mgi-link

An MCP (Model Context Protocol) / API server that grounds mouse-genetics work in Mouse Genome Informatics (MGI, informatics.jax.org). It reproduces the data on an MGI gene/marker page — especially Mutations, Alleles, and Phenotypes — for LLM agents.

mgi-link is a sibling of hgnc-link, gnomad-link, uniprot-link, and gencc-link and shares their architecture: a local SQLite index built from the MGI bulk reports, refreshed by cron, served over a structured MCP surface.

Why

The MGI gene page (e.g. Wt1, MGI:98968) is a rich JS app with no clean JSON API. mgi-link rebuilds that surface from MGI's canonical bulk data reports into a fast, offline, deterministic index and exposes it as MCP tools with structured outputs, response-mode verbosity control, and _meta.next_commands chaining.

Tools

Tool	Purpose
resolve_marker	Resolve a mouse symbol / MGI id / human ortholog → canonical marker
get_marker	Full marker record: location, xrefs, ortholog, summary counts
search_markers	FTS over marker symbol / name / synonyms
get_marker_alleles	Mutations & Alleles + generation-method category counts
get_marker_phenotypes	MP annotations (allelic composition, background, PubMed) + summary
get_phenotype_overview	The 27-system Phenotype Overview grid
get_marker_diseases	Human-mouse disease models (DO/OMIM)
get_marker_ortholog	Mouse ↔ human ortholog (HGNC/Entrez/Ensembl/OMIM)
get_mp_term	Mammalian Phenotype ontology term (parents/children/systems)
search_phenotype_terms	FTS over MP terms
find_markers_by_phenotype	Reverse: MP term → mouse genes (descendants included)
get_server_capabilities, get_mgi_diagnostics	Discovery

Data sources

The local index is built from the MGI bulk reports at https://www.informatics.jax.org/downloads/reports/: MRK_List2, MGI_PhenotypicAllele, MGI_GenePheno, VOC_MammalianPhenotype, MPheno_OBO.ontology, HOM_MouseHumanSequence, MGI_DO (+ MRK_ENSEMBL). A live MouseMine (InterMine) enrichment client is reserved for v2.

Quick start

make install      # uv sync --group dev
make data         # download the MGI reports and build the local SQLite index
make dev          # run the unified server (FastAPI /health + MCP /mcp)
make mcp-serve    # run the stdio MCP server
make test         # run the test suite

Register with Claude:

claude mcp add mgi-link -- uv run mgi-link-mcp

Data & license

MGI data are freely available for research use; please cite MGI / The Jackson Laboratory. The Mammalian Phenotype Ontology is licensed CC BY 4.0. Research use only; not for clinical decision support, diagnosis, treatment, or patient management.

Development

make ci-local is the definition-of-done gate (format-check, lint, 500-line budget, mypy strict, tests). See AGENTS.md for engineering conventions and docs/ for architecture and deployment.