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Tools

Six tools for protein-first research over UniProt — discovery search is the entry point, uniprot_map_ids is the bridge that turns any sibling identifier into a UniProtKB accession, and the rest fetch curated records, proteomes, taxonomy, and sequences:

Tool	Description
uniprot_search_proteins	Search UniProtKB by plain text or a Lucene field query, with the reviewed (Swiss-Prot) filter foregrounded and optional server-side facet counts. Cursor-paginated. The discovery entry point.
uniprot_get_entry	Fetch full curated entries by accession in one batch (up to 20) — function, catalytic activity, disease, variants, isoforms, GO terms, cross-references. Partial-success output; an oversized record returns a section outline.
uniprot_map_ids	Translate identifiers across databases via UniProt's async ID-mapping service — gene names, Ensembl, RefSeq, ChEMBL, PDB, GeneID ↔ UniProtKB accessions. Polls within a budget; returns a resumable ticket on overflow.
uniprot_get_proteome	Fetch a reference proteome by UPID or NCBI taxon ID — protein count, BUSCO completeness, genome assembly inline, plus an opt-in capped page of the proteins.
uniprot_get_taxonomy	Resolve a taxonomy record by NCBI taxon ID or scientific name — name, rank, parent, full lineage, and optionally the immediate children.
uniprot_get_sequence	Fetch the canonical amino-acid sequence (FASTA) for an accession, with length and parsed header — and optionally the isoform sequences. The cheap sequence-only path.

uniprot_search_proteins

Search UniProtKB and return curated protein records — the discovery entry point.

• text_search for plain language (the 80% case) or query for full Lucene field syntax (gene, organism_id, keyword, go, reviewed, protein_name, family, length, existence, accession) — exactly one
• reviewed defaults to true (Swiss-Prot only) so the agent isn't drowned in TrEMBL predictions; set false to include them
• organism_id convenience filter ANDed onto the query
• Optional facets for server-side count breakdowns (e.g. reviewed, model_organism)
• Forward cursor pagination (UniProtKB has no offset paging); totalResults and the effective query echoed back
• Every hit carries reviewed, annotationScore, and proteinExistence so curation quality is weighable

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uniprot_get_entry

Fetch full curated UniProtKB entries by accession in batch — this tool does not search.

• Batch up to 20 accessions in one round trip
• Sectioned record: function, catalytic activity, cofactors, subcellular location, disease, PTMs, natural variants, isoforms, domains, GO terms, keywords, cross-references
• Partial-success output — resolved entries in succeeded[], unknown/withdrawn ones in failed[]; the whole batch never aborts on one bad accession
• fields trims the upstream projection; identity and provenance fields are always retained
• A single oversized record returns kind: "outline" (a section listing) instead of overflowing context — re-call the same accession with sections: [...] to pull only what's needed
• Accessions come from uniprot_search_proteins or uniprot_map_ids; strip any -N isoform suffix first

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uniprot_map_ids

Translate identifiers across databases via UniProt's ID-mapping service — the bridge from any sibling server's identifier into a UniProtKB accession.

• from_db / to_db are validated enums (e.g. Gene_Name, Ensembl, RefSeq_Protein, ChEMBL, PDB, GeneID, UniProtKB_AC-ID) so an unsupported pair fails before the upstream call
• Target UniProtKB-Swiss-Prot for reviewed accessions only (the usual intent), or UniProtKB / UniProtKB_AC-ID to include unreviewed TrEMBL
• The job runs asynchronously; the tool submits it and polls within a budget. Finishes in time → status: "finished" with the mappings; runs long → status: "running" with a resumable ticket — re-call with the ticket alone (the job is held server-side)
• Pair a gene-symbol from_db with tax_id to disambiguate species
• Reports unmapped input IDs alongside the resolved mappings

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uniprot_get_proteome

Fetch the reference proteome for an organism by UPID or NCBI taxon ID — provide exactly one.

