Ols Tools

Configuration File: ols_tools.json Tool Type: Local Tools Count: 7

This page contains all tools defined in the ols_tools.json configuration file.

Available Tools

ols_find_similar_terms (Type: OLSTool)

Find similar terms using LLM-based similarity

ols_find_similar_terms tool specification

Tool Information:

  • Name: ols_find_similar_terms

  • Type: OLSTool

  • Description: Find similar terms using LLM-based similarity

Parameters:

  • operation (string) (optional) The operation to perform (find_similar_terms)

  • term_iri (string) (optional) The IRI of the term to find similar terms for

  • ontology (string) (required) The ontology ID

  • size (integer) (optional) Number of similar terms to return (default: 10)

  • term_id (string) (optional) Alias for term_iri. Short-form ontology ID (e.g., GO:0008150) or full IRI.

Example Usage:

query = {
    "name": "ols_find_similar_terms",
    "arguments": {
        "ontology": "example_value"
    }
}
result = tu.run(query)

ols_get_ontology_info (Type: OLSTool)

Get detailed information about an ontology

ols_get_ontology_info tool specification

Tool Information:

  • Name: ols_get_ontology_info

  • Type: OLSTool

  • Description: Get detailed information about an ontology

Parameters:

  • operation (string) (optional) The operation to perform (get_ontology_info)

  • ontology_id (string) (optional) The ID of the ontology to retrieve

  • ontology (string) (optional) Alias for ontology_id. The ontology abbreviation (e.g. mondo, hp, go, ordo).

Example Usage:

query = {
    "name": "ols_get_ontology_info",
    "arguments": {
    }
}
result = tu.run(query)

ols_get_term_ancestors (Type: OLSTool)

Get ancestor terms of a specific term in an ontology. Use term_id with CURIE format (e.g., ‘HP:…

ols_get_term_ancestors tool specification

Tool Information:

  • Name: ols_get_term_ancestors

  • Type: OLSTool

  • Description: Get ancestor terms of a specific term in an ontology. Use term_id with CURIE format (e.g., ‘HP:0001928’) — the ontology is auto-inferred from the prefix. Or supply term_iri + ontology explicitly.

Parameters:

  • operation (string) (optional) The operation to perform (get_term_ancestors)

  • term_iri (string) (optional) The full IRI of the term (e.g., http://www.ebi.ac.uk/efo/EFO_0000408)

  • term_id (string) (optional) Short-form CURIE (e.g., ‘HP:0001928’, ‘GO:0008150’). Ontology is auto-inferred from prefix.

  • ontology (string) (optional) Ontology ID (e.g., ‘hp’, ‘go’, ‘efo’). Auto-inferred from term_id prefix when not supplied.

  • include_obsolete (boolean) (optional) Include obsolete terms (default: false)

  • size (integer) (optional) Number of results to return (default: 20)

Example Usage:

query = {
    "name": "ols_get_term_ancestors",
    "arguments": {
    }
}
result = tu.run(query)

ols_get_term_children (Type: OLSTool)

Get child terms of a specific term in an ontology. Use term_id with CURIE format (e.g., ‘HP:000…

ols_get_term_children tool specification

Tool Information:

  • Name: ols_get_term_children

  • Type: OLSTool

  • Description: Get child terms of a specific term in an ontology. Use term_id with CURIE format (e.g., ‘HP:0001928’) — the ontology is auto-inferred from the prefix. Or supply term_iri + ontology explicitly.

Parameters:

  • operation (string) (optional) The operation to perform (get_term_children)

  • term_iri (string) (optional) The full IRI of the term (e.g., http://www.ebi.ac.uk/efo/EFO_0000408)

  • term_id (string) (optional) Short-form CURIE (e.g., ‘HP:0001928’, ‘GO:0008150’). Ontology is auto-inferred from prefix.

  • ontology (string) (optional) Ontology ID (e.g., ‘hp’, ‘go’, ‘efo’). Auto-inferred from term_id prefix when not supplied.

  • include_obsolete (boolean) (optional) Include obsolete terms (default: false)

  • size (integer) (optional) Number of results to return (default: 20)

Example Usage:

query = {
    "name": "ols_get_term_children",
    "arguments": {
    }
}
result = tu.run(query)

ols_get_term_info (Type: OLSTool)

Get detailed information about a specific term in OLS

ols_get_term_info tool specification

Tool Information:

  • Name: ols_get_term_info

  • Type: OLSTool

  • Description: Get detailed information about a specific term in OLS

Parameters:

  • operation (string) (optional) The operation to perform (get_term_info)

  • id (string) (optional) Ontology term ID or IRI (e.g. HP:0001903, http://purl.obolibrary.org/obo/HP_0001903)

  • term_id (string) (optional) Alias for id — ontology term ID (e.g. HP:0001903)

  • term_iri (string) (optional) Alias for id. Full IRI or short-form ID (e.g., GO:0008150, EFO:0003971). Same as id.

Example Usage:

query = {
    "name": "ols_get_term_info",
    "arguments": {
    }
}
result = tu.run(query)

ols_search_ontologies (Type: OLSTool)

Search for ontologies in OLS

ols_search_ontologies tool specification

Tool Information:

  • Name: ols_search_ontologies

  • Type: OLSTool

  • Description: Search for ontologies in OLS

Parameters:

  • operation (string) (optional) The operation to perform (search_ontologies)

  • search (string) (optional) Search query for ontologies (optional)

  • page (integer) (optional) Page number (default: 0)

  • size (integer) (optional) Number of results per page (default: 20)

Example Usage:

query = {
    "name": "ols_search_ontologies",
    "arguments": {
    }
}
result = tu.run(query)

ols_search_terms (Type: OLSTool)

Search for terms in OLS (Ontology Lookup Service)

ols_search_terms tool specification

Tool Information:

  • Name: ols_search_terms

  • Type: OLSTool

  • Description: Search for terms in OLS (Ontology Lookup Service)

Parameters:

  • operation (string) (optional) The operation to perform (search_terms)

  • query (string) (required) The search query for terms

  • rows (integer) (optional) Number of results to return (default: 10). Alias: size.

  • size (integer) (optional) Alias for rows. Number of results to return (default: 10).

  • ontology (string) (optional) Filter by specific ontology (optional)

  • exact_match (boolean) (optional) Search for exact matches only (default: false)

  • include_obsolete (boolean) (optional) Include obsolete terms (default: false)

  • limit ([‘integer’, ‘null’]) (optional) Alias for rows. Maximum number of results to return (default: 10, max: 100).

Example Usage:

query = {
    "name": "ols_search_terms",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)