Hpo Tools#

Configuration File: hpo_tools.json Tool Type: Local Tools Count: 6

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

Available Tools#

HPO_get_disease_annotations (Type: HPOTool)#

Get the full curated HPO annotation profile for a disease, keyed by a disease ID (OMIM / ORPHA / …

HPO_get_disease_annotations tool specification

Tool Information:

  • Name: HPO_get_disease_annotations

  • Type: HPOTool

  • Description: Get the full curated HPO annotation profile for a disease, keyed by a disease ID (OMIM / ORPHA / DECIPHER), from the JAX HPO network annotations. Returns three things: (1) medical_actions — MAxO curated treatments / management actions, each with TREATS / PREVENTS relations and the specific phenotypes they target; (2) categories — the disease’s phenotypes grouped by body system (e.g., Cardiovascular, Nervous System, Eye), each with frequency / onset; (3) genes — the causative genes (NCBI gene IDs and symbols). Use to retrieve evidence-based management options and the organ-system phenotype breakdown for a known disease. Example: OMIM:154700 (Marfan syndrome) returns 3 medical actions including MAXO:0000653 ‘angiotensin receptor blocker therapy’ (PREVENTS/TREATS aortic root aneurysm), 13 body systems, and gene NCBIGene:2200 (FBN1). Other examples: OMIM:277900 (Wilson disease) → copper chelator / zinc therapy; OMIM:261600 (phenylketonuria) → dietary phenylalanine avoidance.

Parameters:

  • disease_id (string) (required) Disease identifier as an OMIM, ORPHA, or DECIPHER CURIE (e.g., ‘OMIM:154700’ for Marfan syndrome, ‘OMIM:277900’ for Wilson disease, ‘ORPHA:558’).

Example Usage:

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

HPO_get_diseases_by_phenotype (Type: HPOTool)#

Get the diseases that present with an HPO phenotype term, from the JAX HPO network annotations. R…

HPO_get_diseases_by_phenotype tool specification

Tool Information:

  • Name: HPO_get_diseases_by_phenotype

  • Type: HPOTool

  • Description: Get the diseases that present with an HPO phenotype term, from the JAX HPO network annotations. Returns disease IDs (ORPHA/OMIM/DECIPHER), names, and the cross-referenced MONDO ID. Example: HP:0001250 (Seizure) is a feature of thousands of diseases. Use to build a differential diagnosis from a set of observed phenotypes. A phenotype term can be linked to thousands of diseases but ‘limit’ caps a single response at 500 – check metadata.has_more in the response and pass ‘offset’ to page through the rest; a well-known disease for a common phenotype may not appear in the first page.

Parameters:

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

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of results to return (1-500, default 50). Phenotype terms can be linked to thousands of diseases.

  • offset ([‘integer’, ‘null’]) (optional) Number of results to skip before returning ‘limit’ results (default 0). Use with the response’s metadata.has_more/metadata.total to page through phenotypes with more diseases than fit in one call.

Example Usage:

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

HPO_get_genes_by_phenotype (Type: HPOTool)#

Get the genes associated with an HPO phenotype term (genes in which variants cause this phenotype…

HPO_get_genes_by_phenotype tool specification

Tool Information:

  • Name: HPO_get_genes_by_phenotype

  • Type: HPOTool

  • Description: Get the genes associated with an HPO phenotype term (genes in which variants cause this phenotype), from the JAX HPO network annotations. Returns NCBI gene IDs and symbols. Example: HP:0001250 (Seizure) is linked to genes such as RELN, SCN1A, and ~2000 others. Use to go from an observed patient phenotype to candidate disease genes for variant prioritization. A phenotype term can be linked to thousands of genes but ‘limit’ caps a single response at 500 – check metadata.has_more in the response and pass ‘offset’ to page through the rest; a well-known gene for a common phenotype may not appear in the first page.

Parameters:

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

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of results to return (1-500, default 50). Phenotype terms can be linked to thousands of genes.

  • offset ([‘integer’, ‘null’]) (optional) Number of results to skip before returning ‘limit’ results (default 0). Use with the response’s metadata.has_more/metadata.total to page through phenotypes with more genes than fit in one call.

Example Usage:

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

HPO_get_term (Type: HPOTool)#

Get detailed information about an HPO term by ID, including complete synonyms, cross-references, …

HPO_get_term tool specification

Tool Information:

  • Name: HPO_get_term

  • Type: HPOTool

  • Description: Get detailed information about an HPO term by ID, including complete synonyms, cross-references, and every available translation with explicit counts; multilingual names are not limited to the former first five. Also returns definition, comments, descendant count, and obsolete-ID resolution metadata.

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 HPO terms by keyword with complete synonym arrays and explicit synonym_count for every ret…

HPO_search_terms tool specification

Tool Information:

  • Name: HPO_search_terms

  • Type: HPOTool

  • Description: Search HPO terms by keyword with complete synonym arrays and explicit synonym_count for every returned term. Metadata reports total_available and next_offset so all search pages are reachable. Useful for disambiguating clinical phenotype language before querying disease or gene associations.

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).

  • offset (integer) (optional) Zero-based result offset. Continue with metadata.next_offset while has_more is true.

Example Usage:

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