Metadata-Version: 2.4
Name: c3fst-mcp-server
Version: 1.0.0
Summary: MCP server for c3fst biomedical search — FDA drugs, MeSH headings, ClinVar variants
Author-email: Mark Andrews <mark@flamingyak.com>
License: MIT
Project-URL: Homepage, https://github.com/mjandrews1/c3fst
Project-URL: Repository, https://github.com/mjandrews1/c3fst
Project-URL: Issues, https://github.com/mjandrews1/c3fst/issues
Keywords: mcp,biomedical,search,fda,mesh,clinvar,genomics
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
Requires-Python: >=3.10
Description-Content-Type: text/markdown
Requires-Dist: mcp>=2.0.0

# c3fst MCP Server

MCP server for c3fst biomedical search engine.

## Datasets

| Source | Description | Records |
|--------|-------------|---------|
| `products` | FDA Orange Book — drug products, ingredients, manufacturers | 48,502 |
| `mesh` | MeSH medical subject headings — diseases, procedures, anatomy | 1,011,763 |
| `variants` | ClinVar genomic variants — genes, clinical significance, phenotypes | 9,029,235 |

## Tools

- **`search(source, query)`** — BM25-ranked full-text search across any dataset
- **`sources()`** — List available datasets with record counts

## Remote Endpoint

This server runs remotely via SSE transport:

```
https://home.flamingyak.com/sse
```

To connect from an MCP client (Claude Desktop, Cursor, etc.), add to your MCP config:

```json
{
  "mcpServers": {
    "c3fst": {
      "url": "https://home.flamingyak.com/sse"
    }
  }
}
```

## Local Usage

For local development, run the server directly:

```bash
pip install mcp
python server.py
```

Set environment variables as needed:
- `C3FST_BIN` — path to c3fst binary
- `C3FST_DB` — path to RocksDB database
- `C3MCP_TRANSPORT` — `stdio` (default), `sse`, or `http`
- `C3MCP_PORT` — port for SSE/HTTP transport (default: 3000)
- `C3MCP_MAX_RESULTS` — max results per search (default: 20)

## License

MIT

<!-- mcp-name: io.github.mjandrews1/c3fst-biomedical-search -->
