Cbioportal Tools#

Configuration File: cbioportal_tools.json Tool Type: Local Tools Count: 14

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

Available Tools#

cBioPortal_get_cancer_studies (Type: CBioPortalRESTTool)#

Get one page of the cBioPortal study catalogue. This returns a SLICE, not the whole catalogue: `l…

cBioPortal_get_cancer_studies tool specification

Tool Information:

  • Name: cBioPortal_get_cancer_studies

  • Type: CBioPortalRESTTool

  • Description: Get one page of the cBioPortal study catalogue. This returns a SLICE, not the whole catalogue: limit defaults to 20 while cBioPortal currently holds several hundred studies. The response always reports total_available (the full catalogue size) alongside count (studies actually returned), and sets truncated: true with a truncation_note whenever studies were left behind. Never conclude a study is missing from cBioPortal from a truncated page — raise limit to total_available, or page with offset, before drawing that conclusion.

Parameters:

  • limit (integer) (optional) Number of studies to return in this page. The default of 20 covers only a small fraction of the catalogue; set it to the total_available reported in the response to retrieve every study.

  • offset (integer) (optional) 0-based index of the first study to return, for paging through the catalogue. Applied client-side because the cBioPortal /studies endpoint ignores its own pageNumber parameter.

Example Usage:

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

cBioPortal_get_cancer_types (Type: CBioPortalRESTTool)#

Get all cancer types from cBioPortal including TCGA, Pan-Cancer Atlas, and other studies. Returns…

cBioPortal_get_cancer_types tool specification

Tool Information:

  • Name: cBioPortal_get_cancer_types

  • Type: CBioPortalRESTTool

  • Description: Get all cancer types from cBioPortal including TCGA, Pan-Cancer Atlas, and other studies. Returns cancerTypeId, name, and clinical trial keywords for filtering studies.

Parameters:

No parameters required.

Example Usage:

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

cBioPortal_get_clinical_attributes (Type: CBioPortalRESTTool)#

Get available clinical attributes for a cancer study. Returns attribute IDs, names, and data type…

cBioPortal_get_clinical_attributes tool specification

Tool Information:

  • Name: cBioPortal_get_clinical_attributes

  • Type: CBioPortalRESTTool

  • Description: Get available clinical attributes for a cancer study. Returns attribute IDs, names, and data types. Use to know what clinical data can be queried (e.g., stage, grade, survival).

Parameters:

  • study_id (string) (required) Cancer study ID (e.g., ‘brca_tcga’)

Example Usage:

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

cBioPortal_get_clinical_data (Type: CBioPortalRESTTool)#

Get clinical data for samples in a study. Returns patient-level data like tumor stage, histology,…

cBioPortal_get_clinical_data tool specification

Tool Information:

  • Name: cBioPortal_get_clinical_data

  • Type: CBioPortalRESTTool

  • Description: Get clinical data for samples in a study. Returns patient-level data like tumor stage, histology, survival status. Filter by clinical attribute ID for specific data types. Returns one page: page_size defaults to 100 while a single TCGA study can hold tens of thousands of clinical records, so the response reports total_available (all records matching) next to count (records returned), plus truncated/truncation_note when records were left behind.

Parameters:

  • study_id (string) (required) Cancer study ID

  • clinical_attribute_id (string) (optional) Optional clinical attribute ID to filter by

  • page_size (integer) (optional) Number of records to return

Example Usage:

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

cBioPortal_get_copy_number_alterations (Type: CBioPortalRESTTool)#

Get discrete copy-number alteration (CNA) calls per sample from GISTIC profiles for a gene in a c…

cBioPortal_get_copy_number_alterations tool specification

Tool Information:

  • Name: cBioPortal_get_copy_number_alterations

  • Type: CBioPortalRESTTool

  • Description: Get discrete copy-number alteration (CNA) calls per sample from GISTIC profiles for a gene in a cancer study. Returns per-sample alteration values: -2 (deep deletion), -1 (shallow loss), 0 (neutral), 1 (gain), 2 (amplification), plus a count breakdown by category. Use alteration_type to filter to a single category (AMP, GAIN, DIPLOID, HETLOSS, HOMDEL) or ALL for every altered sample. Example: ERBB2 (entrez 2064) AMP in brca_tcga_pan_can_atlas_2018 returns 123 amplified samples.

