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EMBL-EBI Ontology Lookup Service (OLS) · mkurman | DecimalAI

scienceby mkurman

EMBL-EBI Ontology Lookup Service (OLS)

mkurman/embl-ebi-ols

Source mkurman/zorai ↗License MIT

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).

SkillScore32Maintained

Automatic

Research pack

Last verified 8/22/2026

What it changes

Passed 3 of 9 test cases with the skill, and 2 of 9 without it.

Without skill23%

With skill32%

Checks it passed that the model alone missed

Specifies go as the ontology parameter.
Uses suggest_ols.py for partial text completion.
Passes --id efo to identify the target ontology.

and 4 more in the full report

4 fixed3 passed either way13 still failing2 broke

Pass-rate lift: +9 pp
Tokens: +213%
Agent turns: 0%
Response time: -18%

Model gemini-3.6-flashMeasured 8/22/2026v17 of 22 cases passed with skill · 9 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mkurman-embl-ebi-ols/SKILL.md https://app.decimal.ai/s/mkurman-embl-ebi-ols/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mkurman-embl-ebi-ols, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mkurman-embl-ebi-ols/ and pins it in .decimal/skills.lock

decimalai skills add mkurman-embl-ebi-ols

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mkurman-embl-ebi-ols/SKILL.md https://app.decimal.ai/s/mkurman-embl-ebi-ols/SKILL.md

Raw file: /s/mkurman-embl-ebi-ols/SKILL.md ↗ · machine-readable summary at /s/mkurman-embl-ebi-ols.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 4 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 4

Prompt

A user is typing 'diabet' into a search box. Generate the command to get autocomplete suggestions for this partial query and save the result to /tmp/suggest.json.

What was checked, without and with the skill
Checked	Without skill	With skill
Uses suggest_ols.py for partial text completion.	Missed	Passed
Specifies /tmp/suggest.json as the file path in the --output option.	Missed	Passed

case-09 · gemini-3.6-flash · 8/22/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md271 lines10 filesincludes scripts

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 LICENSE_NOTIFICATION.txt does not already exist in this skill 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

Track record

Benchmark

3 / 9

test cases passed, vs 2 / 9 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mkurman / zorai

skills/scientific-skills-gdm/embl_ebi_ols/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1Bundled 9 files · scripts

More skills from the same source and nearby in the registry, with their headline benchmark lift.

Ready to supercharge your AI agents?

See it in action

What's inside

EMBL-EBI Ontology Lookup Service (OLS)

Prerequisites

Core Rules

When to Use — Quick Recipes

Track record

Benchmark

Adoption

SkillSafety

Source

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