/embl_ebi_ols

name: embl-ebi-ols
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.

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:

• **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`

> **Multi-step queries** (e.g., "What is the parent of myocardial infarction?"): > When the user names a term but you don't know its OBO ID, complete in > **exactly 2 steps** — do NOT search across multiple ontologies: > > 1. **Search** in the single most appropriate ontology: `search_ols.py --query > "myocardial infarction" --ontology doid --exact --rows 1 --output > /tmp/step1.json` > 2. **Get relations** using the OBO ID from step 1: `get_term.py --obo_id > DOID:5844 --relations parents --output /tmp/step2.json` > > **Ontology selection rule**: ALWAYS use `doid` for common human diseases > (e.g., diabetes, cancer), `hp` for phenotypes, `go` for gene functions, > `chebi` for chemicals, `uberon` for anatomy, `cl` for cell types. Use `mondo` > ONLY when cross-species context is explicitly mentioned or needed.

Utility Scripts

**1. Search Terms Across Ontologies**

Search for ontology terms by keyword and return clean JSON.

uv run scripts/search_ols.py --query "diabetes" \
  --rows 5 --output /tmp/ols_search_results.json 2>/dev/null

> **Important**: `--output` is required for all scripts. Results are always > written to the specified file. For larger output, you can limit `--rows` > (e.g., 5-10) or paginate using `--start`.

*Returned Fields:* JSON results include `iri`, `label`, `description`, `ontology_name`, `ontology_prefix`, `obo_id`, `short_form`, `type`, `is_defining_ontology`, and `exact_synonyms`.

*Pagination:* Output includes a `pagination` block with `start`, `rows`, and `has_more` so you can decide whether to fetch more results.

*Options:*

• `--query`: Search string (required). Searches labels, synonyms,

descriptions, and identifiers.

• `--ontology`: Filter by ontology ID (e.g., `go`, `doid`, `efo`, `hp`).

**Recommended** when you know which ontology to search — avoids noise from 250+ ontologies.

• `--type`: Filter by entity type: `class`, `property`, `individual`, or

`ontology`.

• `--exact`: Flag for exact label match only. **Use this for entity

resolution** when mapping a user's string to a specific ontology term ID.

• `--defining`: Only return terms from their defining (authoritative)

ontology. E.g., `GO:0005634` only from GO, not cross-referenced copies.

• `--obsolete`: Flag to include obsolete terms in results.
• `--local`: Only return terms in their defining ontology.
• `--childrenOf`: Restrict to children of given term IRI(s), comma-separated.
• `--allChildrenOf`: Restrict to all children including transitive relations

(part of, develops from), comma-separated IRIs.

• `--queryFields`: Comma-separated fields to search in (e.g.,

`label,synonym,description`).

• `--fieldList`: Comma-separated fields to return.
• `--groupField`: Group results by unique IRI.
• `--isLeaf`: Only return leaf terms (no children).
• `--rows`: Number of results to return (default 10).
• `--start`: Pagination offset (default 0).
• `--output`: File path to save results (**required**).

**2. Autocomplete