What is embl-ebi-ols?

A search tool for biomedical ontology terms. Ontologies are organised vocabularies that define concepts and their relationships; this service covers more than 250 of them, including Gene Ontology and disease and phenotype vocabularies.

It helps look up terms, definitions, properties, individuals, parents, children, and ancestors through the EMBL-EBI Ontology Lookup Service.

It avoids manually searching separate biomedical vocabularies when you need a term's definition, related terms, or place in a hierarchy.

embl-ebi-ols — Skill for Claude Code and Codex by google-deepmind

About the project

Science Skills is a collection of add-ons that give AI agents structured instructions, scripts, and references for scientific research, including genomics, structural biology, cheminformatics, and literature search. Researchers use it to guide agents through specialized scientific tasks with information from databases and tools such as AlphaGenome, AFDB, and UniProt. The catalogue entries are individual skills from this collection.

google-deepmind/science-skills · 2,960 stars · on GitHub · antigravity.google

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add google-deepmind/science-skills --skill embl_ebi_ols

Clone the repo

git clone --depth 1 https://github.com/google-deepmind/science-skills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/google-deepmind/science-skills/embl_ebi_ols/github.svg)](https://agentmods.dev/skills/google-deepmind/science-skills/embl_ebi_ols)

Your own site

<a href="https://agentmods.dev/skills/google-deepmind/science-skills/embl_ebi_ols"><img src="https://agentmods.dev/badge/skills/google-deepmind/science-skills/embl_ebi_ols/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/google-deepmind/science-skills/embl_ebi_ols"><img src="https://agentmods.dev/badge/skills/google-deepmind/science-skills/embl_ebi_ols.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 92 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 3,071 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

NVIDIA SkillSpector pass 7 Sept 2026

How audits are shown

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00092	$0.03071
Opus 5	$0.00046	$0.01536
Sonnet 5	$0.00018	$0.00614
Haiku 4.5	$0.00009	$0.00307

Measured 10d ago against content hash fd6b63b2d509, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

embl-ebi-ols scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 10d ago.

The scan reads SKILL.md. This mod also ships 8 executable files (scripts/get_individual.py, scripts/get_ontology.py, scripts/get_property.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

status. NEVER use `curl` or custom Python requests to query API directly.

skills/embl_ebi_ols/SKILL.md · 283 lines

How it starts

The opening of the file, as written. The whole thing — 283 lines — stays where its author put it; the contents beside it link to each section on GitHub.

EMBL-EBI Ontology Lookup Service (OLS)

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is 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 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:

Definition of a disease, phenotype, or term → get_term.py --obo_id <ID> --summary
Subtypes or children of a term → get_term.py --obo_id <ID> --relations children
Parent of a term → get_term.py --obo_id <ID> --relations parents
Ancestors / disease categories / classified under → get_term.py --obo_id <ID> --relations ancestors
Root terms of an ontology → get_term.py --ontology <id> --roots
Hierarchical parents (is-a + part-of) → get_term.py --obo_id <ID> --relations hierarchicalParents
Structures part of / hierarchical children → get_term.py --obo_id <ID> --relations hierarchicalChildren
Compare direct vs hierarchical parents → get_term.py --obo_id <ID> --relations parents,hierarchicalParents
Search for a term (e.g., "apoptosis" in GO) → search_ols.py --query "..." --ontology <id>
Find a GO term matching a function → search_ols.py --query "..." --ontology go --exact
Search in MONDO, CHEBI, CL, UBERON → search_ols.py --query "..." --ontology <id> --defining
Paginate search results / next page → search_ols.py --query "..." --rows N --start <offset>
Autocomplete a partial name → suggest_ols.py --query "..."
Ontology metadata (e.g., EFO info) → get_ontology.py --id <id>
OLS index statistics → get_stats.py

Read the full file on GitHub · 283 lines

Files

What ships with it

10 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

10d ago First seen · 283 lines · 92 tokens per session scan A fd6b63b2d509

Subscribe to this mod's changes

embl-ebi-ols is a skill published in the GitHub repository google-deepmind/science-skills (2,960 stars, last pushed yesterday), licensed Apache-2.0. It adds 92 tokens to every session and 3,071 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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embl-ebi-ols