Parameters:

  • study_id (string) (required) Cancer study ID (e.g., ‘brca_tcga_pan_can_atlas_2018’). The discrete GISTIC profile is resolved automatically.

  • gene_list (string) (required) Comma-separated gene symbols (e.g., ‘ERBB2’ or ‘TP53,ERBB2’)

  • gene (string) (optional) Alias for gene_list: comma-separated gene symbols

  • alteration_type (string) (optional) CNA category filter: ‘AMP’ (amplification), ‘GAIN’, ‘DIPLOID’, ‘HETLOSS’ (shallow loss), ‘HOMDEL’ (deep deletion), or ‘ALL’ for every altered sample (default ‘ALL’).

  • sample_list_id (string) (optional) Optional sample list ID. Defaults to ‘{study_id}_all’.

  • molecular_profile_id (string) (optional) Optional explicit GISTIC molecular profile ID (overrides auto-resolution).

Example Usage:

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

cBioPortal_get_gene_info (Type: CBioPortalRESTTool)#

Get basic information about a specific gene by Entrez Gene ID. Returns the HUGO gene symbol and g…

cBioPortal_get_gene_info tool specification

Tool Information:

  • Name: cBioPortal_get_gene_info

  • Type: CBioPortalRESTTool

  • Description: Get basic information about a specific gene by Entrez Gene ID. Returns the HUGO gene symbol and gene type (e.g., ‘protein-coding’); does not return aliases – use HGNC_fetch_gene_by_symbol or NCBIGene_get_summary for gene aliases/chromosome location.

Parameters:

  • entrez_gene_id (integer) (required) Entrez Gene ID (e.g., 672 for BRCA1)

Example Usage:

query = {
    "name": "cBioPortal_get_gene_info",
    "arguments": {
        "entrez_gene_id": 10
    }
}
result = tu.run(query)

cBioPortal_get_gene_panel_genes (Type: CBioPortalRESTTool)#

Get all genes in a specific gene panel. Essential for understanding what genes are covered when a…

cBioPortal_get_gene_panel_genes tool specification

Tool Information:

  • Name: cBioPortal_get_gene_panel_genes

  • Type: CBioPortalRESTTool

  • Description: Get all genes in a specific gene panel. Essential for understanding what genes are covered when analyzing mutation frequency data from targeted sequencing studies.

Parameters:

  • gene_panel_id (string) (required) Gene panel ID (e.g., ‘IMPACT468’)

Example Usage:

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

cBioPortal_get_gene_panels (Type: CBioPortalRESTTool)#

Get gene panels used in cBioPortal studies. Gene panels define which genes were sequenced in a st…

cBioPortal_get_gene_panels tool specification

Tool Information:

  • Name: cBioPortal_get_gene_panels

  • Type: CBioPortalRESTTool

  • Description: Get gene panels used in cBioPortal studies. Gene panels define which genes were sequenced in a study. Use to understand coverage before querying mutation data. Returns one page: page_size defaults to 50, and the response reports total_available (all panels matching) next to count (panels returned), plus truncated/truncation_note when panels were left behind.

Parameters:

  • page_size (integer) (optional) Number of panels to return

Example Usage:

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

cBioPortal_get_genes (Type: CBioPortalRESTTool)#

Search for genes by keyword or query (gene symbol or alias). Alias: cBioPortal_search.

cBioPortal_get_genes tool specification

Tool Information:

  • Name: cBioPortal_get_genes

  • Type: CBioPortalRESTTool

  • Description: Search for genes by keyword or query (gene symbol or alias). Alias: cBioPortal_search.

