uniprot-mcp-server

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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>
  </p>
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**Public Hosted Server:** [https://uniprot.caseyjhand.com/mcp](https://uniprot.caseyjhand.com/mcp)

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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

---

### `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. 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

---

### `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 → results bounded by a wall-clock budget, with a resumable server-side ticket on overflow