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)#

Retrieve COSMIC mutation records constrained to one gene symbol. Repeated source records are aggr…

COSMIC_get_mutations_by_gene tool specification

Tool Information:

  • Name: COSMIC_get_mutations_by_gene

  • Type: COSMICTool

  • Description: Retrieve COSMIC mutation records constrained to one gene symbol. Repeated source records are aggregated into unique mutations while retaining every distinct cancer context visible in the upstream 500-record window. COSMIC does not permit pagination; metadata explicitly reports truncation and a possibly capped server total.

Parameters:

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

  • gene (string) (required) HGNC-style gene symbol, e.g. BRAF, TP53, HLA-DRA.

  • max_results (integer) (optional) Maximum unique mutations to return from the accessible 500-source-record window (default 100, range 1-500). The upstream API does not support offsets.

  • 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": {
        "gene": "example_value"
    }
}
result = tu.run(query)

COSMIC_search_mutations (Type: COSMICTool)#

Search COSMIC mutation records by gene, mutation ID, or mutation description through NLM Clinical…

COSMIC_search_mutations tool specification

Tool Information:

  • Name: COSMIC_search_mutations

  • Type: COSMICTool

  • Description: Search COSMIC mutation records by gene, mutation ID, or mutation description through NLM Clinical Tables. Repeated source records are aggregated into unique mutations with all cancer contexts visible in the accessible window. COSMIC does not permit pagination: metadata explicitly reports the 500-record upstream window, truncation, and whether the server total may be capped at 10,000.

Parameters:

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

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

  • max_results (integer) (optional) Maximum unique mutations to return from the accessible 500-source-record window (default 20, range 1-500). Increase this value to expose more unique mutations in that one window; the upstream API does not support offsets.

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

Example Usage:

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