Schema Reference

The curation schema lives at curation/schema/genesets_interpretation.yaml. It is a LinkML schema for a single curated interpretation of a non-GO gene set.

Main Classes

• GeneSetInterpretation: one curated gene set interpretation.
• BiologicalContext: ontology terms describing what the set is about, such as cell type, disease, phenotype, perturbagen, or experimental condition.
• TermAssociation: one curated association between the gene set and a GO term.
• Term: an ontology term reference with an ID and label.
• EnrichmentStats: enrichment values that seeded an association.
• EvidenceItem: literature evidence supporting, refuting, or contextualizing a term association.

Important Fields

• gene_set_id: stable source identifier, such as MSIGDB:<SET>.
• contexts: ontology-grounded biological context for the gene set.
• associations.term: the GO term being judged.
• associations.category: curator role judgment.
• associations.confidence: confidence in the biological judgment.
• associations.specificity: how specific the term is to the context.
• associations.recovery_status: whether current annotations and membership make the term recoverable.
• associations.evidence: cited evidence with optional validated snippets.

Validation

Validation has three layers:

• LinkML structural validation checks required fields and enum values.
• linkml-term-validator checks ontology IDs and labels for GO, CL, UBERON, MONDO, CHEBI, PR, HP, NCBITaxon, EFO, and related prefixes.
• linkml-reference-validator checks cited evidence snippets against referenced literature when snippets are provided.

Use:

just curate-validate-schema
just curate-validate

LinkML Browser

A generated LinkML schema browser is useful as reference documentation for the schema. It should complement, not replace, a curated gene set browser. Most users will want pages organized by gene set and biological context; schema docs are organized by classes and slots.