EMBL-EBI OLS (Claude Skill)

Look up biomedical ontology terms, definitions, and hierarchies across 250+ ontologies through the EMBL-EBI Ontology Lookup Service — resolve a label to an ID, walk parent/child relationships, and find the canonical term for a concept.

   
Type Claude Skill
Supplier Google DeepMind
Availability GA
Pricing Free / OSS skill (Apache-2.0 code, CC-BY-4.0 docs); the OLS API is a public EMBL-EBI web service, no key
Capabilities Read-only — Claude runs the skill’s Python locally (uv run) and queries the public OLS4 API
Verified degraded · 2026-07-20 — dir resolves; fixed a stale scienceskillscommon copy line
Security cleared · 2026-07-20 — provenance matches google-deepmind, Apache-2.0, maintained, keyless public API, no OSV advisories

How to install

The google-deepmind/science-skills collection follows the Agent Skills SKILL.md spec. The repo’s primary npx skills add path targets Gemini/Antigravity; for Claude the followable path is a manual copy of the skill directory.

  • Claude Code / Claude Desktop — clone and copy the skill into your skills directory: 
    git clone https://github.com/google-deepmind/science-skills
cp -r science-skills/skills/embl_ebi_ols ~/.claude/skills/
cp -r science-skills/skills/uv ~/.claude/skills/

    (The SKILL.md requires the bundled uv skill for its setup — copy it too.)

  • Prerequisite — the skill runs its utility script via uv run; install uv first if absent: curl -LsSf https://astral.sh/uv/install.sh | sh. Python deps install into an isolated environment on first run.

What it does

Queries the EMBL-EBI Ontology Lookup Service (OLS4) and interprets the results:

  • Term resolution — retrieve a term’s label, definition, synonyms, IRI, and OBO ID from a query, OBO ID, or IRI.
  • Hierarchy navigation — parents, children, ancestors, and descendants of a term.
  • Property and individual lookups within an ontology.
  • Autocomplete suggestions for partial terms.
  • Ontology metadata and statistics — version, term counts, and coverage per ontology.
  • Cross-ontology search with filtering by ontology and relation type.

Covers 250+ ontologies including GO (Gene Ontology), MONDO, DOID (Disease Ontology), HP (Human Phenotype), CHEBI, CL (Cell Ontology), UBERON (anatomy), and EFO. Outputs are JSON.

Primary use cases: normalizing free-text concepts to ontology IDs, building controlled vocabularies, mapping phenotypes/diseases/anatomy/cell-types to canonical terms, enriching annotations with ontology hierarchy.

Notes

The skill mandates use of its bundled utility script for all OLS API interactions — it instructs Claude never to call the API with raw curl or ad-hoc requests, which keeps queries within the skill’s validated paths. It calls the public OLS4 service, so results depend on EMBL-EBI availability. The upstream npx skills add google-deepmind/science-skills/ command is oriented at Gemini/Antigravity (it writes to ~/.gemini/config/skills/); for Claude, the manual copy into ~/.claude/skills/ shown above is the equivalent path. Tagged All: ontology resolution is a cross-cutting need spanning every life-science domain.

Sources

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