uniprot-link

An MCP (Model Context Protocol) + REST server that grounds protein research in the UniProt SPARQL endpoint (https://sparql.uniprot.org/sparql). It wraps a ~232-billion-triple, QLever-backed SPARQL 1.1 service behind intent-named, token-economical tools — and ships a safe raw-SPARQL escape hatch plus UniProt's 126 curated example queries so an LLM can learn and write its own queries.

Part of the *-link family of biomedical MCP servers (gnomad-link, gtex-link, pubtator-link, genereviews-link, …) and follows their stack and conventions.

Features

• 15 MCP tools across discovery, raw SPARQL, the curated example catalog, proteins (UniProtKB), and taxonomy.

• Typed protein tools — get_protein, sequence, features (with FALDO coordinates), natural variants, diseases, GO terms, cross-references, id mapping.

• search_sparql_query — execute any SPARQL 1.1 query (SELECT/ASK/CONSTRUCT/ DESCRIBE, with SERVICE federation); auto-LIMIT on unbounded SELECTs; JSON/XML/ CSV/TSV/Turtle/RDF-XML/N-Triples output.

• Example catalog — search_example_queries / get_example_query expose UniProt's 126 curated, executable queries (backed by the sparql-examples graph).

• Agentic affordances — every response carries _meta.next_commands (ready-to-run {tool, arguments} steps), a structured error taxonomy, and a uniprot://capabilities discovery resource.

• Two transports — unified (REST + MCP/HTTP) and HTTP-only. Streamable HTTP only.

Related MCP server: UniProt MCP Server

Quick start

make install                       # uv sync --group dev
make dev                           # unified server: REST on / and MCP on /mcp (port 8000)
uv run uniprot-link serve --help   # CLI: serve / config / health / version
make ci-local                      # format + lint + loc + typecheck + tests

CLI

The uniprot-link console script is the single entry point (Streamable HTTP only):

uniprot-link serve --transport unified --host 127.0.0.1 --port 8000  # REST + MCP/HTTP
uniprot-link serve --transport http                                  # REST only
uniprot-link config --validate                                       # show + validate config
uniprot-link health --url http://127.0.0.1:8000                      # probe /health
uniprot-link version                                                 # print version

Connect an MCP client

Point a Streamable-HTTP MCP client at the /mcp endpoint of a running server, e.g.:

claude mcp add --transport http uniprot-link --scope user http://127.0.0.1:8000/mcp

Tool catalog

Tool names are unprefixed (the GeneFoundry Tool-Naming Standard v1): the server reports serverInfo.name = "uniprot-link" and its canonical gateway namespace token is uniprot. When federated behind the genefoundry-router gateway, tools surface as uniprot_<tool> (e.g. uniprot_find_proteins); standalone MCP clients already namespace them as mcp__uniprot-link__<tool>.

Configuration

Environment variables (prefix UNIPROT_LINK_, nested with __):

Development

See AGENTS.md for conventions (notably the SPARQL / QLever discipline that keeps queries off the timeout cliff) and docs/ for architecture and usage. research/verify_queries.py validates every query builder against the live endpoint.

Disclaimer

Research use only; not for clinical decision support, diagnosis, treatment, or patient management. UniProt data is licensed CC BY 4.0.

License

MIT