ontology-term-resolution

SUMMARY

What it does

This Agent Skill resolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup Service (OLS4). It is intended for use whenever an ontology identifier must be produced or checked, including 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ENA, BioSamples, CELLxGENE, HCA, or ISA-Tab submission; auditing a metadata table of term IDs; checking whether a term is obsolete and what replaced it; or mapping between ontologies. The skill provides two scripts: resolve_terms.py (text to ID) and validate_terms.py (ID to verdict). It requires Python 3.11+ and network access to https://www.ebi.ac.uk/ols4 (public, no API key). The skill is part of Scientific Agent Skills by K-Dense and is licensed under MIT.