uniprot-mcp-server 1.1.2

Model Context Protocol server for the UniProt protein knowledgebase.

uniprot-mcp

A Model Context Protocol server for the UniProt protein knowledgebase with per-query provenance verification. 41 tools across 8 families. Apache-2.0. Every successful response carries a verifiable Provenance record — UniProt release, retrieval timestamp, resolved URL, and a SHA-256 of the canonical response body — that the agent (or a third party, a year later) can re-check with a single tool call: uniprot_provenance_verify.

The wedge: **per-response SHA-256 + verify primitive + release pinning

• offline replay** is, to the best of my survey of public MCPs as of 2026-04-26, absent from every other bio-MCP server I could find (BioMCP, Augmented-Nature/UniProt-MCP, biothings-mcp, gget-mcp, and others). If you are a regulated-bio-pharma user who needs to prove, years later, that a UniProt-derived claim still holds, this is the mechanism. Comparison and citations: docs/COMPETITIVE_LANDSCAPE.md.

Author: Santiago Maniches · ORCID 0009-0005-6480-1987 · TOPOLOGICA LLC

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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/	25 disease & target worked examples — 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 for machine consumption. Methodology (how compiled, what's verified, what's community-reviewable) at examples/atlas/METHODOLOGY.md.
examples/01..04.jsonl	Full Claude-Desktop transcripts of clinical-variant interpretation (TP53 R175H), drug-target dossier (BRCA1), provenance verification a year later, pathogen drug-discovery (TEM-1).
tests/benchmark/	Pre-registered 30-prompt benchmark with SHA-256 commitments on main. The 2026-04-26 v1.1.0 run verified 30/30 against live UniProt — transcript at tests/benchmark/run-2026-04-26-v1.1.0/.
scripts/replicate.sh	One-command verification that the published PyPI wheel was built from this exact repo (cross-checks SHA-256 across PyPI / GitHub Release / SLSA attestation; runs --self-test; re-runs the benchmark live). POSIX + scripts/replicate.ps1 for Windows.
docs/COMPETITIVE_LANDSCAPE.md	Honest 14-server survey of the bio-MCP space (April 2026) and the specific differentiation this server claims.

Issues / corrections welcome at https://github.com/smaniches/uniprot-mcp/issues. The atlas in particular is community-reviewable — see METHODOLOGY.md for what is machine-verified vs what needs human review.

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What makes this different

	uniprot-mcp	Vanilla LLM + WebFetch	A typical bio-MCP
Tool surface	41 tools, 8 families	none — caller writes URLs	usually 5–10
Provenance on every response	release • date • URL • SHA-256	none	sometimes URL only
Per-query auditability	uniprot_provenance_verify re-checks any prior response	not possible	not possible
Release pinning	--pin-release=YYYY_MM raises on drift	n/a	n/a
Pre-registered benchmark	30 prompts, SHA-256 committed on main + reproducible verifier	n/a	n/a
Local provenance cache	offline replay via UNIPROT_MCP_CACHE_DIR	n/a	n/a
Clinical primitives	sequence chemistry / position-aware features / HGVS variant lookup / disease associations / AlphaFold pLDDT / ClinVar	none	none
Composition tool	uniprot_target_dossier — one call, nine sections	n/a	n/a
Input validation	regex + length cap before any HTTP call	none	partial
Error-channel safety	upstream exception text never echoed to LLM	n/a	partial
Cross-origin allowlist	enumerated, threat-modelled, privacy-listed	n/a	usually unaudited
Supply chain	SLSA build provenance + Sigstore + CycloneDX SBOM (post-flip)	n/a	rare
Test layers	unit + property + contract + client + integration + benchmark	n/a	usually unit only
Mutation testing	weekly + on-demand workflow; baseline measurement on v1.1.0; ≥ 95 % gate planned post-baseline	n/a	rare

The provenance + verify chain is, in my 2026-04-26 survey, absent from every other bio-MCP I could find. A regulated user can take any prior uniprot-mcp answer and prove — without contacting the author — that UniProt still returns the same bytes, or detect exactly how the upstream has drifted. If you find a counter-example I missed, please file an issue and I will update the comparison.

