Add missing info #203
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Add missing info #203
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NGS reads-type columns were missing descriptions because Reads wasn't capitalized Added attribute definitions for GeoMx Tags and GeoMx Tissue Stain (columns already in template)
From updated mappings (will be continuously updated): https://docs.google.com/spreadsheets/d/1LLpSIFAh12YdKnGfzXMxGpoKCaEH90nDx-QvncaIJlk/edit?usp=sharing
Added CODEX to assay values
Updated AR data dictionary CSV with new columns and changed column names to camel case, so they can be directly used when building JSON schema
Updated conventions:
Data model schemas: {org abbreviation}.{Component}-{Release Version Tag}-schema.json
Access Restriction schemas: {org abbreviation}.AccessRequirement-{Project identifier or "Project" if multiple grant conditions are contained in the schema}-{Release Version Tag}-schema.json
Match columns in example expanded AR reference table
AR-related content has been moved to governanceDUO repo and will no longer be maintained here
Add NGS Library Source Material and NGS Library Source Molecule attributes
Add valid values mappings for NGS Library Source Material and NGS Library Source Molecule attributes, from sequencingLevel1/librarySourceMolecule.csv and sequencingLevel1/librarySelection.csv, respectively
NGS Library Source Molecule and NGS Library Source Material
NGS Library Source Molecule and NGS Library Source Material
NGS Library Source Material, NGS Library Source Molecule
schematic 25.4.1
Template is superseded by v10.0.0 JSON; v10.0.0 is valid Synapse JSON. JSON schema is not currently used in our curation workflow - v10.0.0 schema is being maintained as an example of valid JSON schema, since there were some changes that needed to be made previously to create useable JSON schemas from schematic auto-generated outputs
schematic 25.4.1
schematic 25.4.1
aditya-nath-sage
approved these changes
Jun 6, 2025
|
LGTM, would it be useful adding tests or validation to ensure only allowed duoCodes are used? |
I think that could be useful once we've finalized how DCC data models will be used in governance workflows. For now, I think limiting duoCodes to the defined valid values is sufficient. The data sharing plan prep phase will also help us define which DUO codes are applicable, so adjusting the data model to only contain allowed DUO codes is probably not necessary, unless contributors start submitting data sharing plans independently on a regular basis |
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Changelog
CODEXtoassay.csvDCCtofile_formats.csv