Mondo Tools

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

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

Available Tools

Mondo_get_disease (Type: MonarchV3Tool)

Get detailed information about a disease from the Mondo Disease Ontology by its MONDO ID. Returns…

Mondo_get_disease tool specification

Tool Information:

  • Name: Mondo_get_disease

  • Type: MonarchV3Tool

  • Description: Get detailed information about a disease from the Mondo Disease Ontology by its MONDO ID. Returns the disease name, description, synonyms, cross-references (OMIM, Orphanet, DOID, MeSH, ICD-10, NCIT, UMLS, SNOMED-CT), hierarchy (parent diseases), subtypes count, causal genes, inheritance pattern, and association counts (phenotypes, correlated genes, etc.). Essential for understanding disease classification and finding equivalent IDs across ontologies.

Parameters:

  • disease_id (string) (required) Mondo disease identifier. Examples: ‘MONDO:0004975’ (Alzheimer disease), ‘MONDO:0005148’ (type 2 diabetes mellitus), ‘MONDO:0007254’ (breast cancer), ‘MONDO:0018076’ (Huntington disease), ‘MONDO:0009061’ (cystic fibrosis).

Example Usage:

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

Mondo_get_disease_phenotypes (Type: MonarchV3Tool)

Get HPO (Human Phenotype Ontology) phenotypes associated with a Mondo disease. Returns the phenot…

Mondo_get_disease_phenotypes tool specification

Tool Information:

  • Name: Mondo_get_disease_phenotypes

  • Type: MonarchV3Tool

  • Description: Get HPO (Human Phenotype Ontology) phenotypes associated with a Mondo disease. Returns the phenotype IDs (HP:xxxxxxx), names, and the specific disease subtype contributing each phenotype. Data comes from OMIM, Orphanet, and clinical annotations. Use this to understand clinical presentations and symptoms of a disease. First find the Mondo ID using Mondo_search_disease, then query phenotypes here.

Parameters:

  • disease_id (string) (required) Mondo disease identifier. Examples: ‘MONDO:0004975’ (Alzheimer disease, 95 phenotypes), ‘MONDO:0005148’ (type 2 diabetes, 50+ phenotypes), ‘MONDO:0009061’ (cystic fibrosis, 100+ phenotypes).

  • limit (integer) (optional) Maximum number of phenotypes to return (default: 20, max: 200).

Example Usage:

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

Mondo_search_disease (Type: MonarchV3Tool)

Search the Mondo Disease Ontology for diseases by name or keyword. Mondo unifies disease identifi…

Mondo_search_disease tool specification

Tool Information:

  • Name: Mondo_search_disease

  • Type: MonarchV3Tool

  • Description: Search the Mondo Disease Ontology for diseases by name or keyword. Mondo unifies disease identifiers across OMIM, Orphanet, DOID, MeSH, ICD-10, NCIT, and other ontologies into a single MONDO ID. Returns matching disease entries with their Mondo IDs, descriptions, and cross-references. Use this to find the Mondo ID for a disease before querying Mondo_get_disease or Mondo_get_disease_phenotypes. Examples: ‘Alzheimer’ returns MONDO:0004975, ‘breast cancer’ returns MONDO:0007254, ‘diabetes’ returns MONDO:0005015.

Parameters:

  • query (string) (required) Disease name or keyword to search. Examples: ‘Alzheimer’, ‘breast cancer’, ‘type 2 diabetes’, ‘Parkinson’, ‘cystic fibrosis’, ‘sickle cell’.

  • limit (integer) (optional) Maximum number of results to return (default: 10, max: 50).

Example Usage:

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