cBioPortal MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Server capabilities have not been inspected yet.
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| paginate_resultsD | Delegate to utils.pagination.paginate_results with api_client. |
| collect_all_resultsC | Delegate to utils.pagination.collect_all_results with api_client. |
| get_cancer_studiesC | Get a list of cancer studies in cBioPortal with pagination support. |
| get_cancer_typesC | Get a list of all available cancer types in cBioPortal with pagination support. |
| search_studiesC | Search for cancer studies by keyword in their name or description with pagination support. |
| get_study_detailsC | Get detailed information for a specific cancer study. |
| get_multiple_studiesC | Get details for multiple studies concurrently. |
| search_genesC | Search for genes by keyword in their symbol or name with pagination support. |
| get_genesC | Get information about specific genes by their Hugo symbol or Entrez ID using batch endpoint. |
| get_multiple_genesC | Get information about multiple genes concurrently. |
| get_mutations_in_geneC | Get mutations in a specific gene for a given study and sample list, with pagination support. |
| get_samples_in_studyC | Get a list of samples associated with a specific cancer study with pagination support. |
| get_sample_list_idC | Get sample list information for a specific study and sample list ID. |
| get_molecular_profilesC | Get a list of molecular profiles available for a specific cancer study with pagination support. |
| get_clinical_dataC | Get clinical data for patients in a study with pagination support. Can fetch specific attributes or all. |
| get_gene_panels_for_studyC | Get all gene panels in a specific study with pagination support. |
| get_gene_panel_detailsC | Get detailed information for a specific gene panel, including the list of genes. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 17 tools
Most tools have distinct purposes targeting specific resources like studies, genes, or clinical data, but there is some overlap between 'get_genes' and 'get_multiple_genes' which could cause confusion, and 'collect_all_results' and 'paginate_results' are both pagination utilities with unclear boundaries.
Tool names follow a consistent verb_noun pattern throughout, such as 'get_cancer_studies', 'search_genes', and 'get_mutations_in_gene', with no deviations in style or convention, making them predictable and readable.
With 17 tools, the count is slightly high but reasonable for a bioinformatics domain like cBioPortal, covering various data retrieval and search operations without feeling excessively bloated.
The tool set provides comprehensive coverage for querying studies, genes, clinical data, and molecular profiles, with minor gaps such as lacking update or delete operations, but this is typical for a read-only API server focused on data retrieval.