Curation Workflow

The curation workflow turns enrichment output into LinkML-validated biological interpretations of non-GO gene sets.

Local Setup

Use the curation extra from the Python workflow package:

uv run --project python/genesets-workflows --extra curation \
  genesets-workflows curate --help

The justfile provides the common repository commands:

just curate-validate-schema
just curate-validate
just curate-report

Steps

1. Validate the schema’s ontology-backed enum meanings:

   just curate-validate-schema
   

2. Draft a curated interpretation from enrichment output:

   uv run --project python/genesets-workflows --extra curation \
     genesets-workflows curate draft MSIGDB:<SET> \
     --enrichment-tsv path/to/enrichment.tsv \
     -o curation/genesets/<SET>.yaml
   

3. Adjudicate the draft by assigning category, confidence, specificity, and recovery_status. Add curator-only core terms and literature evidence where needed.

4. Validate every curated YAML file:

   just curate-validate
   

5. Build the precision/recall report:

   just curate-report
   

Judgment Model

category is the biological judgment. A term that is central to the gene set’s biology should remain core even if current GO annotations do not recover it.

recovery_status records whether the current annotations and membership make that biological 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.

This separation keeps the corpus useful both as an enrichment eval fixture and as a source of curation targets.