"parentBiospecimenID","The biospecimenID associated with the originating biospecimen for derived or child biospecimens.","","","FALSE","","","","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 microarray map, tissue multiarray map, user manual","","TRUE","","","","string","","","",""
"metadataType","A label further classifying the content of metadata resource.","assay, biospecimen, cell coordinates, clinical, data dictionary, demographics, 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","","","",""
Expand Down Expand Up @@ -122,3 +122,4 @@
"ImmPortAccession","Accession to corresponding information in ImmPort.","","","FALSE","","","regex search ^SDY error","string","","","","^SDY"
"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","","","","^CL:"
"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","","","","^pmc:PMC[0-9]{8}"
"demultiplexMethod","This attribute indicates the general method that needs to be used to demultiplex multispecimen raw data.","genotypic demux, hashtag oligos, sample barcode, slide array map","","TRUE","","","","string","","","",""
3 changes: 2 additions & 1 deletion model_contexts/clinical/ark.clinical_model.csv
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Expand Up @@ -24,7 +24,7 @@
"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_list","","","",""
"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 microarray map, tissue multiarray map, user manual","","TRUE","","","","string","","","",""
"metadataType","A label further classifying the content of metadata resource.","assay, biospecimen, cell coordinates, clinical, data dictionary, demographics, 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","","","",""
Expand Down Expand Up @@ -114,3 +114,4 @@
"ImmPortAccession","Accession to corresponding information in ImmPort.","","","FALSE","","","regex search ^SDY error","string","","","","^SDY"
"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","","","","^CL:"
"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","","","","^pmc:PMC[0-9]{8}"
"demultiplexMethod","This attribute indicates the general method that needs to be used to demultiplex multispecimen raw data.","genotypic demux, hashtag oligos, sample barcode, slide array map","","TRUE","","","","string","","","",""
3 changes: 2 additions & 1 deletion model_contexts/fastq/ark.fastq_model.csv
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"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_list","","","",""
"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 microarray map, tissue multiarray map, user manual","","TRUE","","","","string","","","",""
"metadataType","A label further classifying the content of metadata resource.","assay, biospecimen, cell coordinates, clinical, data dictionary, demographics, 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","","","",""
Expand Down Expand Up @@ -114,3 +114,4 @@
"ImmPortAccession","Accession to corresponding information in ImmPort.","","","FALSE","","","regex search ^SDY error","string","","","","^SDY"
"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","","","","^CL:"
"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","","","","^pmc:PMC[0-9]{8}"
"demultiplexMethod","This attribute indicates the general method that needs to be used to demultiplex multispecimen raw data.","genotypic demux, hashtag oligos, sample barcode, slide array map","","TRUE","","","","string","","","",""
3 changes: 2 additions & 1 deletion model_contexts/fcs/ark.fcs_model.csv
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Expand Up @@ -23,7 +23,7 @@
"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_list","","","",""
"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 microarray map, tissue multiarray map, user manual","","TRUE","","","","string","","","",""
"metadataType","A label further classifying the content of metadata resource.","assay, biospecimen, cell coordinates, clinical, data dictionary, demographics, 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","","","",""
Expand Down Expand Up @@ -113,3 +113,4 @@
"ImmPortAccession","Accession to corresponding information in ImmPort.","","","FALSE","","","regex search ^SDY error","string","","","","^SDY"
"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","","","","^CL:"
"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","","","","^pmc:PMC[0-9]{8}"
"demultiplexMethod","This attribute indicates the general method that needs to be used to demultiplex multispecimen raw data.","genotypic demux, hashtag oligos, sample barcode, slide array map","","TRUE","","","","string","","","",""
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