# uniprot-mcp-server [Health: Active]
**Category:** 🧬 Biology & Bioinformatics
**Repository:** https://github.com/cyanheads/uniprot-mcp-server
**GitHub Stars:** 1
**Views:** 0
**Installs:** 0
**Upvotes:** 0
**Directory Page:** https://allmcps.com/mcp/uniprot-mcp-server
## Description
Protein research over UniProtKB — search by function, fetch curated records, map IDs, proteomes.
## Claude Desktop Quick Installation
Install path detected from listing signals. Uses `bunx` (confidence: high):
```json
"mcpServers": {
"uniprot-mcp-server": {
"command": "bunx",
"args": ["@cyanheads/uniprot-mcp-server@latest"]
}
}
```
## Documentation & README
@cyanheads/uniprot-mcp-server
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.
6 Tools • 2 Resources • 1 Prompt
[](./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/)
[](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)
**Public Hosted Server:** [https://uniprot.caseyjhand.com/mcp](https://uniprot.caseyjhand.com/mcp)
---
## 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; 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. |
| `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
---
### `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
---
### `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. A running job returns `status: "running"` with a ticket — pass that ticket alone to poll the same job
- A completed call returns `status: "finished"` with one upstream page (up to 500 mappings). If `continuation` is present, pass it alone to fetch the next completed page without polling or re-submitting; its absence marks the terminal page
- Pair a gene-symbol `from_db` with `tax_id` to disambiguate species
- `unmappedIds` is populated only from UniProt's `failedIds`, so identifiers UniProt normalizes in successful result rows are not misclassified as failures
---
### `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`
---
### `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
---
### `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`](https://www.npmjs.com/package/@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 bounded by a wall-clock budget, with a running-job ticket and separately paginated completed 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
- Discriminated output contracts — `uniprot_get_entry` returns `kind: "full" | "outline"`, while `uniprot_map_ids` separates a running-job `ticket` from a finished-page `continuation`; 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
### 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 v1.3.0](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` | 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). | `/logs` |
| `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`](https://github.com/cyanheads/uniprot-mcp-server/blob/HEAD/.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 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`](https://github.com/cyanheads/uniprot-mcp-server/blob/HEAD/CLAUDE.md) (and the byte-identical [`AGENTS.md`](https://github.com/cyanheads/uniprot-mcp-server/blob/HEAD/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:
```sh
bun run devcheck
bun run test
```
## License
Apache-2.0 — see [LICENSE](https://github.com/cyanheads/uniprot-mcp-server/blob/HEAD/LICENSE) for details.