Cbioportal Tools

Configuration File: cbioportal_tools.json Tool Type: Local Tools Count: 13

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

Available Tools

cBioPortal_get_cancer_studies (Type: CBioPortalRESTTool)

Get list of cancer studies from cBioPortal

cBioPortal_get_cancer_studies tool specification

Tool Information:

• Name: cBioPortal_get_cancer_studies

• Type: CBioPortalRESTTool

• Description: Get list of cancer studies from cBioPortal

Parameters:

• limit (integer) (optional) Number of studies to return

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 all samples in a study. Returns patient-level data like tumor stage, histol…

cBioPortal_get_clinical_data tool specification

Tool Information:

• Name: cBioPortal_get_clinical_data

• Type: CBioPortalRESTTool

• Description: Get clinical data for all samples in a study. Returns patient-level data like tumor stage, histology, survival status. Filter by clinical attribute ID for specific data types.

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_gene_info (Type: CBioPortalRESTTool)

Get detailed information about a specific gene by Entrez Gene ID. Returns gene symbol, aliases, t…

cBioPortal_get_gene_info tool specification

Tool Information:

• Name: cBioPortal_get_gene_info

• Type: CBioPortalRESTTool

• Description: Get detailed information about a specific gene by Entrez Gene ID. Returns gene symbol, aliases, type, and 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 all gene panels used in cBioPortal studies. Gene panels define which genes were sequenced in …

cBioPortal_get_gene_panels tool specification

Tool Information:

• Name: cBioPortal_get_gene_panels

• Type: CBioPortalRESTTool

• Description: Get all gene panels used in cBioPortal studies. Gene panels define which genes were sequenced in a study. Use to understand coverage before querying mutation data.

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 (gene symbol or alias)

cBioPortal_get_genes tool specification

Tool Information:

• Name: cBioPortal_get_genes

• Type: CBioPortalRESTTool

• Description: Search for genes by keyword (gene symbol or alias)

Parameters:

• keyword (string) (required) Gene symbol or alias to search for

Example Usage:

query = {
    "name": "cBioPortal_get_genes",
    "arguments": {
        "keyword": "example_value"
    }
}
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

cBioPortal_get_patients tool specification

Tool Information:

• Name: cBioPortal_get_patients

• Type: CBioPortalRESTTool

• Description: Get all patients in a cancer study

Parameters:

• study_id (string) (required) Cancer study ID

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

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

cBioPortal_get_samples tool specification

Tool Information:

• Name: cBioPortal_get_samples

• Type: CBioPortalRESTTool

• Description: Get all samples in a cancer study

Parameters:

• study_id (string) (required) Cancer study ID

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

Example Usage:

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

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