| name | ols-search |
| description | Search EMBL-EBI Ontology Lookup Service (OLS) for biomedical ontology terms, definitions, and hierarchies across 250+ ontologies (GO, DOID, HP, UBERON, CL). Use for term search, term details, or navigating parents/children/ancestors. Public API, no credential needed. |
| license | Apache-2.0 |
Ols Search (Codex-native)
Codex-native adaptation of Google DeepMind's embl-ebi-ols skill
(science-skills, Apache-2.0).
Uses the public API directly through Codex's own tools.
Gates (ask before proceeding)
- Terms notice: on first use in a workspace, tell the user to review the
source's terms of use and record the notice in provenance.
- Network / install: read-only public access; be polite about rate limits.
Write large responses to a file and parse them; if you write helper code, run
it via
uv run, never bare python3. Ask before installs or large downloads.
Endpoints
- OLS4 API
https://www.ebi.ac.uk/ols4/api (docs at /ols4/api-docs)
Workflow
Search across ontologies first with science_search_ols; use OLS4 directly for
ontology scoping and hierarchy traversal.
- Search a term with
/ols4/api/search?q=<term> (optionally scope by ontology=).
- Fetch details and navigate the hierarchy (parents, children, ancestors) via the term IRI endpoints.
- Provenance & review: record queries, endpoints, and cited identifiers with
$science-provenance; check claims with $science-review before presenting.
Boundaries
- Always report the ontology and term IRI/CURIE (e.g.
GO:0006915); labels alone are ambiguous.
- Cite only terms actually returned.
