Omics

A Model Context Protocol server for retrieving -omics data from various online sources.

Colby T. Ford, Ph.D.

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

1. 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.

2. Install the MCPHost package:

go install github.com/mark3labs/mcphost@latest
## Make sure mcphost is in your PATH 
# export PATH="$HOME/go/bin:$PATH"

3. Run MCPHost with the model you pulled from Ollama:

mcphost -m ollama:qwen2.5:0.5b --config .mcphost.json

4. 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."