• Metadata inline: proteome type, total protein count, BUSCO completeness (score, complete/fragmented/missing counts, lineage dataset), genome assembly accession
• The protein set is opt-in via include_proteins (it is large — human is ~147,506) and returns a capped page with a forward cursor and truncation disclosure
• Narrow the protein list with the query filter (UniProtKB Lucene syntax) for a subset
• Resolve an organism name to a taxon ID first with uniprot_get_taxonomy

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uniprot_get_taxonomy

Resolve a taxonomy record by NCBI taxon ID or scientific name — provide exactly one.

• Returns scientific and common name, mnemonic, rank, parent, and the full lineage (root → near ancestor)
• include_children fetches the immediate child taxa via a follow-up search (not inline on the record)
• Turns an organism name into the taxon ID that uniprot_search_proteins (organism_id) and uniprot_get_proteome (taxon_id) expect

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uniprot_get_sequence

Fetch the canonical amino-acid sequence (FASTA) for an accession — the cheap, sequence-only path (for the full functional record use uniprot_get_entry).

• Returns the canonical sequence with its length and parsed FASTA header
• include_isoforms also returns the alternatively-spliced isoform sequences
• Accessions come from uniprot_search_proteins or uniprot_map_ids; strip any -N isoform suffix first

Resources and prompts

Type	Name	Description
Resource	uniprot://entry/{accession}	A curated UniProtKB entry by accession — the resource mirror of uniprot_get_entry for a single accession.
Resource	uniprot://taxonomy/{taxonId}	A taxonomy record by NCBI taxon ID — name, rank, parent, full lineage. The mirror of uniprot_get_taxonomy by ID.
Prompt	uniprot_protein_dossier	Guided protein-research workflow — resolve an identifier, fetch the curated entry, pull disease and variants, and surface cross-references for structure, citations, and bioactivity.

All resource data is also reachable via tools — tool-only clients lose nothing. UniProtKB is far too large to enumerate, so there is no resource list(); discovery is uniprot_search_proteins's job.

Features

Built on @cyanheads/mcp-ts-core:

• Declarative tool, resource, and prompt definitions — single file per primitive, framework handles registration and validation
• Unified error handling — handlers throw, framework catches, classifies, and formats
• Pluggable auth: none, jwt, oauth
• Swappable storage backends: in-memory, filesystem, Supabase, Cloudflare KV/R2/D1
• Structured logging with optional OpenTelemetry tracing
• STDIO and Streamable HTTP transports

UniProt-specific:

• Keyless — UniProt REST requires no API key; works against any rest.uniprot.org-compatible base (override UNIPROT_BASE_URL for a private mirror)
• One thin fetch client over all four REST collections (UniProtKB, ID Mapping, Proteomes, Taxonomy) with retry/backoff and HTML-error-page detection
• Batch entry fetch — N accessions in one round trip, cross-referenced against the request to flag any missing
• Async ID-mapping run → poll → results bounded by a wall-clock budget, with a resumable server-side ticket on overflow

Agent-friendly output:

• Provenance is data, not decoration — reviewed, annotationScore, proteinExistence, and per-field PubMed/ECO evidence ship on every record so the agent can weigh manual vs. predicted annotation
• Graceful partial failure — uniprot_get_entry returns per-accession succeeded[] / failed[] rows instead of aborting the batch
• Discriminated output contracts — uniprot_get_entry returns kind: "full" | "outline", uniprot_map_ids returns status: "finished" | "running"; callers branch on data, not string parsing
• Sparsity preserved — absent upstream fields stay absent, never fabricated (most curated sections are legitimately missing on TrEMBL entries)

Getting started

Add the following to your MCP client configuration file. UniProt REST is keyless — no API key required.

{
  "mcpServers": {
    "uniprot-mcp-server": {
      "type": "stdio",
      "command": "bunx",
      "args": ["@cyanheads/uniprot-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}

Or with npx (no Bun required):

{
  "mcpServers": {
    "uniprot-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@cyanheads/uniprot-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}

Or with Docker:

{
  "mcpServers": {
    "uniprot-mcp-server": {
      "type": "stdio",
      "command": "docker",
      "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/uniprot-mcp-server:latest"]
    }
  }
}

For Streamable HTTP, set the transport and start the server:

MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
# Server listens at http://localhost:3010/mcp

Prerequisites

• Bun v1.3.11 or higher (or Node.js v24+).
• No API key — UniProt REST is keyless and open. Data is UniProt, CC BY 4.0.

