Update documentation to include assay models - #256
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Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Removed a duplicate Biospecimen Key entry from visiumRNALevel2's manifest and re-ran the valid-values sync so Study/shared data-use-code fields match the current DUO ontology IDs in duo.csv instead of stale short codes. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…ence Adds docs pages, download templates, and Standard Terms wiring for 24 models across modules: Biospecimen, Individual, Model, Imaging, NanoString GeoMx, Sequencing, 10x Visium. Reworks generate_linked_table() so each model's Full Field Reference is built from its live DependsOn list cross-checked against its JSON Schema export, sourced from the fully-collated mc2.model.csv rather than each module's own fragmentary CSV - this fixes missing/stale columns (e.g. Biospecimen was missing its foreign-key columns, Study still listed access-requirement fields already moved to governance). Reorganizes the Data Models nav into Sample, Administrative, Resource Sharing, and assay-specific subgroups. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Review needed for markdown files added to docs/models (biospecimen.md, etc.):
Next steps (ongoing in separate branch, https://github.com/mc2-center/data-models/tree/docs-with-mapping-updates):