Hpo Tools

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

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

Available Tools

HPO_get_term (Type: HPOTool)

Get detailed information about a Human Phenotype Ontology (HPO) term by its ID. HPO provides stan…

HPO_get_term tool specification

Tool Information:

  • Name: HPO_get_term

  • Type: HPOTool

  • Description: Get detailed information about a Human Phenotype Ontology (HPO) term by its ID. HPO provides standardized descriptions of phenotypic abnormalities in human disease with over 18,000 terms. Returns the term name, definition, synonyms, cross-references to UMLS/SNOMED, descendant count, and translations. Example: HP:0001250 (Seizure) returns definition, 346 descendants, synonyms including ‘Epileptic seizure’ and ‘Epilepsy’, and cross-references to UMLS and SNOMED-CT.

Parameters:

  • term_id (string) (required) HPO term identifier. Must start with ‘HP:’ followed by 7 digits. Examples: ‘HP:0001250’ (Seizure), ‘HP:0001263’ (Global developmental delay), ‘HP:0000252’ (Microcephaly), ‘HP:0001249’ (Intellectual disability).

Example Usage:

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

HPO_get_term_hierarchy (Type: HPOTool)

Get the parent or child terms of an HPO phenotype term in the ontology hierarchy. HPO is organize…

HPO_get_term_hierarchy tool specification

Tool Information:

  • Name: HPO_get_term_hierarchy

  • Type: HPOTool

  • Description: Get the parent or child terms of an HPO phenotype term in the ontology hierarchy. HPO is organized as a directed acyclic graph (DAG) where more specific phenotypes are children of broader terms. Use direction=’children’ to find more specific sub-phenotypes, or direction=’parents’ to find broader categories. Example: children of HP:0001250 (Seizure) include ‘Bilateral tonic-clonic seizure’, ‘Focal-onset seizure’, ‘Febrile seizure’, and others. Parents include ‘Abnormal nervous system physiology’.

Parameters:

  • term_id (string) (required) HPO term identifier (e.g., ‘HP:0001250’). Must start with ‘HP:’ followed by 7 digits.

  • direction ([‘string’, ‘null’]) (optional) Direction to traverse: ‘children’ (more specific terms, default) or ‘parents’ (broader terms).

Example Usage:

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

HPO_search_terms (Type: HPOTool)

Search for Human Phenotype Ontology (HPO) terms by keyword. HPO contains over 18,000 standardized…

HPO_search_terms tool specification

Tool Information:

  • Name: HPO_search_terms

  • Type: HPOTool

  • Description: Search for Human Phenotype Ontology (HPO) terms by keyword. HPO contains over 18,000 standardized phenotype terms used in clinical genetics and rare disease research. Returns matching terms with definitions, synonym counts, and descendant counts. Useful for finding the correct HPO ID for a clinical phenotype before querying disease or gene associations. Example: searching ‘seizure’ returns terms like ‘Bilateral tonic-clonic seizure’ (HP:0007334), ‘Generalized-onset seizure’ (HP:0002197), ‘Focal-onset seizure’ (HP:0007359).

Parameters:

  • query (string) (required) Search keyword for phenotype terms. Examples: ‘seizure’, ‘intellectual disability’, ‘cardiomyopathy’, ‘scoliosis’, ‘microcephaly’.

  • max_results ([‘integer’, ‘null’]) (optional) Maximum number of results to return (default 10, max 50).

Example Usage:

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