Medgen Tools#

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

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

Available Tools#

MedGen_get_clinical_features (Type: MedGenTool)#

Get HPO clinical features (phenotypes) associated with a genetic condition from NCBI MedGen. Retu…

MedGen_get_clinical_features tool specification

Tool Information:

  • Name: MedGen_get_clinical_features

  • Type: MedGenTool

  • Description: Get HPO clinical features (phenotypes) associated with a genetic condition from NCBI MedGen. Returns feature names, HPO IDs, UMLS CUIs, and definitions. Useful for phenotype-driven diagnosis. Example: uid=’41393’ (cystic fibrosis) returns bronchiectasis, meconium ileus, male infertility, etc.

Parameters:

  • uid (string) (optional) MedGen UID (e.g., ‘41393’ for cystic fibrosis).

  • cui (string) (optional) UMLS CUI (e.g., ‘C0010674’ for cystic fibrosis). Alternative to uid.

  • concept_id ([‘string’, ‘null’]) (optional) Alias for cui. UMLS CUI identifier (e.g., “C0017205” for Gaucher disease).

Example Usage:

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

MedGen_get_condition (Type: MedGenTool)#

Get detailed information about a specific genetic condition from NCBI MedGen by UID or UMLS CUI. …

MedGen_get_condition tool specification

Tool Information:

  • Name: MedGen_get_condition

  • Type: MedGenTool

  • Description: Get detailed information about a specific genetic condition from NCBI MedGen by UID or UMLS CUI. Returns the complete synonym and clinical-feature arrays present in MedGen, with explicit synonym_count and clinical_feature_count; no fixed 20/30-item truncation is applied.

Parameters:

  • uid (string) (optional) MedGen UID (e.g., ‘41393’ for cystic fibrosis). Get from MedGen_search_conditions.

  • cui (string) (optional) UMLS Concept Unique Identifier (e.g., ‘C0010674’ for cystic fibrosis). Alternative to uid.

  • concept_id ([‘string’, ‘null’]) (optional) Alias for cui. UMLS CUI identifier (e.g., “C0017205” for Gaucher disease).

Example Usage:

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

MedGen_search_conditions (Type: MedGenTool)#

Search NCBI MedGen for genetic conditions, diseases, or syndromes by keyword. Use the zero-based …

MedGen_search_conditions tool specification

Tool Information:

  • Name: MedGen_search_conditions

  • Type: MedGenTool

  • Description: Search NCBI MedGen for genetic conditions, diseases, or syndromes by keyword. Use the zero-based start offset and next_start while has_more is true to retrieve all matches. Returns condition names, definitions, OMIM IDs, and associated genes.

Parameters:

  • query (string) (required) Search term (e.g., ‘cystic fibrosis’, ‘BRCA1’, ‘Marfan syndrome’, ‘autosomal recessive’).

  • max_results (integer) (optional) Maximum number of results (default 10, max 50).

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

Example Usage:

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