Efo Tools

Configuration File: efo_tools.json Tool Type: Local Tools Count: 6

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

Available Tools

OSL_get_efo_id_by_disease_name (Type: EFOTool)

Legacy helper to find an EFO term ID from a disease name using EMBL-EBI OLS search.

Returns the …

OSL_get_efo_id_by_disease_name tool specification

Tool Information:

  • Name: OSL_get_efo_id_by_disease_name

  • Type: EFOTool

  • Description: Legacy helper to find an EFO term ID from a disease name using EMBL-EBI OLS search.

Returns the best match as {efo_id, name} (or null if none). Note: the tool name contains a legacy typo (OSL_ vs OLS_). If you need richer ontology data (IRI, synonyms, children), use the newer ols_* tools in efo_tools.json.

Parameters:

  • disease (string) (required) Disease name or free-text query (e.g., ‘diabetes mellitus’).

Example Usage:

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

ols_get_efo_ontology_info (Type: OLSRESTTool)

Get metadata about the EFO ontology itself (version, status, number of terms, title/description).

ols_get_efo_ontology_info tool specification

Tool Information:

  • Name: ols_get_efo_ontology_info

  • Type: OLSRESTTool

  • Description: Get metadata about the EFO ontology itself (version, status, number of terms, title/description).

Parameters:

No parameters required.

Example Usage:

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

ols_get_efo_term (Type: OLSRESTTool)

Get details for a single EFO term by iri (recommended) or obo_id (e.g., ‘EFO:0000400’). Use `…

ols_get_efo_term tool specification

Tool Information:

  • Name: ols_get_efo_term

  • Type: OLSRESTTool

  • Description: Get details for a single EFO term by iri (recommended) or obo_id (e.g., ‘EFO:0000400’). Use ols_search_efo_terms first to discover IDs.

iri example: ‘http://www.ebi.ac.uk/efo/EFO_0000400’.

Parameters:

  • iri (string) (optional) Term IRI returned by ols_search_efo_terms.

  • obo_id (string) (optional) OBO ID like ‘EFO:0000400’ (will be converted to an EFO IRI).

Example Usage:

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

ols_get_efo_term_children (Type: OLSRESTTool)

List children of an EFO term (ontology hierarchy). Provide iri or obo_id.

Tip: use `ols_sear…

ols_get_efo_term_children tool specification

Tool Information:

  • Name: ols_get_efo_term_children

  • Type: OLSRESTTool

  • Description: List children of an EFO term (ontology hierarchy). Provide iri or obo_id.

Tip: use ols_search_efo_terms first, then pass the returned obo_id or iri.

Parameters:

  • iri (string) (optional) Term IRI returned by ols_search_efo_terms.

  • obo_id (string) (optional) OBO ID like ‘EFO:0000400’ (will be converted to an EFO IRI).

  • size (integer) (optional) Maximum number of children to return.

Example Usage:

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

ols_list_ontologies (Type: OLSRESTTool)

List available ontologies in OLS (not limited to EFO). Useful to discover ontologyId, sizes, an…

ols_list_ontologies tool specification

Tool Information:

  • Name: ols_list_ontologies

  • Type: OLSRESTTool

  • Description: List available ontologies in OLS (not limited to EFO). Useful to discover ontologyId, sizes, and status.

Parameters:

  • size (integer) (optional) Maximum number of ontologies to return.

Example Usage:

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

ols_search_efo_terms (Type: OLSRESTTool)

Search EFO terms (OLS v4). Use this to find term IRIs and OBO IDs for a concept, then pass the `i…

ols_search_efo_terms tool specification

Tool Information:

  • Name: ols_search_efo_terms

  • Type: OLSRESTTool

  • Description: Search EFO terms (OLS v4). Use this to find term IRIs and OBO IDs for a concept, then pass the iri (or obo_id) into ols_get_efo_term / ols_get_efo_term_children.

Example: search for ‘diabetes mellitus’ to discover obo_id like ‘EFO:0000400’ and iri like ‘http://www.ebi.ac.uk/efo/EFO_0000400’.

Parameters:

  • query (string) (required) Search query (free text).

  • rows (integer) (optional) Maximum number of results to return.

Example Usage:

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