smaniches/uniprot-mcp

Produce verifiable, release-aware protein evidence packages from UniProt and linked scientific sources.
Use this MCP server to find proteins, assemble protein, target, and variant evidence, and keep a checkable record of where each result came from. Each successful response records the UniProt release, retrieval time, resolved source URL, and a SHA-256 digest. uniprot_provenance_verify can later determine whether the upstream record is unchanged or has drifted.
The complete tool catalog remains available for specialized research workflows.
> Author: **Santiago Maniches** · ORCID 0009-0005-6480-1987 · TOPOLOGICA LLC
**Research authorship:** Santiago Maniches independently maintains this server and is the sole scientific author of its project-specific research contributions. AI-assisted tools have supported development, testing, and internal review under his direction. UniProt records, linked source data, and underlying third-party methods retain their original authorship; internal tool-assisted review is not external scientific validation.
**Run it in one line:**
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Verifiable provenance (the receipts)
Every answer this server returns is traceable to a primary-source URL **and**
a content hash you can re-compute yourself. The walkthrough below is a real
run against the live server (UniProt release 2026_01), independently
confirmed against the UniProt REST API.
**Question.** What is the function of human p53 (UniProt P04637), what
heritable cancer syndrome is it associated with, and is the R175H mutation
a documented disease variant?
**Answer, with its provenance footer (verbatim from the server):**
- **Function.** *Cellular tumor antigen p53* (gene TP53, *Homo sapiens*,
393 aa). "Multifunctional transcription factor that induces cell cycle
arrest, DNA repair or apoptosis... Acts as a tumor suppressor in many tumor
types."
- **Disease.** *Li-Fraumeni syndrome* (acronym LFS, UniProt disease id
DI-01904, OMIM 151623) — "an autosomal dominant familial cancer
syndrome... Four types of cancers account for 80% of tumors occurring in
TP53 germline mutation carriers."
- **Variant.** R175H — "in LFS; germline mutation and in sporadic cancers;
somatic mutation; does not induce SNAI1 degradation; reduces interaction
with ZNF385A; dbSNP:rs28934578."
Reproduce it
**1. Run the server and ask the same question** (any MCP client; tool calls shown):
**2. Confirm the hash re-verifies** (re-fetches the URL and re-checks the
release + canonical hash with the server's own code):
**3. Confirm the values against the primary source — no server in the loop:**
**What this proves:** every returned claim is traceable to a primary-source
URL and a content hash. The gene, protein name, disease (with OMIM id), and
variant the server reports all match the live UniProt entry; the footer
SHA-256 is reproducible byte-for-byte from the primary source using a
documented, server-independent recipe. A third party can re-run all three
checks today, or a year from now, without trusting this server.
> Note on the hash: the footer SHA-256 is of the *canonical* UniProt response
> body — the JSON re-serialized with sorted keys and compact separators
> (json.dumps(obj, sort_keys=True, separators=(",", ":"), ensure_ascii=False)),
> so harmless key-order changes within a release do not break verification. A raw
> curl | sha256sum of the bytes will therefore differ; apply the same
> canonicalization (step 3 above) or use uniprot_provenance_verify.
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Installation
Run without installing (recommended):
Or install into an environment:
> **Note:** There is an unrelated package named uniprot-mcp on PyPI
> (different author, 5 tools, MIT). This package is uniprot-mcp-server.
> Running pip install uniprot-mcp will install the wrong package silently.
For researchers — where to start
If you are a biomedical researcher visiting this repo, the highest-signal places to look are:
| Resource | What it gives you |
|---|---|
| **examples/atlas/** | Two artifacts with deliberately different scopes: • **Curated atlas (25 entries).** TP53, BRCA1, CFTR, HTT, EGFR, BRAF, KRAS, TEM-1 β-lactamase, more — each linking the canonical UniProt accession to MONDO / OMIM / PharmGKB / ARO IDs and the relevant tool sequence. JSON-LD manifest at examples/atlas/atlas.json. • **Comprehensive index (11,590 rows).** UniProt's curated disease + pathogen surface as two TSVs (comprehensive_index.tsv 7,250 human disease rows, comprehensive_index_pathogens.tsv 4,340 pathogen rows). Each row carries a UniProt disease ID and an OMIM cross-reference where available. MONDO / PharmGKB / ARO mappings exist only in the 25-entry curated atlas, not in the 11,590-row index. SHA-256 reproducibility manifest at examples/atlas/manifest.json. Methodology (how compiled, what's verified, what's community-reviewable) at examples/atlas/METHODOLOGY.md. |