# Embl Ebi Ols

Query and search the EMBL-EBI Ontology Lookup Service (OLS) for biomedical ontology...

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Engineering
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill embl-ebi-ols -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill embl-ebi-ols -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill embl-ebi-ols -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill embl-ebi-ols -g -a gemini-cli -y`

## Description

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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# EMBL-EBI Ontology Lookup Service (OLS)

## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **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 use `curl` or 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:

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/embl_ebi_ols/SKILL.md