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@Bankso Bankso commented Mar 12, 2025

Changelog

  • Added grant numbers from recent grant curation to grant_number.csv
  • Added Institutions for Grant View annotation
    • Update institution_name.csv
    • Update institution_alias.csv
  • Add DUOplus attributes and identify existing Study attributes that map to some DUOplus elements
  • Add controlled vocab CSVs and update mapping.yml for DUOplus-related Study attributes
    • Study Source Geography + study/sourceGeography.csv
    • Study Data Permission + study/dataPermission.csv
    • Study Data Tier + study/dataTier.csv
  • Add additional licenses available to Synapse contributors via studyLicense.csv
  • Add Biospecimen Treatment Type attribute; Biospecimen Tumor Status attribute and valid values
  • Update Individual Sex and Model Sex to be required attributes
  • Add 'Not Applicable' to dataset_species.csv
  • Add Individual Vital Status and vitalStatus.csv + mapping in mapping.yml
  • Include Biospecimen Tumor Status in Biospecimen model
  • Add templates for Dataset View and DUO code <--> AR mapping JSON schemas, which can be bound to Synapse entities
  • Update File Longitudinal Event Type description
  • Add a schematic-compatible version of the Synapse Data Catalog model
  • Add attribute Grant End Date to Grant View (was accidentally omitted from previous version)

Add Not Applicable as a valid value
Update format and content of auto-generate Dataset View JSON schema
Template for Synapse project schema that relates DUO codes to access restrictions
Remove maxItems from JSON schema
Adjust File Longitudinal Event Type description to better describe intent of attribute
Added Data Catalog attributes, descriptions, and model definition. Descriptions contain notes on equivalent annotations in other MC2 data model components
Add Grant End Date as attribute and include in Grant View model
Add mapping of assay annotations to portal icon tags for the CCKP
To help prepare resource content tags for the CCKP, this file relates valid values for assay with high level categorical labels. This is intended to be used as input during portal sync operations.
Add DUOplus attributes and identify existing Study attributes that map to some DUOplus elements
Add valid value mappings for DUOplus analogs Study Source Geography, Study Data Permission, Study Data Tier
Add additional licenses described in DUOplus6
Add valid values to all_valid_values.csv and new Study attributes
Collate model CSV and convert to JSON-LD with schematic 24.12.1
@Bankso Bankso requested a review from aditigopalan as a code owner March 12, 2025 19:45
@Bankso Bankso added the minor PR label for a minor update label Mar 12, 2025
Bankso added 26 commits March 19, 2025 12:43
Add valid value mappings for dataCatalog model
Allow multiple assays to be designated for a file. For example, allow selection of "Hematoxylin and Eosin Staining Method" and "Imaging" or "Immunohistochemistry Staining Method" and "Fluorescence Microscopy"
schematic 24.12.1
Add item typing to template JSON schema
Indicate duoCodes annotation is required to satisfy if statement and trigger ARs
Add duoCodes requirement to template if statement
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Bankso commented Apr 4, 2025

@aditigopalan could you look over this PR when you have a chance?

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Took me a while to go through everything, lgtm 🚀

@aditigopalan aditigopalan merged commit 498c8d1 into main Apr 8, 2025
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@aditigopalan aditigopalan deleted the 145-update-grant-values branch April 8, 2025 15:10
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3 participants