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Tools (41)

Eight endpoint families. All read-only (readOnlyHint: true). All but uniprot_replay_from_cache interact with at least one upstream service (openWorldHint: true). No UniProt API key required.

Core UniProtKB (10)

Tool	Purpose
uniprot_get_entry	Full UniProt entry (e.g. P04637 for p53). Function, gene, organism, disease, cross-refs.
uniprot_search	UniProt query language — gene, organism, taxon ID, reviewed flag, free text.
uniprot_get_sequence	FASTA. PIR-style provenance comment block above the first record (BLAST+ / biopython compatible).
uniprot_get_features	Domains, binding sites, PTMs, signal peptides — optional type filter.
uniprot_get_variants	Natural variants and disease mutations.
uniprot_get_go_terms	GO annotations grouped by aspect (F / P / C).
uniprot_get_cross_refs	Raw cross-references to PDB, Pfam, Ensembl, Reactome, KEGG, STRING …
uniprot_id_mapping	Map IDs between databases (Gene_Name → UniProtKB, PDB → UniProtKB, …).
uniprot_batch_entries	Up to 100 entries in one call; invalid accessions filtered client-side.
uniprot_taxonomy_search	Search UniProt taxonomy by organism name.

Controlled vocabularies (4)

Tool	Purpose
uniprot_get_keyword	Keyword by ID (e.g. KW-0007 = Acetylation). Definition, synonyms, GO refs, hierarchy.
uniprot_search_keywords	Free-text keyword search.
uniprot_get_subcellular_location	Subcellular-location term by ID (e.g. SL-0039 = Cell membrane).
uniprot_search_subcellular_locations	Free-text location search.

Sequence archives & clusters (4)

Tool	Purpose
uniprot_get_uniref	UniRef cluster by ID (UniRef50_P04637, UniRef90_P04637, UniRef100_P04637).
uniprot_search_uniref	Cluster search with identity_tier filter (50 / 90 / 100).
uniprot_get_uniparc	Sequence-archive record by UPI (UPI000002ED67).
uniprot_search_uniparc	UniParc full-text search.

Proteomes & literature (4)

Tool	Purpose
uniprot_get_proteome	Proteome by UP ID (UP000005640 = human). Counts, BUSCO score, components.
uniprot_search_proteomes	Filter by organism / type / completeness.
uniprot_get_citation	Citation record by ID (typically a PubMed numeric ID).
uniprot_search_citations	Index search across UniProt citations.

Structured cross-DB resolvers (4)

Gateway-only — no calls leave the UniProt origin. These extract the relevant cross-references from a UniProt entry and return structured records (typed lists / objects, not passthrough strings).

Tool	Purpose
uniprot_resolve_pdb	PDB structures: id + method + resolution + chain coverage.
uniprot_resolve_alphafold	AlphaFold model id + EBI viewer URL (model id only — for pLDDT call the dedicated tool below).
uniprot_resolve_interpro	InterPro signatures: id + entry name.
uniprot_resolve_chembl	ChEMBL drug-target id + EBI target-card URL.

Biomedical features (7)

Pure-Python compositions over the entry — no extra origin. The first four answer per-residue and per-variant questions; the last three are the v1.1.0 expansion targeting drug discovery, therapeutic-protein engineering, and pathogen-secretion analysis: each is a filter over the entry's features array, with a structured grouping by feature type and an honest empty-set advisory.

Tool	Purpose
uniprot_compute_properties	Derived sequence chemistry from the FASTA: MW / pI / GRAVY / aromaticity / charge / ε₂₈₀.
uniprot_features_at_position	Every feature overlapping a residue position. Critical for variant-effect interpretation.
uniprot_lookup_variant	HGVS-shorthand match (R175H, V600E, R248*) against UniProt's natural-variant features.
uniprot_get_disease_associations	Structured disease records from DISEASE-type comments: name + acronym + UniProt disease ID + OMIM cross-ref + description.
uniprot_get_active_sites	Catalytic and ligand-binding residues: active sites, binding sites, sites, metal binding, DNA binding. The residue-level chemistry of the protein.
uniprot_get_processing_features	Maturation features: signal peptide, propeptide, transit peptide, initiator methionine, chain, peptide. Essential for therapeutic-protein engineering and pathogen-secretion analysis.
uniprot_get_ptms	Post-translational modifications: modified residues (phospho/acetyl/methyl), glycosylation, lipidation (GPI/prenyl/palmitoyl), disulfide bonds, cross-links.

