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
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:
Search in the single most appropriate ontology: search_ols.py --query "myocardial infarction" --ontology doid --exact --rows 1 --output /tmp/step1.json
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.
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 / Suggest
Get autocomplete suggestions for partial term names.
--ontology: Filter by ontology ID(s), comma-separated.
--rows: Number of suggestions (default 10).
--start: Pagination offset (default 0).
--output: File path to save results (default: stdout).
3. Get Term Details
Retrieve full details for a specific ontology term by its OBO ID or IRI.
uv run scripts/get_term.py --obo_id "GO:0005634" \
--output /tmp/ols_term.json 2>/dev/null
Returned Fields: JSON includes iri, label, description, obo_id,
synonyms, ontology_name, is_obsolete, is_defining_ontology,
has_children, is_root, annotation, in_subset, and any requested
relations.
Summary Mode: Use --summary to get a clean, human-readable block on stdout
(Label, OBO ID, Ontology, Definition, Synonyms). The full JSON is always saved
to the --output file.
uv run scripts/get_term.py --obo_id "GO:0005634" --summary \
--output /tmp/nucleus_full.json
Options:
--obo_id: OBO-style identifier (e.g., GO:0005634, DOID:9351). Mutually
exclusive with --iri. Auto-converts to IRI with double encoding.
--iri: Full IRI of the term. Mutually exclusive with --obo_id.
--ontology: Ontology ID (auto-derived from --obo_id if not provided).
--relations: Comma-separated list of relations to fetch.
Direct (is-a only):parents, children, ancestors,
descendants
Note: Use hierarchical variants for anatomical/developmental
ontologies (UBERON, CL) where transitive relations like "part of" and
"develops from" are critical for navigating the hierarchy.
--roots: List root terms of the ontology (requires --ontology).
--preferred_roots: List preferred root terms (requires --ontology).
--summary: Human-readable summary on stdout, full JSON to --output.
--output: File path to save results (default: stdout).
4. Get Property Details
Retrieve details for an ontology property (relation type) with hierarchy.
uv run scripts/get_property.py --obo_id "BFO:0000051" --ontology go \
--output /tmp/ols_property.json 2>/dev/null
Options:
--obo_id: OBO-style ID of the property. Mutually exclusive with --iri.
--iri: Full IRI of the property. Mutually exclusive with --obo_id.
--obo_id: OBO-style ID. Mutually exclusive with --iri.
--iri: Full IRI. Mutually exclusive with --obo_id.
--ontology: Ontology ID (required with --iri).
--types: Fetch the direct types (classes) of this individual.
--alltypes: Fetch all types including ancestor classes.
--output: File path to save results (default: stdout).
6. Get Ontology Information
List available ontologies or retrieve details for a specific one.
uv run scripts/get_ontology.py --id go \
--output /tmp/ols_ontology.json 2>/dev/null
Options:
--id: Specific ontology ID (e.g., go, efo, doid). If omitted, lists
all ontologies.
--page: Page number for pagination (default 0).
--size: Number of ontologies per page (default 20).
--output: File path to save results (default: stdout).
7. Get OLS Statistics
Retrieve index statistics (total ontologies, classes, properties, individuals).
uv run scripts/get_stats.py --output /tmp/ols_stats.json 2>/dev/null
Options:
--output: File path to save results (default: stdout).
Reference
API Reference: See
references/api_reference.md for common ontology
IDs, OBO ID format, and key API endpoints.
Workflow
Use suggest_ols.py for autocomplete when you have a partial term name.
Search for terms using search_ols.py. Use --defining to prioritize
authoritative definitions. Use --exact for entity resolution.
If full details are needed, use get_term.py with the OBO ID or IRI. Use
--summary for a concise view.
To explore a term's hierarchy, use get_term.py --relations parents,children for is-a only, or --relations hierarchicalParents,hierarchicalChildren for "part of" etc.
To explore from the top down, use get_term.py --ontology go --roots.
For properties or individuals, use get_property.py or get_individual.py.
To discover available ontologies, use get_ontology.py.
