mcp-omics
A Model Context Protocol server that enables retrieval of -omics data from sources like PDB, ChEMBL, UniProt, PubChem, and HUGO.
README
mcp-omics
A Model Context Protocol server for retrieving -omics data from various online sources.
<h3 align="right">Colby T. Ford, Ph.D.</h3>
Run the MCP server
To run the MCP server, you need to have FastMCP installed. You can install it using pip:
pip install -r requirements.txt
Then, you can check that the server will run using the following command:
fastmcp run server.py
Example: Communicate with the MCP server locally in Ollama using MCPHost
- Pull your desired model from Ollama:
ollama pull qwen2.5:0.5b
Note that you can use any of the models that support "tools". Avoid the "thinking" models, as their outputs are overly verbose for this use case.
- Install the MCPHost package:
go install github.com/mark3labs/mcphost@latest
## Make sure mcphost is in your PATH
# export PATH="$HOME/go/bin:$PATH"
- Run MCPHost with the model you pulled from Ollama:
mcphost -m ollama:qwen2.5:0.5b --config .mcphost.json
- Run some examples:
- PDB - "From the Protein Data Bank, tell me about PDB 5JXE."
- ChEMBL - "In the ChEMBL database, what are the other names for the compound with ID 'CHEMBL112'?"
- UniProt - "What is the UniProt ID P43220?"
- PubChem - "What is the PubChem CID 2244?"
- HUGO - "Tell me about the gene BRCA1."
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