Disease Ontology Tools

Configuration File: disease_ontology_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

DiseaseOntology_get_parents (Type: DiseaseOntologyTool)

Get the parent disease terms for a Disease Ontology term, enabling navigation of the disease hier…

DiseaseOntology_get_parents tool specification

Tool Information:

  • Name: DiseaseOntology_get_parents

  • Type: DiseaseOntologyTool

  • Description: Get the parent disease terms for a Disease Ontology term, enabling navigation of the disease hierarchy. Returns the direct parent(s) via ‘is_a’ relationships, their definitions, and their own parents, allowing you to trace the full path from a specific disease to the root. Example: DOID:10283 (prostate cancer) has parent DOID:2998 (testicular cancer -> male reproductive gland cancer -> reproductive organ cancer -> urogenital system cancer).

Parameters:

  • doid (string) (required) Disease Ontology identifier in format ‘DOID:XXXX’. Examples: ‘DOID:10283’ (prostate cancer), ‘DOID:162’ (cancer), ‘DOID:9352’ (type 2 diabetes).

Example Usage:

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

DiseaseOntology_get_term (Type: DiseaseOntologyTool)

Get detailed information about a disease from the Disease Ontology (DO) by its DOID identifier. R…

DiseaseOntology_get_term tool specification

Tool Information:

  • Name: DiseaseOntology_get_term

  • Type: DiseaseOntologyTool

  • Description: Get detailed information about a disease from the Disease Ontology (DO) by its DOID identifier. Returns the disease name, definition, synonyms, parent diseases in the ontology hierarchy, cross-references to ICD-10, ICD-9, MeSH, NCI Thesaurus, SNOMED-CT, UMLS, and OMIM, and which DO classification subsets it belongs to (cancer slim, AGR slim, FlyBase slim, etc.). The Disease Ontology is a standardized ontology for human disease terms used widely in bioinformatics. Example: DOID:162 returns ‘cancer’ with 4 synonyms, 7 cross-references (ICD10CM, MeSH, NCI, SNOMED, UMLS), and membership in 6 subsets including cancer_slim.

Parameters:

  • doid (string) (required) Disease Ontology identifier in format ‘DOID:XXXX’. Examples: ‘DOID:162’ (cancer), ‘DOID:9352’ (type 2 diabetes mellitus), ‘DOID:10283’ (prostate cancer), ‘DOID:2531’ (hematologic cancer), ‘DOID:684’ (hepatocellular carcinoma), ‘DOID:4’ (disease - root term).

Example Usage:

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