PomBase MCP Server

An MCP (Model Context Protocol) server that gives AI agents structured access to PomBase, the comprehensive database for the fission yeast Schizosaccharomyces pombe. It wraps PomBase's public, unauthenticated JSON API (https://www.pombase.org/api/v1/dataset/latest/data, see the API documentation) so agents can look up genes, GO annotations, phenotypes, orthologs, protein domains, and interactions without scraping the website.

No API key or account is required — PomBase's API is free and open for academic/research use.

Features

• 🔎 Keyword search across all ~12,700 curated S. pombe genes
• 🧬 Gene summaries, protein domains, GO annotations, phenotypes, orthologs, and interactions
• 📊 A multi-gene comparison tool for quickly triaging gene lists (e.g. screen hits)
• 📝 Markdown (human-readable) or JSON (machine-readable) output for every tool
• ⚡ Async I/O throughout, with an in-memory cache for the large gene-summary dataset

Available Tools

Tool	Description
pombase_search_genes	Search/browse genes by name, systematic ID, or product keyword. Use this to resolve a gene name (e.g. cdc2) to its systematic ID (e.g. SPBC11B10.09). Supports pagination.
pombase_get_gene_summary	Core identifying info for a gene: name, product, synonyms, genomic location, taxon, UniProt/BioGRID IDs, characterisation status, deletion viability.
pombase_get_gene_domains	Protein domain/motif annotations: InterPro matches (source DB, coordinates, descriptions) and transmembrane domain coordinates.
pombase_get_gene_go_annotations	Gene Ontology annotations (Molecular Function, Biological Process, Cellular Component), optionally filtered to one aspect.
pombase_get_gene_phenotypes	FYPO (Fission Yeast Phenotype Ontology) annotations plus the gene's deletion viability (essential vs. non-essential).
pombase_get_gene_orthologs	Curated human and S. cerevisiae orthologs of the gene.
pombase_get_gene_interactions	Curated physical and/or genetic interactions, with interactor names, evidence, and source references.
pombase_compare_genes	Workflow tool: fetches 2-10 genes in parallel and returns a side-by-side comparison (product, viability, characterisation status, ortholog counts).

Every tool accepts a response_format of "markdown" (default, human-readable) or "json" (structured, for programmatic use).

Requirements

• Python 3.10+
• uv (recommended) or pip

Installation

Clone or download this repository, then choose one of the install paths below.

git clone [pombase-mcp](https://github.com/ubcd-ibfg/pombase-mcp)
cd pombase-mcp

Option A: uv (recommended — no separate install step needed)

uv can run the server directly from the project directory with uv run, resolving dependencies automatically. This is the command used in the client configs below.

Option B: pip

pip install -e .

This installs the pombase-mcp console command (defined in pyproject.toml) on your PATH.

---

Connecting to Claude Code

Claude Code can register MCP servers with the claude mcp add CLI command.

Using uv (from the cloned project directory):

claude mcp add pombase -- uv run --directory /absolute/path/to/pombase-mcp pombase-mcp

Using a pip install:

claude mcp add pombase -- pombase-mcp

Verify it's connected:

claude mcp list

Then just ask Claude Code things like "Use PomBase to find the human ortholog of cdc2 in fission yeast" — it will discover and call the tools automatically.

To remove it later: claude mcp remove pombase.

Project-scoped config (checked into a repo)

Alternatively, add a .mcp.json file to your project root:

{
  "mcpServers": {
    "pombase": {
      "command": "uv",
      "args": ["run", "--directory", "/absolute/path/to/pombase-mcp", "pombase-mcp"]
    }
  }
}

---

Connecting to Claude Desktop

Edit your Claude Desktop config file:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%\Claude\claude_desktop_config.json
• Linux: ~/.config/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "pombase": {
      "command": "uv",
      "args": ["run", "--directory", "/absolute/path/to/pombase-mcp", "pombase-mcp"]
    }
  }
}

(If you installed via pip install -e . instead, replace "command"/"args" with "command": "pombase-mcp", "args": [], using the full path to the executable if it's not on Claude Desktop's PATH.)

Restart Claude Desktop after saving. The PomBase tools will appear under the 🔌 connector icon.

---

Connecting to Cursor

Add to .cursor/mcp.json in your project (or the global ~/.cursor/mcp.json):

{
  "mcpServers": {
    "pombase": {
      "command": "uv",
      "args": ["run", "--directory", "/absolute/path/to/pombase-mcp", "pombase-mcp"]
    }
  }
}

---

Connecting to Windsurf

Add to ~/.codeium/windsurf/mcp_config.json:

{
  "mcpServers": {
    "pombase": {
      "command": "uv",
      "args": ["run", "--directory", "/absolute/path/to/pombase-mcp", "pombase-mcp"]
    }
  }
}

---

Connecting to OpenCode

OpenCode is a web-based IDE with built-in MCP support. To connect PomBase MCP:

1. Open your OpenCode workspace
2. Go to Settings → MCP Servers
3. Add a new server with the following configuration:

{
  "pombase": {
    "command": "uv",
    "args": ["run", "--directory", "/absolute/path/to/pombase-mcp", "pombase-mcp"]
  }
}

Replace /absolute/path/to/pombase-mcp with the full path to your cloned repository.

Alternatively, if you've installed via pip install -e .:

{
  "pombase": {
    "command": "pombase-mcp",
    "args": []
  }
}

Save the configuration and the PomBase tools will be available in your OpenCode AI assistant.

---

Connecting to any other MCP-compatible client (generic stdio config)

Most agent platforms (Cline, Continue, LibreChat, Zed, custom MCP clients, etc.) accept the same shape of config — a command to launch the server over stdio:

{
  "mcpServers": {
    "pombase": {
      "command": "uv",
      "args": ["run", "--directory", "/absolute/path/to/pombase-mcp", "pombase-mcp"]
    }
  }
}

or, if installed with pip:

{
  "mcpServers": {
    "pombase": {
      "command": "pombase-mcp",
      "args": []
    }
  }
}

Consult your client's docs for where this config file lives.

---

Running and testing manually

Run the server directly over stdio:

uv run --directory /absolute/path/to/pombase-mcp pombase-mcp
# or, if pip-installed:
pombase-mcp

Inspect and test tool calls interactively with the official MCP Inspector:

npx @modelcontextprotocol/inspector uv run --directory /absolute/path/to/pombase-mcp pombase-mcp

Example prompts once connected

• "Search PomBase for kinase genes and show me the first 10."
• "What is the product of SPBC11B10.09, and is it essential?"
• "What GO biological process terms is pom1 (SPAC2F7.03c) annotated with?"
• "What are the human orthologs of cdc2?"
• "List the physical interactions for ase1."
• "Compare cdc2, cdc13, and wee1 — which are essential and what are their human orthologs?"

Data source and licensing

All data is served live from PomBase (https://www.pombase.org/api/v1/dataset/latest/data) and is not bundled with this server. PomBase is funded by the Wellcome Trust and run by a consortium comprising the University of Cambridge, University College London, and the Babraham Institute. If you use PomBase data in your research, please cite PomBase — see https://www.pombase.org/help/citing-pombase.

This project is an independent, unofficial MCP wrapper and is not developed or endorsed by the PomBase team.

License

MIT — see LICENSE.