Embl Ebi Ols
Query and search the EMBL-EBI Ontology Lookup Service (OLS) for biomedical ontology...
Install
npx skills add google-deepmind/science-skills --skill embl-ebi-ols -g -a claude-code -y- Repository
- google-deepmind/science-skills3.4k
- Category
- Engineering
- Updated
- 12d ago
- License
- Apache-2.0
- Context cost
- Mediumabout 2,745 tokens
- Runs scripts
- Yes, review before use
What it does
Query and search the EMBL-EBI Ontology Lookup Service (OLS) for biomedical ontology terms, definitions, and hierarchies across 250+ ontologies (e.g., GO, DOID, HP). Use when the user asks to search for terms, retrieve details, navigate hierarchies (parents, children, ancestors), look up properties and individuals, get autocomplete suggestions, or access ontology metadata and statistics.
EMBL-EBI Ontology Lookup Service (OLS)
Prerequisites
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- User Notification: If .licenses/embl_ebi_ols_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://www.ebi.ac.uk/ols4/api-docs, then (2) create the file recording the notification text and timestamp.
Core Rules
-
[!IMPORTANT] Use the Utility Scripts: You MUST ALWAYS use the provided utility script under
scripts/for all API interactions, including checking status. NEVER usecurlor custom Python requests to query API directly. -
Rate Limiting & Resilience: You MUST respect EBI's Terms of Use with a maximum 5 requests per second. The provided utility scripts automatically enforce this.
-
Notification: If this skill is used, ensure this is mentioned in the output.
When to Use, Quick Recipes
Use this skill whenever a user query matches one of these patterns:
