Genefoundry

Name: Genefoundry
Author: berntpopp

by berntpoppversion 0.10.10i★ –iRuns in the cloud

Registry nameio.github.berntpopp/genefoundry

Install

Overview

Description from the maker (original English)

MCP gateway federating 22 biomedical MCP servers behind one endpoint: gnomAD, ClinVar, HPO, VEP.

PopNx MCP’s three pillars

These three are never merged into one score: opinions, measurements and popularity are different things.

User voiceiNo reviews yetReviews open together with accounts in a later step
Our basic checksi3 of 3 passedChecked from public information; code not scanned yet
UsageiNot measured yet★ –

What you can do with it

We have not written a plain-language summary for this one yet. Below are the facts we read from the registry.

Connection: Runs in the cloud
Transport: Streamable HTTP
Category: Clinics & health

Install

Pick the AI app you use, then copy the settings.

Before you install

Basic checks: 3 of 3 passed
Runs on the maker’s server: what you ask it goes through their server.
The registry lists no key to fill in.

You need

Runs in the cloudNothing to install; it connects over the internet

Which app do you use?

ClaudeClaude CodeCursorVS CodeChatGPT

Pick your app above. We remember it, so next time the button says “Install in …”.

Works in Claude on the web, desktop and mobile:

Open Settings → Connectors
Press Add custom connector
Paste the address below and press Add
If it asks you to sign in, sign in with the maker

https://genefoundry.org/mcp

Run this in your terminal

claude mcp add --transport http genefoundry https://genefoundry.org/mcp

Open in Cursor

Or copy the settings yourself

Paste into .cursor/mcp.json in your project, or ~/.cursor/mcp.json

{
  "mcpServers": {
    "genefoundry": {
      "url": "https://genefoundry.org/mcp"
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

Open in VS Code

Or copy the settings yourself

Paste into .vscode/mcp.json in your project

{
  "servers": {
    "genefoundry": {
      "type": "http",
      "url": "https://genefoundry.org/mcp"
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

ChatGPT connects only to servers on the internet:

Open ChatGPT on the web → Settings → Connectors (Apps)
Press Create or Add (some plans need Developer mode under Advanced first)
Paste the address below, give it a name and save
If it asks you to sign in, sign in with the maker

https://genefoundry.org/mcp

Menu names can differ slightly by plan and over time.

Your choice stays on this device in a cookie; no account needed.

These settings are generated from the maker’s registry entry. If the README says otherwise, follow the README.

What it can do

The server asks you to sign in before it lists its tools.

Basic checksi

We check information anyone can see; we have not read the code. Checks that do not apply are left out of the count. · Checked Nov 7, 2026

✓ Pass
Maker matches the repo
The registry name was verified with the GitHub account berntpopp, which owns the repo
… Not checked yet
Still maintained
We have not read this repo from GitHub yet
… Not checked yet
Has a licence
We have not read this repo from GitHub yet
✓ Pass
Endpoint responds
Responded in 830 ms (HTTP 401)
✓ Pass
Sign-in with OAuth
Declares OAuth sign-in, so your AI app can take you to log in
… Not checked yet
No hidden instructions in tool descriptions
Not checked yet; we read the tool list when we check the endpoint

Compared with others in Clinics & healthi

More stars than 0% of the other 871 servers in this category
Published to the registry more recently than 71% of the other 871 servers in this category
Basic checks equal to or better than 100% of the other 871 servers in this category

Compared with every active server in this category in the registry. Stars count only when the publisher owns the repo.

Common questions

Is Genefoundry safe?

It passed 3 of 3 applicable basic checks. We have not read the code. Before adding a key or token, see what access the server asks for and use a key with only the permissions you need.

What keys or codes does it need?

The registry does not list a required key, though some servers ask you to sign in on first use.

Does it run on my computer or in the cloud?

It runs in the maker’s cloud. Connect over the internet with nothing to install, but what you send passes through the maker’s servers.

Is it still maintained?

The GitHub repo last changed –, and the latest version (0.10.10) reached the registry 10 days ago.

Which apps can use it?

Apps that support MCP, such as Claude Desktop, Claude Code, Cursor and VS Code. It connects by URL, so apps that accept remote MCP servers work too, such as ChatGPT in developer mode.

