Civic MCP Server

@pipeworx/civic

Expert-curated clinical interpretation of cancer variants from CIViC — which somatic alterations are clinically actionable, in which disease, with which therapy, and the graded published evidence behind each claim.

Part of Pipeworx — an MCP gateway connecting AI agents to 1683+ live data sources.

Tools

• civic_search_genes(query, limit?) — cancer genes and fusions by name, with variant / evidence / assertion counts and the CIViC feature id.
• civic_gene_variants(gene, variant_name?, limit?) — the curated variants of a gene, with associated diseases and therapies.
• civic_variant_evidence(molecular_profile | variant_id, evidence_type?, disease?, therapy?, limit?) — individual evidence items with type, level A-E, direction, significance, 1-5 star rating and the PubMed/ASCO source.
• civic_assertions(molecular_profile? | disease? | therapy?, limit?) — the AMP/ASCO/CAP-tiered rollups, with FDA companion-test and regulatory-approval flags, ACMG codes and NCCN guideline.

Auth

Keyless. Public GraphQL endpoint; CIViC's content is CC0.

Data sources

• https://civicdb.org/api/graphql — POST, {query, variables}.

Things that will otherwise cost you an afternoon:

• An explicitly null variable is a FILTER, not an absent filter — and it returns HTTP 200. Measured 2026-09-17: evidenceItems(molecularProfileName: "BRAF V600E") reports 249 matches; adding variantId: null reports 0, diseaseName: null reports 245, therapyName: null reports 313. Unset filters must be omitted from the variables map entirely. omitNulls() in src/index.ts exists for exactly this and removing it produces a silent zero.
• browseVariants.totalCount and browseFeatures.totalCount ignore their own filter arguments. browseVariants(featureName: "BRAF") and an unfiltered browseVariants both report 5029, the whole catalogue. evidenceItems and assertions DO filter their totalCount. This pack only reports the count for the two that mean it.
• description on the BrowseFeature type 500s the entire query. It is in the schema and it is not callable. The gene summary lives on the Gene type, which is why civic_search_genes makes a second call.
• genes takes entrezSymbols/entrezIds, not name. Free-text gene search is browseFeatures(featureName:) (substring, unranked — this pack re-ranks exact matches first) or featureTypeahead(queryTerm:).
• Evidence and assertion status can be SUBMITTED as well as ACCEPTED; a submitted item has not been through CIViC review yet.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "civic": {
      "url": "https://gateway.pipeworx.io/civic/mcp"
    }
  }
}

What this endpoint actually serves

tools/list at https://gateway.pipeworx.io/civic/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 1683+ data sources. The only difference is which pack's tools are listed directly; ask_pipeworx reaches all of them from either one.

No MCP client? Call it over HTTP

curl -X POST https://gateway.pipeworx.io/v1/tools/civic_search_genes \
  -H 'Content-Type: application/json' \
  -d '{"query":"BRAF","limit":5}'

No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/civic_search_genes. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.

Standalone (no gateway account)

This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:

{
  "mcpServers": {
    "civic": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-civic"]
    }
  }
}

Or run it directly to confirm it starts:

npx -y @pipeworx/mcp-civic

It speaks MCP over stdin/stdout and answers initialize/tools/list/tools/call for only this pack's tools — none of the shared meta-tools the gateway connection above adds. Same source, same tools, no ask_pipeworx routing.

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 Civic data" })

The gateway picks the right tool and fills the arguments automatically.

More

• Docs and guides
• pipeworx.io

License

MIT