Cross-origin enrichment (3)

The only tools that consult origins outside rest.uniprot.org. Each is documented in PRIVACY.md and in the threat model.

Tool	Origin	Purpose
uniprot_get_alphafold_confidence	alphafold.ebi.ac.uk	pLDDT mean + four-band distribution; lets the agent decide whether to trust the model.
uniprot_resolve_clinvar	eutils.ncbi.nlm.nih.gov	ClinVar significance + condition + review status by gene + optional HGVS shorthand.
uniprot_get_publications	rest.uniprot.org	Pure-Python over the entry's references — listed here because it complements the cross-origin enrichment.

Composition + provenance (5)

Tool	Purpose
uniprot_resolve_orthology	Group orthology cross-references by source DB (KEGG / OMA / OrthoDB / eggNOG / 8 more).
uniprot_get_evidence_summary	Aggregate ECO codes (Evidence and Conclusion Ontology) across an entry. Distinguishes wet-lab confirmed from inferred-by-similarity from automatic.
uniprot_target_dossier	One-call comprehensive characterisation: nine sections — identity / function / chemistry / structure / drug-target / disease / variants / functional annotations / cross-refs.
uniprot_provenance_verify	Re-fetch a previously recorded URL and compare release tag + canonical response SHA-256. Five verdicts (verified, release_drift, hash_drift, release_and_hash_drift, url_unreachable) each with an advice string.
uniprot_replay_from_cache	Read a cached UniProt response without hitting the upstream. Opt-in via UNIPROT_MCP_CACHE_DIR.

---

Provenance & verification

Every successful tool response includes a footer like:

---
_Source: UniProt release 2026_01 (28-January-2026) • Retrieved 2026-04-25T17:09:00Z_
_Query: https://rest.uniprot.org/uniprotkb/P04637_
_SHA-256: 0040d79bb39e2f7386d55f81071e87858ec2e5c2cd9552e93c3633897f78345e_

A year later, an auditor can call uniprot_provenance_verify with those exact fields:

> uniprot_provenance_verify(
    url="https://rest.uniprot.org/uniprotkb/P04637",
    release="2026_01",
    response_sha256="0040d79bb39e2f7386d55f81071e87858ec2e5c2cd9552e93c3633897f78345e"
  )

## Provenance Verification

**Status:** verified

**URL:** https://rest.uniprot.org/uniprotkb/P04637
- ✓ URL resolves (HTTP 200)
- ✓ Release: recorded '2026_01', current '2026_01'
- ✓ Response SHA-256: recorded 0040d79bb39e2f73…, current 0040d79bb39e2f73…

**Advice:** Both checks passed. The recorded provenance is reproducible against the live UniProt API.

If UniProt has moved on, the tool tells you exactly how:

Verdict	Meaning	Advice
verified	Both release and hash match	The provenance is reproducible
release_drift	UniProt released a new version	Pin via the FTP snapshot if you need the historical answer
hash_drift	Same release, body changed	An in-release edit; investigate or re-fetch
release_and_hash_drift	Both moved on	Use a release-specific FTP snapshot
url_unreachable	Endpoint dropped or rate-limited	Retry or report to UniProt

For strict reproducibility, opt into release pinning:

export UNIPROT_PIN_RELEASE=2026_01
uniprot-mcp
# every response is checked against the pinned release;
# any drift raises `ReleaseMismatchError`, which the server surfaces
# as an agent-actionable error envelope.

For offline replay (post-cache-population):

export UNIPROT_MCP_CACHE_DIR=~/.uniprot-mcp-cache
uniprot-mcp
# every successful response is mirrored to disk; later replay via
# uniprot_replay_from_cache(url) without touching the upstream.

A live end-to-end demonstration is committed at tests/benchmark/run-2026-04-25-roundtrip/transcript.md — real values, real verdicts, no mocks.

---

Pre-registered benchmark

tests/benchmark/ ships a 30-prompt evaluation (Tier A / B / C × 10) with SHA-256-committed expected answers on main. The plaintext expected.jsonl is held local-only until a benchmark run is published; the cryptographic commitments mean the author cannot rewrite "correct" answers post-hoc.

