Idmap Tools#

Configuration File: idmap_tools.json Tool Type: Local Tools Count: 3

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

Available Tools#

OpenTargets_get_disease_ids_by_efoId (Type: OpenTarget)#

Given a disease ID (e.g. a MONDO ID), retrieve all cross-referenced external disease IDs includin…

OpenTargets_get_disease_ids_by_efoId tool specification

Tool Information:

  • Name: OpenTargets_get_disease_ids_by_efoId

  • Type: OpenTarget

  • Description: Given a disease ID (e.g. a MONDO ID), retrieve all cross-referenced external disease IDs including EFO, OMIM, MeSH, MedDRA, NCIt, ICD10, Orphanet, UMLS.

Parameters:

  • efoId (string) (required) The disease ID (e.g. a MONDO ID such as MONDO_0008383). Legacy EFO disease IDs no longer resolve in OpenTargets.

Example Usage:

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

OpenTargets_get_disease_ids_by_name (Type: OpenTarget)#

Given a disease or phenotype name, find candidate diseases and their cross-referenced external ID…

OpenTargets_get_disease_ids_by_name tool specification

Tool Information:

  • Name: OpenTargets_get_disease_ids_by_name

  • Type: OpenTarget

  • Description: Given a disease or phenotype name, find candidate diseases and their cross-referenced external IDs (e.g., OMIM, MONDO, MeSH, ICD10, UMLS, MedDRA, NCIt, Orphanet) using Open Targets GraphQL full-text search. Returns up to 5 ranked candidates, not a single guaranteed match – OpenTargets’ relevance ranking can surface an unrelated top hit for multi-word or qualified phrasing (e.g. ‘localized prostate cancer’ or ‘high-risk prostate cancer’ rank an unrelated disease/trait above ‘prostate cancer’ itself). Always check each hit’s ‘name’ against the disease you intended before using its dbXRefs; prefer a plain, unqualified disease name (e.g. ‘prostate cancer’ rather than ‘localized prostate cancer’) if the top hit’s name looks wrong.

Parameters:

  • name (string) (required) The name of the disease or phenotype (e.g. ‘rheumatoid arthritis’).

Example Usage:

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

OpenTargets_map_any_disease_id_to_all_other_ids (Type: OpenTarget)#

Given any known disease or phenotype ID (EFO, OMIM, MONDO, UMLS, ICD10, MedDRA, etc.), return all…

OpenTargets_map_any_disease_id_to_all_other_ids tool specification

Tool Information:

  • Name: OpenTargets_map_any_disease_id_to_all_other_ids

  • Type: OpenTarget

  • Description: Given any known disease or phenotype ID (EFO, OMIM, MONDO, UMLS, ICD10, MedDRA, etc.), return all known cross-referenced IDs including the EFO ID.

Parameters:

  • inputId (string) (required) Any known disease ID (e.g. OMIM:604302, UMLS:C0003873, ICD10:M05, MONDO_0008383, etc.)

Example Usage:

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