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Merged
jmvera255 merged 12 commits into from
Jan 29, 2026
Merged

2026.01.R1 updates #86

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af14eff
add ARK_data_model_dev/2026-01-09_model_updates updates from issue #84"
jmvera255 Jan 28, 2026
0d86b6b
Add new attribute 'sampleCollectionBatch' to biospecimen templates
jmvera255 Jan 28, 2026
1196e25
add cell type related attributes to BDM file annotation templates
jmvera255 Jan 28, 2026
ccde84e
create context-specific set of platform valid values issue #84
jmvera255 Jan 28, 2026
418dd31
Merge ccde84ee98f33d87385b993fefec27b41b6e5c97 into f7946c6c8a1e649b1…
jmvera255 Jan 29, 2026
9dbdde5
GitHub Action: commit results of ci-schema-convert workflow
jmvera255 Jan 29, 2026
37815c8
add new updates from 2026-01-09_model_updates
jmvera255 Jan 29, 2026
07d766f
Merge 37815c8d1471c299eccf1339093b0d16b0efd9e2 into f7946c6c8a1e649b1…
jmvera255 Jan 29, 2026
3032eb8
GitHub Action: commit results of ci-schema-convert workflow
jmvera255 Jan 29, 2026
d1f477e
incorporate changes from 2026-01-27_models_review
jmvera255 Jan 29, 2026
e51bb4c
Merge d1f477ea12f79f375ec7e40146e367340ee6fefe into f7946c6c8a1e649b1…
jmvera255 Jan 29, 2026
4fc742e
GitHub Action: commit results of ci-schema-convert workflow
jmvera255 Jan 29, 2026
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17 changes: 9 additions & 8 deletions ark.all_attributes.csv
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34 changes: 17 additions & 17 deletions model_contexts/biospecimen/ark.biospecimen_context.csv
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Original file line number Diff line number Diff line change
@@ -1,17 +1,17 @@
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, 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",,,,,,,
suction blister fluid,Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.,,"skinSiteStatus, anatomicalSite",,,,,,,
saliva,Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.,,salivaCollectionProcedure,,,,,,,
synovial tissue,Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.,,"synovialCollectionProcedure, anatomicalSite, krennInflammatory, krennLining, krennStroma, krennSynovitisScore",,,,,,,
synovial fluid,Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.,,"synovialCollectionProcedure, anatomicalSite",,,,,,,
flow-sorted cells,A valid value of 'biospecimenSubtype' that triggers conditional dependencies for additional attributes.,,"FACSPopulation, cellOntologyID, cellType, userDefinedCellType",,,,,,,
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,,,,,,,
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
"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, notes, sampleCollectionBatch","","","","","","",""
"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, sampleCollectionBatch","","","","","","",""
"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","","","","","","",""
"suction blister fluid","Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.","","skinSiteStatus, anatomicalSite","","","","","","",""
"saliva","Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.","","salivaCollectionProcedure","","","","","","",""
"synovial tissue","Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.","","synovialCollectionProcedure, anatomicalSite, krennInflammatory, krennLining, krennStroma, krennSynovitisScore","","","","","","",""
"synovial fluid","Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.","","synovialCollectionProcedure, anatomicalSite","","","","","","",""
"flow-sorted cells","A valid value of 'biospecimenSubtype' that triggers conditional dependencies for additional attributes.","","FACSPopulation, cellOntologyID, cellType, userDefinedCellType","","","","","","",""
"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","","","","","","",""
"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"
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