Oncokb Tools

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

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

Available Tools

OncoKB_annotate_copy_number (Type: OncoKBTool)

Annotate copy number alterations (amplification/deletion) for oncogenic potential. Returns eviden…

OncoKB_annotate_copy_number tool specification

Tool Information:

  • Name: OncoKB_annotate_copy_number

  • Type: OncoKBTool

  • Description: Annotate copy number alterations (amplification/deletion) for oncogenic potential. Returns evidence for gene amplification or deletion in cancer. Example: ERBB2 amplification in breast cancer, CDKN2A deletion.

Parameters:

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

  • gene (string) (required) Gene symbol (e.g., ERBB2, MYC, CDKN2A)

  • copy_number_type (string) (optional) Type of copy number alteration (case-insensitive: AMPLIFICATION or DELETION)

  • tumor_type (string) (optional) Optional OncoTree tumor type code

  • copy_number_alteration (string) (optional) Alias for copy_number_type. Amplification or Deletion.

Example Usage:

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

OncoKB_annotate_mutations (Type: OncoKBTool)

Annotate a cancer mutation using OncoKB. Accepts query string like ‘BRAF V600E’ or separate gene/…

OncoKB_annotate_mutations tool specification

Tool Information:

  • Name: OncoKB_annotate_mutations

  • Type: OncoKBTool

  • Description: Annotate a cancer mutation using OncoKB. Accepts query string like ‘BRAF V600E’ or separate gene/variant parameters. Returns oncogenicity, mutation effect, and FDA-approved therapies. Alias for OncoKB_annotate_variant with query-string parsing. Demo mode available for BRAF, TP53, ROS1.

Parameters:

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

  • query (string) (optional) Mutation query string, e.g. ‘BRAF V600E’ or ‘EGFR T790M’. Gene and variant separated by space.

  • gene (string) (optional) Gene symbol (e.g., BRAF, EGFR, TP53)

  • variant (string) (optional) Protein change (e.g., V600E, T790M)

  • tumor_type (string) (optional) Optional OncoTree tumor type code (e.g., MEL, LUAD)

Example Usage:

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

OncoKB_annotate_variant (Type: OncoKBTool)

Annotate a cancer variant for oncogenic potential and treatment implications using OncoKB. Return…

OncoKB_annotate_variant tool specification

Tool Information:

  • Name: OncoKB_annotate_variant

  • Type: OncoKBTool

  • Description: Annotate a cancer variant for oncogenic potential and treatment implications using OncoKB. Returns evidence level, oncogenicity, mutation effect, and FDA-approved therapies. Requires ONCOKB_API_TOKEN env var (demo mode available for BRAF, TP53, ROS1). Example: BRAF V600E in melanoma.

Parameters:

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

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

  • gene_symbol (string) (optional) Alias for gene. Gene symbol (e.g., BRAF, EGFR, TP53, KRAS).

  • variant (string) (optional) Variant notation - protein change (e.g., V600E, T790M, G12D)

  • tumor_type (string) (optional) Optional OncoTree tumor type code (e.g., MEL for melanoma, LUAD for lung adenocarcinoma)

  • alteration (string) (optional) Alias for variant. Protein change notation (e.g., “V600E”, “T790M”, “G12D”).

Example Usage:

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

OncoKB_get_cancer_genes (Type: OncoKBTool)

Get list of all cancer genes curated in OncoKB. Returns genes classified as oncogenes and/or tumo…

OncoKB_get_cancer_genes tool specification

Tool Information:

  • Name: OncoKB_get_cancer_genes

  • Type: OncoKBTool

  • Description: Get list of all cancer genes curated in OncoKB. Returns genes classified as oncogenes and/or tumor suppressors. Useful for checking if a gene is a known cancer driver. Requires ONCOKB_API_TOKEN env var.

Parameters:

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

Example Usage:

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

OncoKB_get_gene_info (Type: OncoKBTool)

Get gene-level oncogenic information from OncoKB. Returns whether gene is an oncogene, tumor supp…

OncoKB_get_gene_info tool specification

Tool Information:

  • Name: OncoKB_get_gene_info

  • Type: OncoKBTool

  • Description: Get gene-level oncogenic information from OncoKB. Returns whether gene is an oncogene, tumor suppressor, or both. Includes curated background information. Requires ONCOKB_API_TOKEN env var (demo mode available for BRAF, TP53, ROS1).

Parameters:

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

  • gene (string) (optional) Gene symbol (e.g., BRAF, TP53, ROS1). Without ONCOKB_API_TOKEN only BRAF, TP53, and ROS1 are available (demo mode).

  • gene_symbol (string) (optional) Gene symbol alias — alternative to gene parameter

Example Usage:

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

OncoKB_get_levels (Type: OncoKBTool)

Get OncoKB evidence level definitions. Returns descriptions of all therapeutic actionability leve…

OncoKB_get_levels tool specification

Tool Information:

  • Name: OncoKB_get_levels

  • Type: OncoKBTool

  • Description: Get OncoKB evidence level definitions. Returns descriptions of all therapeutic actionability levels (1, 2, 3A, 3B, 4, R1, R2). Level 1 = FDA-approved, Level 2 = Standard care, Level 3A = Compelling clinical evidence, etc.

Parameters:

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

Example Usage:

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