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 phenotypes associated with a Mondo disease using exact offset pagination. Metadata report…

Mondo_get_disease_phenotypes tool specification

Tool Information:

  • Name: Mondo_get_disease_phenotypes

  • Type: MonarchV3Tool

  • Description: Get HPO phenotypes associated with a Mondo disease using exact offset pagination. Metadata reports total_phenotypes, has_more and next_offset.

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) Phenotypes per page (1-200).

  • offset (integer) (optional) Zero-based offset. Continue with metadata.next_offset.

Example Usage:

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

Mondo_search_disease (Type: MonarchV3Tool)#

Search Mondo diseases by name or keyword with exact offset pagination. Metadata reports total_res…

Mondo_search_disease tool specification

Tool Information:

  • Name: Mondo_search_disease

  • Type: MonarchV3Tool

  • Description: Search Mondo diseases by name or keyword with exact offset pagination. Metadata reports total_results, has_more and next_offset; continue until has_more is false.

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) Disease results per page (1-50).

  • offset (integer) (optional) Zero-based offset. Continue with metadata.next_offset.

Example Usage:

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