Curated Gene Set Interpretations

The curation corpus stores expert GO interpretations of non-GO gene sets. It is both a precision/recall fixture for enrichment reports and the source content for a future curated gene set browser.

Interpretations live in curation/genesets/*.yaml. Each file conforms to the LinkML schema at curation/schema/genesets_interpretation.yaml and is validated with:

• LinkML structural validation;
• linkml-term-validator for ontology IDs and labels;
• linkml-reference-validator for cited literature snippets.

What A Curated File Contains

Each curated interpretation records:

• stable source identifier and source collection;
• biological context terms such as cell type, disease, phenotype, perturbagen, or experimental condition;
• curated GO term associations;
• curator role category, confidence, and specificity;
• recovery status, distinguishing annotation gaps from gene set membership gaps;
• enrichment stats that seeded an association;
• optional cited evidence and curator notes.

The current corpus includes MSigDB C8 cell-type signatures, KEGG legacy disease and pathway sets, Reactome and Hallmark sets, and a C7 perturbation contrast. The manifest at curation/genesets/manifest.tsv is the index of curated sets.

Why This Is Separate From Evals

Eval result tables say which GO terms a run recovered. The curation corpus says which GO terms are biologically appropriate for a gene set. Keeping those separate lets reports measure precision and recall without rewriting biological truth to match the current state of GO annotations.

category is the biological judgment. recovery_status explains whether the current annotation and membership state makes that judgment recoverable:

• annotation_supported: current annotations recover the term;
• annotation_gap: relevant genes are present, but GO annotation is too shallow;
• membership_gap: the gene set lacks genes needed to support the term.

Local Commands

Validate the corpus and build the current curation report:

just curate-validate
just curate-report

See Curation Workflow for the full workflow and Schema Reference for the LinkML model.

Browser Direction

The curated corpus should become browsable as generated pages or a static site. The source of truth should remain the validated YAML files, with generated JSON and HTML/Markdown as read models.

Use LinkML-generated docs for schema reference. Use generated per-gene-set pages for the corpus itself. See Static Browser Plan.