{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_2qbwutkx2dy6","handle":"uniprotkb-mcp","url":"https://wellknown.network/agents/uniprotkb-mcp","links":{"self":"https://wellknown.network/agents/uniprotkb-mcp/record.json","html":"https://wellknown.network/agents/uniprotkb-mcp","markdown":"https://wellknown.network/agents/uniprotkb-mcp/record.md","api":"https://wellknown.network/api/v1/agents/uniprotkb-mcp","status":"https://wellknown.network/api/v1/agents/uniprotkb-mcp/status","claim":"https://wellknown.network/agents/uniprotkb-mcp/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/uniprotkb-mcp/claim.json","badge":"https://wellknown.network/agents/uniprotkb-mcp/badge.svg","openapi":"https://wellknown.network/openapi.json"},"ard":{"identifier":"urn:air::server:uniprotkb-mcp","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"uniprotkb-mcp","summary":"Production-quality MCP server exposing the UniProt REST API (search, entries, FASTA, ID mapping, taxonomy) to LLM clients over stdio.","description":"# uniprot-mcp\n\n[![CI](https://github.com/fzlzjerry/uniprot-mcp/actions/workflows/ci.yml/badge.svg)](https://github.com/fzlzjerry/uniprot-mcp/actions/workflows/ci.yml)\n\n> GitHub repo: `fzlzjerry/uniprot-mcp` · PyPI package & command: **`uniprotkb-mcp`**\n> (the Python import package is `uniprot_mcp`).\n\nA production-quality **MCP server** that exposes the [UniProt REST API](https://rest.uniprot.org)\nto LLM clients (Claude Code, Claude Desktop, …) over **stdio**. Built with\n[FastMCP](https://gofastmcp.com) and managed with [`uv`](https://docs.astral.sh/uv/).\n\nTools return **compact, token-efficient summaries by default** and full payloads\nonly on request, with robust error handling and an embedded UniProt query\ncheat-sheet so the model writes valid queries.\n\n## Tools\n\n| Tool | What it does |\n|------|--------------|\n| `search_uniprotkb` | Search UniProtKB with native query syntax. `reviewed` / `organism_id` filters are added for you. Summary, FASTA, or TSV output. |\n| `get_entry` | One entry as a curated digest (function, names, organism, length, subcellular location, family/domains, key features, PTMs, keywords, PDB/AlphaFold/Ensembl/RefSeq/InterPro/GO cross-refs) or `json`/`fasta`/`txt`/`gff`. |\n| `get_fasta` | Raw FASTA for one accession or a batch. |\n| `map_ids` | Convert ids across databases via UniProt's async ID-mapping (e.g. `RefSeq_Protein`→`UniProtKB`, `UniProtKB_AC-ID`→`PDB`). Returns mapped pairs **and** unmapped ids; validates the db pair against the live config. |\n| `get_taxonomy` | Resolve an organism name or taxon id → taxon id, names, rank, lineage. Turn \"human\" into `organism_id:9606`. |\n| `search_uniref` | Search UniRef100/90/50 sequence-similarity clusters. |\n| `search_proteomes` | Search proteomes (whole-organism protein sets); reference-proteome filter. |\n\nPlus an MCP **resource** `resource://uniprot/query-cheatsheet` documenting the\nUniProtKB query syntax (`gene:`, `organism_id:`, `reviewed:true`,\n`length:[X TO Y]`, `keyword:`, `ec:`, boolean `AND…","publisher":{"name":"uniprot-mcp","url":null},"homepage":"https://github.com/fzlzjerry/uniprot-mcp","repository":"https://github.com/fzlzjerry/uniprot-mcp","version":"0.1.0","license":null,"protocols":["mcp"],"tags":["bioinformatics","fastmcp","llm","mcp","proteins","uniprot"],"pricing":null,"endpoints":[{"url":"pypi:uniprotkb-mcp","type":"package_pypi","auth":null,"probeable":false}],"skills":null,"tools":null,"extra":null,"attribution":{"kind":"pypi","name":"pypi","repoUrl":"pypi","summary":"pypi","version":"pypi","description":"pypi","homepageUrl":"pypi","publisherName":"pypi"}},"derived":{"capabilities":[{"slug":"data.database","name":"Databases","confidence":0.791,"provenance":"derived"},{"slug":"dev.docs-lookup","name":"Documentation Lookup","confidence":0.791,"provenance":"derived"},{"slug":"dev.package-management","name":"Packages & Dependencies","confidence":0.768,"provenance":"derived"}],"categories":["data","dev"],"language":"en"},"observed":{"status":"unknown","statusReason":"Distributed as a package to run locally; no network endpoint to check.","lastOkAt":null,"lastProbedAt":null,"statusComputedAt":null,"reliability30d":null,"latestObservations":[],"tools":null,"package":{"name":"uniprotkb-mcp","registry":"pypi","observedAt":"2026-09-10T14:24:46.394Z","publishedAt":"2026-06-14T14:32:18.277711Z","latestVersion":"0.1.0"}},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"uniprotkb-mcp","url":"https://pypi.org/project/uniprotkb-mcp/","firstSeenAt":"2026-09-10T14:23:59.991Z","fetchedAt":"2026-09-10T14:23:59.991Z","normalizedAt":"2026-09-10T14:23:59.991Z"}]},"firstSeenAt":"2026-09-10T14:23:59.991Z","updatedAt":"2026-09-10T14:24:46.394Z"}