ontology-term-resolution
Resolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup Service (OLS4). Use whenever an ontology identifier must be produced or checked - annotating tissue, cell type, disease, phenotype, assay, chemical, organism, sex, or developmental stage fields; preparing metadata for GEO, ENA, BioSamples, CELLxGENE, HCA, or ISA-Tab submission; auditing a metadata table of term IDs; checking whether a term is obsolete and what replaced it; or mapping between ontologies. Triggers include "ontology term", "ontology ID", "CURIE", "controlled vocabulary", "UBERON", "CL:", "MONDO", "HPO", "EFO", "ChEBI", "NCBITaxon", "GO term", "PATO", "annotate this tissue/cell type/disease", and any request to emit or verify an identifier shaped like PREFIX:0001234.
- Version
- 1.0
- License
- MIT
- Compatibility
- Requires Python 3.11+. Scripts use only the standard library - no third-party packages. Needs network access to https://www.ebi.ac.uk/ols4 (public, no API key).
Pinned to revision de66e10cd0c8, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
- Read
- Write
- Edit
- Bash
Files
- skills/ontology-term-resolution/SKILL.md
- skills/ontology-term-resolution/references/curation-rules.md
- skills/ontology-term-resolution/references/ols4-api.md
- skills/ontology-term-resolution/references/ontology-registry.md
- skills/ontology-term-resolution/scripts/ols_client.py
- skills/ontology-term-resolution/scripts/resolve_terms.py
- skills/ontology-term-resolution/scripts/validate_terms.py
Every link opens the file at its source, pinned to the revision this page describes.