Installation

1. Clone the repository:

git clone https://github.com/cyanheads/uniprot-mcp-server.git

2. Navigate into the directory:

cd uniprot-mcp-server

3. Install dependencies:

bun install

Configuration

All configuration is validated at startup via Zod schemas in src/config/server-config.ts. UniProt REST is keyless, so every server-specific variable below is an optional override.

Variable	Description	Default
UNIPROT_BASE_URL	UniProt REST base URL. Override for a private mirror or testing.	https://rest.uniprot.org
UNIPROT_TIMEOUT_MS	Per-request HTTP timeout in ms.	30000
UNIPROT_ID_MAPPING_BUDGET_MS	Wall-clock budget for the inline ID-mapping poll loop before returning a resumable ticket. Must be less than UNIPROT_TIMEOUT_MS.	8000
UNIPROT_DEFAULT_PAGE_SIZE	Default page size for search and proteome protein listing when the caller leaves it unset.	25
MCP_TRANSPORT_TYPE	Transport: stdio or http.	stdio
MCP_HTTP_PORT	Port for HTTP server.	3010
MCP_AUTH_MODE	Auth mode: none, jwt, or oauth.	none
MCP_LOG_LEVEL	Log level (RFC 5424).	info
LOGS_DIR	Directory for log files (Node.js only).	<project-root>/logs
STORAGE_PROVIDER_TYPE	Storage backend.	in-memory
OTEL_ENABLED	Enable OpenTelemetry instrumentation (spans, metrics, completion logs).	false

See .env.example for the full list of optional overrides.

Running the server

Local development

• Build and run:

  # One-time build
  bun run rebuild
  
  # Run the built server
  bun run start:stdio
  # or
  bun run start:http
  

• Run checks and tests:

  bun run devcheck   # Lint, format, typecheck, security
  bun run test       # Vitest test suite
  bun run lint:mcp   # Validate MCP definitions against spec
  

Docker

docker build -t uniprot-mcp-server .
docker run --rm -e MCP_TRANSPORT_TYPE=stdio ghcr.io/cyanheads/uniprot-mcp-server:latest

The Dockerfile defaults to HTTP transport, stateless session mode, and logs to /var/log/uniprot-mcp-server. OpenTelemetry peer dependencies are installed by default — build with --build-arg OTEL_ENABLED=false to omit them.

Project structure

Directory	Purpose
src/index.ts	createApp() entry point — registers tools/resources/prompts and inits the UniProt service.
src/config	Server-specific environment variable parsing and validation with Zod.
src/mcp-server/tools	Tool definitions (*.tool.ts). Six tools over UniProtKB, ID mapping, proteomes, taxonomy, and sequences.
src/mcp-server/resources	Resource definitions (*.resource.ts). Entry and taxonomy by-ID mirrors.
src/mcp-server/prompts	Prompt definitions (*.prompt.ts). The protein-dossier workflow prompt.
src/services/uniprot	The rest.uniprot.org REST client — search, batch entries, ID mapping, proteomes, taxonomy, FASTA — plus normalized domain types.
tests/	Unit and integration tests mirroring src/.

Development guide

See CLAUDE.md (and the byte-identical AGENTS.md) for development guidelines and architectural rules. The short version:

• Handlers throw, framework catches — no try/catch in tool logic
• Use ctx.log for request-scoped logging, ctx.state for tenant-scoped storage
• Register new tools and resources in the createApp() arrays
• Wrap the UniProt API: validate raw → normalize to domain type → return the output schema; never fabricate missing fields

Contributing

Issues and pull requests are welcome. Run checks and tests before submitting:

bun run devcheck
bun run test

License

Apache-2.0 — see LICENSE for details.