Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| base-url | No | The URL of a cBioPortal API instance | https://www.cbioportal.org/api |
Schema
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| paginate_results | Delegate to utils.pagination.paginate_results with api_client. |
| collect_all_results | Delegate to utils.pagination.collect_all_results with api_client. |
| get_cancer_studies | Get a list of cancer studies in cBioPortal with pagination support. |
| get_cancer_types | Get a list of all available cancer types in cBioPortal with pagination support. |
| search_studies | Search for cancer studies by keyword in their name or description with pagination support. |
| get_study_details | Get detailed information for a specific cancer study. |
| get_multiple_studies | Get details for multiple studies concurrently. |
| search_genes | Search for genes by keyword in their symbol or name with pagination support. |
| get_genes | Get information about specific genes by their Hugo symbol or Entrez ID using batch endpoint. |
| get_multiple_genes | Get information about multiple genes concurrently. |
| get_mutations_in_gene | Get mutations in a specific gene for a given study and sample list, with pagination support. |
| get_samples_in_study | Get a list of samples associated with a specific cancer study with pagination support. |
| get_sample_list_id | Get sample list information for a specific study and sample list ID. |
| get_molecular_profiles | Get a list of molecular profiles available for a specific cancer study with pagination support. |
| get_clinical_data | Get clinical data for patients in a study with pagination support. Can fetch specific attributes or all. |
| get_gene_panels_for_study | Get all gene panels in a specific study with pagination support. |
| get_gene_panel_details | Get detailed information for a specific gene panel, including the list of genes. |