Summary
This connects Claude to the Human Protein Atlas through Pipeworx's gateway, letting you query protein expression data, tissue distribution, and cellular localization without managing API keys. The source doesn't list specific tools, but it's part of a larger gateway that routes requests through ask_pipeworx, where you phrase questions in plain English and it handles the underlying API calls. You'd reach for this when working with proteomics data, analyzing gene expression patterns, or building biology research workflows. Works via streamable HTTP, so no local installation needed. Can be used standalone or as part of the full Pipeworx gateway with 823+ data sources.
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mcp-protein-atlas
Human Protein Atlas (HPA) MCP — keyless.
Part of Pipeworx — an MCP gateway connecting AI agents to 1476+ live data sources.
Tools
| Tool | Description |
|---|---|
search_genes | Search the Human Protein Atlas for human genes/proteins by gene symbol or keyword. Returns each gene with its Ensembl gene id (needed by get_protein and top_tissues), synonyms, and description. Keyless. |
get_protein | Get a trimmed Human Protein Atlas profile for one protein by Ensembl gene id (e.g. "ENSG00000146648"): gene, description, protein class, biological process, molecular function, RNA tissue specificity/distribution, subcellular location, and disease involvement. Use search_genes to find the Ensembl id. Keyless. |
top_tissues | List a protein's top-expressing human tissues by RNA expression (nTPM), highest first, for one Ensembl gene id. Use search_genes to find the Ensembl id. Keyless. |
Quick Start
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"protein-atlas": {
"url": "https://gateway.pipeworx.io/protein-atlas/mcp"
}
}
}
What this endpoint actually serves
tools/list at https://gateway.pipeworx.io/protein-atlas/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 Protein Atlas 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/protein_atlas_search_genes \
-H 'Content-Type: application/json' \
-d '{"query":"EGFR"}'
No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/protein_atlas_search_genes. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.
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Download Free life-time →Integrate web data into your AI product. One API to scrape website & brand data.
Get API Key Now →belt cli automatically finds the best tools and skills for your agent. image, video, music, tts...
one prompt install →Connect your Claude agent to live crypto prices and trading routes via 1inch
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