@cyanheads/uniprot-mcp-server
by cyanheads
README.md
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<h1>@cyanheads/uniprot-mcp-server</h1>
<p><b>Search UniProtKB by protein function, fetch curated records, map IDs across databases, and pull reference proteomes, taxonomy, and sequences via MCP. STDIO or Streamable HTTP.</b>
<div>6 Tools • 2 Resources • 1 Prompt</div>
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[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/uniprot-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/uniprot-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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[](https://github.com/cyanheads/uniprot-mcp-server/releases/latest/download/uniprot-mcp-server.mcpb) [](https://cursor.com/en/install-mcp?name=uniprot-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvdW5pcHJvdC1tY3Atc2VydmVyIl19) [](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22uniprot-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Funiprot-mcp-server%22%5D%7D)
[](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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**Public Hosted Server:** [https://uniprot.caseyjhand.com/mcp](https://uniprot.caseyjhand.com/mcp)
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---
## Overview
Protein research over UniProtKB. Search by function or gene, fetch curated records, map identifiers from Ensembl, ChEMBL, RefSeq, PDB, and more, and pull reference proteomes, taxonomy, and sequences.
### Tools
| 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; running jobs return a ticket and completed pages return a continuation. |
| `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, cursor-paginated. |
| `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. |
### Resources
| Resource | Description |
|:---|:---|
| `uniprot://entry/{accession}` | A curated UniProtKB entry by accession — the resource mirror of `uniprot_get_entry` for a single accession. |
| `uniprot://taxonomy/{taxonId}` | A taxonomy record by NCBI taxon ID — name, rank, parent, full lineage. The mirror of `uniprot_get_taxonomy` by ID. |
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.
### Prompts
| Prompt | Description |
|:---|:---|
| `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. |
## Capability reference
### `uniprot_search_proteins` <sub>tool</sub>
- `text_search` for plain language **or** `query` for Lucene field syntax (`gene`, `organism_id`, `keyword`, `go`, `reviewed`, `protein_name`, `family`, `length`, `existence`, `accession`) — exactly one. `organism_id` filters the whole query; unbalanced parentheses are rejected. Optional `facets` return count breakdowns (e.g. `reviewed`, `model_organism`)
- `reviewed` defaults to `true` (Swiss-Prot only); `false` searches both tiers (put `reviewed:false` in `query` for TrEMBL only). Every hit carries `reviewed`, `annotationScore`, and `proteinExistence`
- Forward-only cursor pagination; returns `totalResults` and the effective query. A cursor UniProt can't continue from fails `invalid_cursor`: restart without it
- Inactive accessions (merged, demerged, or deleted) go in `inactive[]` with the reason and replacements, not in `results[]`
---
### `uniprot_get_entry` <sub>tool</sub>
- Up to 20 accessions per call, from `uniprot_search_proteins` or `uniprot_map_ids` (strip any `-N` isoform suffix). Sectioned record: function, catalytic activity, cofactors, subcellular location, disease, PTMs, natural variants, isoforms, domains, GO terms, keywords, cross-references. `fields` trims the output; identity and provenance fields are always kept
- Resolved entries come back in `succeeded[]`, unknown or inactive ones in `failed[]`, so one bad accession doesn't abort the batch. An inactive accession's error names the merge target, the demerge products, or the UniParc ID
- An oversized record returns `kind: "outline"` (a section listing); re-call one accession with `sections: [...]` for the parts you need. A very large list section pages with `section_limit` (1–500) and `section_offset`, reporting `totalCount` and `nextOffset`
---
### `uniprot_map_ids` <sub>tool</sub>
- `from_db` / `to_db` are validated enums (e.g. `Gene_Name`, `Ensembl`, `RefSeq_Protein`, `ChEMBL`, `PDB`, `GeneID`, and `UniProtKB_AC-ID` as a source); an unknown database fails before any request. Target `UniProtKB-Swiss-Prot` for reviewed accessions only, or `UniProtKB` to include TrEMBL. Pair a gene-symbol `from_db` with `tax_id` to pick the species
- Submits the job and polls within a time budget. A job still running returns `status: "running"` with a ticket; pass that ticket alone to poll it. A finished call returns `status: "finished"` with one page, and `continuation` (pass it alone) fetches the next; no `continuation` means the last page
- `unmappedIds` lists only identifiers UniProt reports as failed. A row whose UniProtKB target is inactive (merged, demerged, or deleted) carries an `inactive` marker with the reason and replacements
---
### `uniprot_get_proteome` <sub>tool</sub>
- Provide exactly one of `upid` (e.g. `UP000005640`) or `taxon_id`; both or neither fails validation. Resolve an organism name to a taxon ID first with `uniprot_get_taxonomy`
- Returns proteome type, total protein count, BUSCO completeness (score, complete/fragmented/missing counts, lineage dataset), and genome assembly accession
- Proteins are opt-in via `include_proteins` (human has ~147,506) and come back as a capped page with a forward cursor; narrow with `query` (UniProtKB Lucene syntax). A cursor UniProt can't continue from fails `invalid_cursor`
---
### `uniprot_get_taxonomy` <sub>tool</sub>
- Provide exactly one of `taxon_id` (NCBI numeric ID) or `name` (scientific name); both or neither fails validation. Gives the taxon ID that `uniprot_search_proteins` (`organism_id`) and `uniprot_get_proteome` (`taxon_id`) expect
