genefoundry-router
A thin FastMCP 3.x aggregator that federates the GeneFoundry *-link MCP fleet behind a
single Streamable-HTTP endpoint. A host adds one server — genefoundry — and gets every
biomedical backend with collision-free <namespace>_<tool> naming and search-based discovery.
IMPORTANT
Research use only. Not clinical decision support. Do not use for diagnosis,
treatment, triage, or patient management.
Why
An MCP host that mounted all 21 backends directly would face a wall of several hundred
tools — more than a model can reason over, and a guarantee of name collisions. The router
collapses that into one endpoint and replaces the flat catalog with a search surface, so
a model finds the right tool by intent instead of by scrolling.
It is a client to each backend and a server to hosts: it namespaces and shapes the
surface, but never rewrites a backend's data. The caller's token is never forwarded
upstream.
Quick start
The fleet is hosted — no install required:
claude mcp add --transport http genefoundry https://genefoundry.org/mcp
Health check: genefoundry.org/health.
To run your own against the live fleet (Python 3.12+, uv):
uv sync --group dev
cp .env.example .env
uv run genefoundry-router run --host 127.0.0.1 --port 8000
curl -s localhost:8000/health | python -m json.tool
An offline fake fleet (make dev-fleet + make run-dev, or one-shot make test-e2e) runs
the real router against impersonated backends over real Streamable-HTTP — no Docker, no
network.
The router does not surface the federated catalog flat. A model sees three things:
| Tool | Purpose |
|---|
search_tools | Relevance search over the entire federated catalog |
call_tool | Invoke a hit by its <namespace>_<tool> name |
| pinned entry points | Each backend's front-door tool, always visible — declared per-backend as entrypoints: in servers.yaml |
search_tools(query="splicing prediction") # → spliceai_predict_splicing (+ schema)
call_tool(name="spliceai_predict_splicing", arguments={...})
Pinning makes each domain's canonical tool reachable deterministically rather than by
relevance luck. See How discovery works — including the two traps that
bite MCP clients.
Federated backends
22 backends, 285 tools, each surfaced namespaced — e.g. gnomad_search_genes.
Data & provenance
The router serves no data of its own; each backend owns its sources, licences and
citation guidance, and the router mirrors their disclaimers.
What it does own is integrity of the tool surface. A backend can serve a clean tool at
review time and later change its definition — the channel for a rug pull. The router
fingerprints every normalized tool definition and diffs the live fleet against a reviewed,
packaged baseline (genefoundry_router/data/fleet-baseline.json), enforced at startup and
on a schedule. See Deployment → drift detection.
Documentation
Contributing
See AGENTS.md for engineering conventions. make ci-local is the
definition-of-done gate: format, lint, line budget, README standard, mypy, and tests.
License
MIT © Bernt Popp. Each federated backend carries the licence and citation terms
of its upstream data source; see that backend's repository.