Gencc Tools

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

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

Available Tools

GenCC_get_classifications (Type: GenCCTool)

Get summary statistics of gene-disease validity classifications from GenCC (Gene Curation Coaliti…

GenCC_get_classifications tool specification

Tool Information:

  • Name: GenCC_get_classifications

  • Type: GenCCTool

  • Description: Get summary statistics of gene-disease validity classifications from GenCC (Gene Curation Coalition). Returns counts for each classification level (Definitive, Strong, Moderate, Limited, etc.), total submissions, unique genes, unique diseases, and top contributing organizations. Useful for understanding the landscape of curated gene-disease evidence.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_classifications)

  • submitter (string) (optional) Optional filter by submitting organization name (e.g., ‘ClinGen’, ‘Ambry’, ‘Genomics England’)

Example Usage:

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

GenCC_search_disease (Type: GenCCTool)

Find genes with validity evidence for a disease from GenCC (Gene Curation Coalition). Search by d…

GenCC_search_disease tool specification

Tool Information:

  • Name: GenCC_search_disease

  • Type: GenCCTool

  • Description: Find genes with validity evidence for a disease from GenCC (Gene Curation Coalition). Search by disease name or MONDO/OMIM identifier. Returns gene-disease validity classifications from multiple expert curators. Useful for identifying established gene-disease relationships for clinical interpretation.

Parameters:

  • operation (string) (optional) Operation type (fixed: search_disease)

  • disease (string) (required) Disease name or ID to search (e.g., ‘Marfan syndrome’, ‘MONDO:0007947’, ‘breast cancer’)

  • classification (string) (optional) Optional filter by classification level (e.g., Definitive, Strong)

Example Usage:

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

GenCC_search_gene (Type: GenCCTool)

Get gene-disease validity classifications for a gene from GenCC (Gene Curation Coalition). Return…

GenCC_search_gene tool specification

Tool Information:

  • Name: GenCC_search_gene

  • Type: GenCCTool

  • Description: Get gene-disease validity classifications for a gene from GenCC (Gene Curation Coalition). Returns curated evidence levels (Definitive, Strong, Moderate, Limited, Disputed, Refuted) from multiple expert panels including ClinGen, Ambry Genetics, Genomics England PanelApp, and Orphanet. Essential for assessing clinical validity of gene-disease associations in genetic testing.

Parameters:

  • operation (string) (optional) Operation type (fixed: search_gene)

  • gene_symbol (string) (required) HGNC gene symbol (e.g., BRCA2, TP53, FBN1, CFTR)

  • classification (string) (optional) Optional filter by classification level (e.g., Definitive, Strong, Moderate, Limited)

Example Usage:

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