kleonai/biogrid-mcp-server

BioGRID MCP server

This is a Model-Context-Protocol (MCP) endpoint server that unlocks BioGRID’s 2 × 10⁷ curated genetic and physical interactions for any LLM or autonomous agent to access the BioGRID API. This repository provides tools for your agent stack to go from raw gene symbols to publication-backed interaction networks, TSV edge lists, and ready-to-analyse statistics—all through schema-validated JSON calls. These tools self-describe inputs/outputs, so agents can discover, validate and correct calls on their own.

Tools

1. get_interactions: Retrieve every BioGRID interaction that involves one gene.
2. get_neighbors: Lightweight wrapper returning first-degree partners for a single gene.
3. export_edge_list: Produce a TSV/CSV edge list for a set of genes – ready for Cytoscape or graph-tool.
4. search_genes: Fuzzy search BioGRID’s gene table to look up ambiguous symbols/aliases.
5. interaction_stats: Quick network summary for a gene list (counts, degree distribution, physical/genetic ratio).

Resource templates

1. biogrid://edge-list/{gene1,gene2,…}: TSV edge list for a gene set (same as export_edge_list but cached & shareable)
2. biogrid://interaction/{biogrid_id}: Lets an agent cite one interaction as evidence without parsing the whole TSV.
3. biogrid://gene/{gene_symbol}: Quick “knowledge card” a model can quote when introducing a gene.
4. biogrid://publications/{pubmed_id}: Enables citation-aware answers or RAG pipelines without hitting NCBI.
5. biogrid://dataset/{dataset_id}: Bulk download of a specific BioGRID dataset release (tar/zip).

Example Use-Cases

Quick Install

1. Clone & Install

git clone https://github.com/<you>/biogrid-mcp-server.git
cd biogrid-mcp-server
npm install

2. Set your BioGRID API key

https://webservice.thebiogrid.org/ This is free for academic usages.

   export BIOGRID_API_KEY=YOUR_KEY_HERE

3. Run the sever

stdio mode is the best for local LLMs

npm run start

HTTP mode – expose on a port for remote agents (choose any free port):

npm run start:http -- --port 3335

You should see something like:

[BIOGRID-MCP] server ready – manifest at /.well-known/mcp/manifest.json

5. Tool call example

{
  "name": "get_neighbors",
  "arguments": {
    "gene_symbol": "TP53",
    "species": 9606,
    "type": "genetic",
    "limit": 250
  }
}

9606 here stands for the species 'human'. Sample that you'll get

{
  "query": {"gene":"TP53","species":9606,"type":"genetic"},
  "neighbors": [
    {
      "partner": "MDM2",
      "biogridId": "111",
      "experimentalSystem": "Dosage Rescue",
      "pubmedIds": [12345]
    }
    /* … */
  ],
  "meta": {
    "total": 187,
    "timestamp": "YYYY-MM-DDTHH:MM:SSZ",
    "biogrid_version": "4.4.229"
  }
}

Workflow examples across several MCP servers

1. Variant triage: search_genes → get_interactions → filter by genetic evidence → rank partners by PubMed support.

2. Module building: get_neighbors (seed genes) → export_edge_list → feed into GRAPH-MCP for clustering → overlay_expression.

3. Cross-DB enrichment: search_genes → STRING-MCP get_functional_enrichment → Reactome-MCP pathway overlay.

Coming soon: http://github.com/kleonai/bio-mcp-servers for a list of Biology MCP servers and usage guides.

Development guide

• src/api.ts – thin axios wrapper around BioGRID /interactions/ and /gene/ endpoints
• src/parsers.ts – converts TSV ➞ typed objects
• src/tools.ts – declare tool schemas and handlers
• src/server.ts – wire up MCP transport (stdio + express)
• Add new analytics (e.g., centrality, clustering) in src/analytics.ts

Prerequisites

The server has been developed by https://kleonlab.com/