Summary
Connects Claude to the National Cancer Institute's Genomic Data Commons, the central repository for cancer genomics data from programs like TCGA and TARGET. The source documentation is sparse on specific tools, but GDC's API typically handles queries for cases, files, mutations, and clinical data across thousands of cancer patients. Part of the Pipeworx gateway ecosystem, which routes requests through a unified endpoint and includes an ask_pipeworx function that translates natural language questions into the appropriate API calls. Reach for this when you need programmatic access to large scale cancer genomics datasets without managing authentication and API pagination yourself.
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mcp-gdc
NCI Genomic Data Commons (GDC) MCP.
Part of Pipeworx — an MCP gateway connecting AI agents to 1476+ live data sources.
Tools
| Tool | Description |
|---|---|
list_projects | List NCI Genomic Data Commons cancer-genomics projects (TCGA, TARGET, CPTAC, etc.), ranked by case count. Returns project_id, name, program, primary site(s) and disease type(s). Keyless, open-access metadata. |
get_project | Look up a single NCI GDC project by project_id (e.g. "TCGA-BRCA") and get its details plus summary counts (case_count, file_count). Keyless, open-access metadata. |
search_cases | Search NCI GDC cancer cases (patients/samples) by primary site and/or project. Returns case_id, submitter_id, primary site, disease type and project_id. Keyless, open-access metadata. |
search_files | Search NCI GDC genomic data files by project and/or data category (e.g. "Transcriptome Profiling", "Simple Nucleotide Variation", "DNA Methylation"). Returns file_id, file_name, data category/type/format, access level and file size. Keyless, open-access metadata. |
Quick Start
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"gdc": {
"url": "https://gateway.pipeworx.io/gdc/mcp"
}
}
}
What this endpoint actually serves
tools/list at https://gateway.pipeworx.io/gdc/mcp returns the tools in the table
above plus the shared Pipeworx meta-tools — ask_pipeworx,
discover_tools, search_within, remember/recall and the rest of the
gateway-wide set. So the tool count you see is larger than this table: a
single-pack endpoint currently lists roughly 30 shared tools alongside the
pack's own. The connection's initialize response states its exact scope, and
is the authoritative answer for a given day.
This is deliberate, not multiplexing by accident. The meta-tools are what let a
scoped connection answer a question this pack does not cover — via
ask_pipeworx, which routes across the whole catalog — without you adding a
second MCP server. There is currently no way to mount a pack endpoint without
them; if the extra schemas cost you more context than the routing is worth,
connect to the full gateway once rather than to several pack endpoints.
Or connect to the full Pipeworx gateway to get every pack's tools listed directly, instead of just this one's:
{
"mcpServers": {
"pipeworx": {
"url": "https://gateway.pipeworx.io/mcp"
}
}
}
Both URLs reach the same gateway and the same 1476+ data sources. The
only difference is which pack's tools are listed directly; ask_pipeworx
reaches all of them from either one.
Using with ask_pipeworx
Instead of calling tools directly, you can ask questions in plain English — this works on the pack endpoint above as well as on the full gateway:
ask_pipeworx({ question: "your question about Gdc data" })
The gateway picks the right tool and fills the arguments automatically.
More
License
MIT
No MCP client? Call it over HTTP
curl -X POST https://gateway.pipeworx.io/v1/tools/gdc_list_projects \
-H 'Content-Type: application/json' \
-d '{"size":20}'
No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/gdc_list_projects. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.
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