What can I use instead?

In the same category: Mirobody, FHIR MCP Server, Google Health MCP

Alternatives

Servers in the same category from other makers, sorted by stars.

Reading a card:★ GitHub starsiThree pillars: reviews · checks · usageiUpdated = latest version published to the registryi

Mirobody

by thetahealth

Lab results to LOINC codes and UCUM units, symptoms and diagnoses to ICPC-3. Offline, no API key.

Runs on your computer★ 1,408Apache-2.0Updated 6 days ago

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FHIR MCP Server

by wso2

MCP server providing seamless access to FHIR APIs for AI tools and healthcare applications

Runs on your computer★ 137Apache-2.0Updated 9 days ago

Install

Google Health MCP

by davidmosiah

Privacy-first unofficial Google Health API v4 MCP server for health, sleep, activity, HR agents

Runs on your computer★ 79MITUpdated 4 months ago

Install

README from the maker

Open the README

Copied from the maker’s repo as written. PopNx MCP has not reviewed or endorsed it. HTML, images and scripts are removed. Links lead off this site.

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 _ 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 3.14+, uv):

uv sync --group dev

cp .env.example .env # set GF_*_URL backend URLs and GF_AUTH_MODE 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.

Tools

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 `_` 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.

Namespace	Domain	Data source	Tools	Repo
`pubtator`	Literature & entity annotation	PubTator3	35	pubtator-link
`gnomad`	Variant / gene / population frequency	gnomAD	22	gnomad-link
`orphanet`	Rare disease ontology & associations	Orphadata	19	orphanet-link
`clingen`	Gene–disease curation	ClinGen	17	clingen-link
`hpo`	Phenotype ontology & associations	Human Phenotype Ontology	17	hpo-link
`mavedb`	Variant-effect assay scores	MaveDB	15	mavedb-link
`uniprot`	Protein function	UniProt	15	uniprot-link
`clinpgx`	Pharmacogenomics / gene-drug guidelines	ClinPGx	13	clinpgx-link
`genereviews`	Gene–disease literature	GeneReviews	13	genereviews-link
`mgi`	Mouse phenotype & models	MGI	13	mgi-link
`mondo`	Disease ontology / cross-references	Mondo	13	mondo-link
`gencc`	Gene–disease curation	GenCC	12	gencc-link
`metadome`	Protein tolerance landscapes	MetaDome	11	metadome-link
`stringdb`	Protein–protein interaction networks	STRING	10	stringdb-link
`gtex`	Tissue expression	GTEx Portal	9	gtex-link
`hgnc`	Gene nomenclature	HGNC	9	hgnc-link
`panelapp`	Diagnostic gene panels & curation	PanelApp	9	panelapp-link
`autopvs1`	Variant ACMG PVS1	AutoPVS1	7	autopvs1-link
`spliceai`	Splicing prediction	SpliceAI Lookup	7	spliceailookup-link
`vep`	Variant annotation / consequence	Ensembl VEP	7	vep-link
`clinvar`	Variant clinical significance	ClinVar	6	clinvar-link
`litvar`	Variant literature	LitVar2	6	litvar-link

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

Configuration & authentication — every GF_* variable, the OAuth/JWT resource-server modes, and the startup guards.
Deployment — container release, digest pinning, rollback, and drift detection.
How discovery works — the search surface, entry-point pinning, and how discoverability is measured.
Design spec — the architecture and why it is shaped this way.
Fleet standards — Tool-Naming · Response-Envelope · MCP-Behaviour · Tool-Surface-Budget · Tool-Schema-Documentation · Container-Hardening · Versioning · README.

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.

Genefoundry

Overview

PopNx MCP’s three pillars

What you can do with it

Install

Before you install

What it can do

Basic checksi

Maker matches the repo

Still maintained

Has a licence

Endpoint responds

Sign-in with OAuth

No hidden instructions in tool descriptions

Compared with others in Clinics & healthi

Common questions

Alternatives

Mirobody

FHIR MCP Server

Google Health MCP

README from the maker

genefoundry-router

Why

Quick start

Tools

Federated backends

Data & provenance

Documentation

Contributing

License