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 direct parents for a Disease Ontology term and expand each parent by one additional level. Th…

DiseaseOntology_get_parents tool specification

Tool Information:

  • Name: DiseaseOntology_get_parents

  • Type: DiseaseOntologyTool

  • Description: Get direct parents for a Disease Ontology term and expand each parent by one additional level. This is a depth-2 view, not a complete path to the root. Every relation includes type and source; each parent has fetch_complete, while metadata reports failed_parent_fetches, parent_expansion_complete, hierarchy_depth_returned=2, and full_ancestry_complete so a failed or deliberately shallow traversal cannot appear complete. Live DOID:10283 has two direct parents: prostate disease and male reproductive organ 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 a complete semantic Disease Ontology term by DOID. The returned ID is verified and the wrappe…

DiseaseOntology_get_term tool specification

Tool Information:

  • Name: DiseaseOntology_get_term

  • Type: DiseaseOntologyTool

  • Description: Get a complete semantic Disease Ontology term by DOID. The returned ID is verified and the wrapper preserves name, definition, synonyms, parent relationship/source, external references, subsets, alternate IDs, and broad/exact/narrow SKOS mappings. Only the internal neo4jid is intentionally omitted and named in metadata. Live DOID:162 currently has 3 synonyms, 7 external references, and 7 subsets.

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)