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Static Browser Plan

The curated interpretation corpus should become browsable from docs or a dedicated static site before it needs a deployed dynamic service.

Generate static pages from curation/genesets/*.yaml:

curation/genesets/*.yaml
  -> validate with LinkML, term validator, and reference validator
  -> materialize a small JSON index
  -> generate one page per curated gene set
  -> generate collection, context, category, and recovery-status index pages

The generator should live in the Python workflow package, for example as:

genesets-workflows curate build-pages \
  --dir curation/genesets \
  --out-dir docs/src/generated/curation

Those generated pages can be committed while the corpus is small, or built in CI for a static docs deploy once the corpus grows.

Page Shape

Each gene set page should show:

  • source ID, name, collection, taxon, direction, and gene count;
  • biological contexts with ontology IDs and labels;
  • curated GO associations grouped by role category;
  • confidence, specificity, and recovery status;
  • enrichment stats and overlap genes when present;
  • evidence references and curator notes;
  • links to neighboring index pages by collection, context, GO term, category, and recovery status.

LinkML Browser Role

Use generated LinkML docs for the schema reference. Use generated corpus pages for the curated instances. A schema browser explains what TermAssociation means; an instance browser explains what MSIGDB:HAY_BONE_MARROW_DENDRITIC_CELL means.

Web UI Relationship

The current web explorer browses eval report bundles. A future curated gene set browser can reuse the same principles but should read curated corpus artifacts instead of report bundles:

  • source of truth remains the validated YAML corpus;
  • generated JSON gives the browser a stable read model;
  • static pages support simple hosting and durable links;
  • a richer client-side UI can be added later over the same JSON.

Do not add curated-browser behavior to the Rust compute engine. If enrichment is needed to refresh stats, run that through workflows and write artifacts back to the curation/report layer.