CIViC MCP: Integrating Large Language Models with the Clinical Interpretations of Variants in Cancer

Abstract

SummaryThe Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase provides a community-driven, open-source platform for discussing the biological and clinical significance of molecular variants in cancer. To enable users to make complex connections between CIViC information, we developed the CIViC Model Context Protocol (MCP) server, which allows users to interface with the CIViC API through natural language via large language models (LLMs), facilitating the rapid summarization of expertly curated cancer variant interpretations. Availability and implementationThe CIViC MCP server is detailed at https://github.com/griffithlab/civic-mcp-server. The repository includes instructions for accessing the server through the Claude desktop app (our recommended approach; Supplementary Figure 1) and hosting it locally with GPT-5, as well as a Python script for directly querying the MCP server. We also provide an MCP-supported Chatbot for CIViC users at https://civicdb.org/mcp-chat. Supplemental informationSupplementary data are available at Bioinformatics Advances online.