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
pip install -r requirements.txtThe 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"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?" 
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
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.
MIT License with Academic Citation Requirement - see LICENSE.md