CIViC MCP Server
MCP-supported Chatbot for CIViC users: https://civicdb.org/mcp-chat
Preprint: https://www.biorxiv.org/content/10.1101/2025.10.13.682185v1
This is a Cloudflare Workers-based Model Context Protocol (MCP) server that provides tools for querying the CIViC (Clinical Interpretation of Variants in Cancer) API.
The CIViC database is a crowd-sourced repository of clinical interpretations of cancer variants. This MCP server enables structured queries and data analysis of cancer genomics information through natural language interactions with AI assistants.
Python 3.11.7 ``bash pip install -r requirements.txt ``
Directly Querying the MCP Server
The MCP Server can be called directly from the command line with the optional arguments disease and therapy to get CIViC evidence items:
python MCP_query_evidence.py --mp "EGFR" --disease "Lung Non-small Cell Carcinoma" --therapy "Erlotinib"Locally Hosting The CIViC MCP Server
We provide an example of doing this with GPT4o-mini. A personal API key is required, update the variable OPENAI_API_KEY in local_hosting/message_MCP_CIViC.py
python local_hosting/message_MCP_CIViC.py --msg "What is the clinical significance of EGFR variants in CIViC?" Adding as a Claude Connector
<img width="3217" height="1094" alt="Claude connector setup" src="https://github.com/user-attachments/assets/b939db57-4a59-4cdf-a38e-620d9516cee4" />
Usage
The server provides two main tools:
get_variant_evidence: Return up to 50 evidence items for a CIViC molecular profileget_variant_assertions: Return CIViC assertions for a molecular profile
Evaluation Scripts
All evaluation files are located in eval_QA_experiment. The file agent_mode_run_results.csv contains the agent mode prompts and responses; the associated chat URLs were created but may no longer be available. QA_triplet_dataset.csv contains the 100 unique (Molecular Profile, Disease, Therapy) triplets along with their expected answers.
License
MIT License with Academic Citation Requirement - see LICENSE.md
