Cosmic Tools

Configuration File: cosmic_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

COSMIC_get_mutations_by_gene (Type: COSMICTool)

Get all somatic mutations for a specific gene from COSMIC database. Returns comprehensive mutatio…

COSMIC_get_mutations_by_gene tool specification

Tool Information:

  • Name: COSMIC_get_mutations_by_gene

  • Type: COSMICTool

  • Description: Get all somatic mutations for a specific gene from COSMIC database. Returns comprehensive mutation data for a gene symbol including CDS changes, amino acid changes, cancer types, and genomic positions. Useful for exploring the mutational landscape of cancer genes like BRAF, TP53, EGFR, KRAS, etc.

Parameters:

  • operation (string) (required) Operation type (fixed: get_by_gene)

  • gene (string) (required) Gene symbol (e.g., BRAF, TP53, EGFR, KRAS, PIK3CA)

  • max_results (integer) (optional) Maximum number of mutations to return (default: 100, max: 500)

  • genome_build (integer) (optional) Genome build version: 37 (GRCh37/hg19) or 38 (GRCh38/hg38). Default: 37

Example Usage:

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

COSMIC_search_mutations (Type: COSMICTool)

Search COSMIC database for somatic mutations in cancer. COSMIC is the world’s largest expert-cura…

COSMIC_search_mutations tool specification

Tool Information:

  • Name: COSMIC_search_mutations

  • Type: COSMICTool

  • Description: Search COSMIC database for somatic mutations in cancer. COSMIC is the world’s largest expert-curated database of somatic mutations in human cancer. Search by gene name, mutation ID, or mutation description. Returns mutation IDs, gene names, CDS changes, and amino acid changes. No authentication required.

Parameters:

  • operation (string) (required) Operation type (fixed: search)

  • terms (string) (required) Search query - gene name (e.g., BRAF), mutation (e.g., V600E), or mutation ID (e.g., COSM476)

  • max_results (integer) (optional) Maximum number of results to return (default: 20, max: 500)

  • genome_build (integer) (optional) Genome build version: 37 (GRCh37/hg19) or 38 (GRCh38/hg38). Default: 37

Example Usage:

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