- Returns scientific and common name, mnemonic, rank, parent, and the full lineage (root → near ancestor)
- `include_children` adds the immediate child taxa, 100 per page with the total count and a `cursor` for the next page. A cursor sent with a different taxon fails `invalid_cursor`
---
### `uniprot_get_sequence` <sub>tool</sub>
- Returns the canonical sequence with its length and parsed FASTA header; `include_isoforms` adds the isoform sequences. Accessions come from `uniprot_search_proteins` or `uniprot_map_ids` (strip any `-N` isoform suffix)
- A merged accession returns its merge target's sequences, with the requested accession in `mergedFrom`; a demerged or deleted one fails `not_found` naming its replacements or UniParc ID
---
### `uniprot://entry/{accession}` <sub>resource</sub>
- Same record as `uniprot_get_entry` for a single accession, addressed by URI. An inactive accession (merged, demerged, or deleted) fails `not_found`
- A very large entry returns an identity summary (accession, entry name, protein name, genes, organism, length, reviewed status, annotation score, protein existence) plus a section outline; fetch specific sections with `uniprot_get_entry` (`sections: [...]`), since the URI takes no sections parameter
---
### `uniprot://taxonomy/{taxonId}` <sub>resource</sub>
- Addressed by NCBI taxon ID, e.g. `uniprot://taxonomy/9606` for human
- Returns scientific and common name, mnemonic, rank, parent, and full lineage — same shape as `uniprot_get_taxonomy` without `include_children`
- Tool-only clients reach the same data via `uniprot_get_taxonomy`
---
### `uniprot_protein_dossier` <sub>prompt</sub>
- Arguments: `identifier` required (gene name, accession, or protein name); `organism` optional to disambiguate
- Five-step workflow embedded in the generated message: resolve identifier → fetch entry → summarize function/localization/provenance → pull disease & variants → surface cross-references for structure (PDB), bioactivity (ChEMBL), and citations (PubMed)
- Returns a single user-role message carrying the full instructions — no separate assistant framing message
## Features
Built on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core): stdio and Streamable HTTP transports, pluggable auth (`none` / `jwt` / `oauth`), swappable storage (`in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`), structured logging with optional OpenTelemetry tracing.
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)
- Batch entry fetch — N accessions in one round trip, with any missing ones flagged
- Async ID mapping with a bounded poll, a resumable ticket for running jobs, and paginated results
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
- Explicit output shapes — `uniprot_get_entry` returns `kind: "full" | "outline"`, and `uniprot_map_ids` returns either a `ticket` or a `continuation`
- Sparsity preserved — absent upstream fields stay absent, never fabricated (most curated sections are legitimately missing on TrEMBL entries)
## Getting started
### Public Hosted Instance
A public instance is available at `https://uniprot.caseyjhand.com/mcp` — no installation required. Point any MCP client at it via Streamable HTTP:
```json
{
"mcpServers": {
"uniprot-mcp-server": {
"type": "streamable-http",
"url": "https://uniprot.caseyjhand.com/mcp"
}
}
}
```
### Self-Hosted / Local
Add the following to your MCP client configuration file. UniProt REST is keyless — no API key required.
```json
{
"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):
```json
{
"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:
```json
{
"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:
```sh
MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
# Server listens at http://localhost:3010/mcp
```
### Prerequisites
- [Bun v1.4.0](https://bun.sh/) or higher (or Node.js v24+).
- No API key — UniProt REST is keyless and open. Data is [UniProt](https://www.uniprot.org), CC BY 4.0.
### Installation
1. **Clone the repository:**
```sh
git clone https://github.com/cyanheads/uniprot-mcp-server.git
```
2. **Navigate into the directory:**
```sh
cd uniprot-mcp-server
```
3. **Install dependencies:**
```sh
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` | Time budget for the ID-mapping poll before returning a 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_SESSION_MODE` | HTTP session mode: `auto`, `stateful`, or `stateless`. The server is stateless by default. | `stateless` |
| `MCP_LOG_LEVEL` | Log level (RFC 5424). | `info` |
| `LOGS_DIR` | Directory for log files (Node.js only). | `<project-root>/logs` |
| `LOG_TOOL_FAILURE_PAYLOADS` | Log each failed tool call's arguments and result, redacted by key name and capped at `LOG_TOOL_FAILURE_PAYLOAD_MAX_BYTES` (default `16384`). A secret inside a free-form value is not redacted. | `false` |
| `STORAGE_PROVIDER_TYPE` | Storage backend. | `in-memory` |
| `OTEL_ENABLED` | Enable [OpenTelemetry instrumentation](https://github.com/cyanheads/mcp-ts-core/tree/main/docs/telemetry) (spans, metrics, completion logs). | `false` |
See [`.env.example`](./.env.example) for the full list of optional overrides.
## Running the server
### Local development
- **Build and run:**
```sh
# One-time build
bun run rebuild
# Run the built server
bun run start:stdio
# or
bun run start:http
```
- **Run checks and tests:**
```sh
bun run devcheck # Lint, format, typecheck, security
bun run test # Vitest test suite
bun run test:coverage # Test suite with coverage, enforcing the framework thresholds
bun run lint:mcp # Validate MCP definitions against spec
```
### Docker
```sh
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`](./CLAUDE.md) (and the byte-identical [`AGENTS.md`](./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 are welcome. Run checks and tests before submitting:
```sh
bun run devcheck
bun run test
```
## License
Apache-2.0 — see [LICENSE](LICENSE) for details.
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