igvf-catalog-mcp

# IGVF Catalog MCP Server An MCP (Model Context Protocol) server providing LLM-friendly access to the IGVF Catalog genomics knowledge graph. ## Features - **Smart Entity Lookup**: Auto-detects entity type from ID patterns (genes, variants, proteins, etc.) - **Genomic Region Search**: Flexible region format parsing with multi-entity queries - **Relationship Discovery**: Find eQTLs, GWAS associations, protein interactions, and more - **ID Translation**: Convert between variant ID formats (rsID, SPDI, HGVS, etc.) - **Data Source Discovery**: Dynamically discover available datasets and filters ## Installation The server is published on PyPI as [`igvf-catalog-mcp`](https://pypi.org/project/igvf-catalog-mcp/). Run it without installing anything using [uv](https://docs.astral.sh/uv/): ```bash uvx igvf-catalog-mcp ``` or install it with pip and run the `igvf-catalog-mcp` command: ```bash pip install igvf-catalog-mcp igvf-catalog-mcp ``` To use it from an MCP client such as Claude Desktop or Claude Code, register it as a stdio server: ```json { "mcpServers": { "igvf-catalog": { "command": "uvx", "args": ["igvf-catalog-mcp"] } } } ``` ## Usage Configure the API URL (optional): ```bash export IGVF_CATALOG_API_URL=https://api.catalogkg.igvf.org # default # or for development: export IGVF_CATALOG_API_URL=https://catalog-api-dev.demo.igvf.org export IGVF_CATALOG_API_URL=http://localhost:2023 ``` `/api` is appended to the URL if it is not already there. ## Tools ### 1. `igvf_catalog_get_entity` Look up any entity by ID with automatic type detection. ```json {"id": "BRCA1"} {"id": "rs12345"} {"id": "ENSG00000141510"} {"id": "lupus", "hint": "disease", "limit": 50, "page": 1} ``` ### 2. `igvf_catalog_search_region` Find all entities within a genomic region. ```json {"region": "chr17:41000000-42000000"} ``` ### 3. `igvf_catalog_find_associations` Discover relationships between entities. ```json {"entity_id": "TP53", "relationship": "regu…