Parameters:

  • keyword (string) (optional) Gene symbol or alias to search for (e.g., ‘BRCA1’, ‘TP53’)

  • query (string) (optional) Alias for keyword: gene symbol or alias to search for

Example Usage:

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

cBioPortal_get_molecular_profiles (Type: CBioPortalRESTTool)#

Get molecular profiles for a cancer study. Molecular profiles include mutation data, copy number …

cBioPortal_get_molecular_profiles tool specification

Tool Information:

  • Name: cBioPortal_get_molecular_profiles

  • Type: CBioPortalRESTTool

  • Description: Get molecular profiles for a cancer study. Molecular profiles include mutation data, copy number alterations, mRNA expression, etc.

Parameters:

  • study_id (string) (required) Cancer study ID

Example Usage:

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

cBioPortal_get_mutations (Type: CBioPortalRESTTool)#

Get mutation data for specific genes in a cancer study. This uses the updated cBioPortal API that…

cBioPortal_get_mutations tool specification

Tool Information:

  • Name: cBioPortal_get_mutations

  • Type: CBioPortalRESTTool

  • Description: Get mutation data for specific genes in a cancer study. This uses the updated cBioPortal API that requires molecular profiles.

Parameters:

  • study_id (string) (required) Cancer study ID (e.g., ‘brca_tcga’)

  • gene_list (string) (required) Comma-separated gene symbols (e.g., ‘BRCA1,BRCA2’)

  • sample_list_id (string) (optional) Optional sample list ID. If not provided, uses all samples in the study.

Example Usage:

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

cBioPortal_get_patients (Type: CBioPortalRESTTool)#

Get all patients in a cancer study. Returns the full cohort by default; the response is a bare ar…

cBioPortal_get_patients tool specification

Tool Information:

  • Name: cBioPortal_get_patients

  • Type: CBioPortalRESTTool

  • Description: Get all patients in a cancer study. Returns the full cohort by default; the response is a bare array with no truncation marker, so lower page_size only when you deliberately want a sample. Use this count as the denominator for mutation-frequency calculations.

Parameters:

  • study_id (string) (required) Cancer study ID

  • page_size (integer) (optional) Maximum number of patients to return. Defaults high enough to return every patient in a study; a smaller value silently truncates the cohort, which will corrupt any frequency denominator computed from it.

  • page_number (integer) (optional) 0-based page index, used with page_size to page through very large studies.

Example Usage:

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

cBioPortal_get_sample_lists (Type: CBioPortalRESTTool)#

Get all sample lists (cohort definitions) in a cancer study. Sample lists define groups like ‘sam…

cBioPortal_get_sample_lists tool specification

Tool Information:

  • Name: cBioPortal_get_sample_lists

  • Type: CBioPortalRESTTool

  • Description: Get all sample lists (cohort definitions) in a cancer study. Sample lists define groups like ‘samples with mutations’, ‘samples with CNA data’. Use for targeted queries.

Parameters:

  • study_id (string) (required) Cancer study ID

Example Usage:

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

cBioPortal_get_samples (Type: CBioPortalRESTTool)#

Get all samples in a cancer study. Returns the full cohort by default; the response is a bare arr…

cBioPortal_get_samples tool specification

Tool Information:

  • Name: cBioPortal_get_samples

  • Type: CBioPortalRESTTool

  • Description: Get all samples in a cancer study. Returns the full cohort by default; the response is a bare array with no truncation marker, so lower page_size only when you deliberately want a sample. Use this count as the denominator for mutation-frequency calculations.

Parameters:

  • study_id (string) (required) Cancer study ID

  • page_size (integer) (optional) Maximum number of samples to return. Defaults high enough to return every sample in a study; a smaller value silently truncates the cohort, which will corrupt any frequency denominator computed from it.

  • page_number (integer) (optional) 0-based page index, used with page_size to page through very large studies.

Example Usage:

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