A reviewer can re-derive every Tier A and B answer from primary-source UniProt REST in two commands:

python tests/benchmark/verify_answers.py tests/benchmark/expected.jsonl
# OK: all 30 prompts verified against https://rest.uniprot.org

python tests/benchmark/verify.py tests/benchmark/expected.jsonl tests/benchmark/expected.hashes.jsonl
# OK: 30 commitments verified

See tests/benchmark/AUDIT.md for the per-prompt source attribution and the formal independence statement (uniprot-mcp was not used during answer authoring).

---

Install

pip install uniprot-mcp-server   # PyPI distribution
# or, for a pinned, isolated install:
uvx --from uniprot-mcp-server uniprot-mcp

Why three different names? This is the standard Python packaging pattern, exactly because PyPI's namespace is global and collisions force disambiguation:

Concept	Value	What it is
GitHub repository	smaniches/uniprot-mcp	source code + issue tracker
PyPI distribution	uniprot-mcp-server	what you pip install (the bare uniprot-mcp name was already claimed on PyPI when this project published)
Python module	uniprot_mcp	what you import (PEP-8 underscore form)
Console script + MCP server identity	uniprot-mcp	what you run from the shell and what Claude Desktop sees

Cross-checks that prove the wheel you installed was built from this repo: each release ships a Sigstore signature, SLSA build provenance, and a CycloneDX SBOM, all attached to the v1.1.0 GitHub Release. Run bash scripts/replicate.sh (POSIX) or pwsh scripts/replicate.ps1 (Windows) to verify the full chain end-to-end. Common precedents for the same one-thing-three-names pattern: pillow/PIL, python-dateutil/dateutil, beautifulsoup4/bs4, python-Levenshtein/Levenshtein.

From source:

git clone https://github.com/smaniches/uniprot-mcp.git
cd uniprot-mcp
pip install -e .

Claude Desktop

claude_desktop_config.json:

{
  "mcpServers": {
    "uniprot": {
      "command": "uniprot-mcp"
    }
  }
}

For pinned, reproducibility-grade access:

{
  "mcpServers": {
    "uniprot": {
      "command": "uniprot-mcp",
      "args": ["--pin-release=2026_01"]
    }
  }
}

For offline replay via the local provenance cache:

{
  "mcpServers": {
    "uniprot": {
      "command": "uniprot-mcp",
      "env": {
        "UNIPROT_MCP_CACHE_DIR": "/absolute/path/to/cache"
      }
    }
  }
}

Claude Code (CLI)

claude mcp add uniprot -- uniprot-mcp

Self-test (live UniProt smoke check)

uniprot-mcp --self-test
# [tools] registered: 41/41
# [live] P04637 -> TP53 OK
# [PASS]

---

Example workflows

1. Clinical-variant interpretation packet for TP53 R175H.

> What's at residue 175 of P04637? Is R175H a known variant? Pull
> the UniProt and ClinVar evidence and tell me how confident the
> AlphaFold model is at that residue.
→ uniprot_features_at_position("P04637", 175)
→ uniprot_lookup_variant("P04637", "R175H")
→ uniprot_resolve_clinvar("P04637", change="R175H")
→ uniprot_get_alphafold_confidence("P04637")

2. Drug-target dossier in one call.

> Give me a complete drug-target characterisation of human BRCA1.
→ uniprot_target_dossier("P38398")
   # nine sections, two upstream calls (entry + FASTA), one tool call.

3. Sequence chemistry for buffer choice / expression-system selection.

> What's the molecular weight, pI, and hydrophobicity of human insulin?
→ uniprot_compute_properties("P01308")
   # MW 11,981 Da, pI 4.93, ε₂₈₀ 24,980 M⁻¹·cm⁻¹ — pure Python on the FASTA.

4. Provenance round-trip — proving an answer is reproducible.

> [later, with the provenance footer from a prior session in hand]
> Verify the recorded provenance for P04637.
→ uniprot_provenance_verify(
    url="https://rest.uniprot.org/uniprotkb/P04637",
    release="2026_01",
    response_sha256="0040d79bb39e2f7386d55f81071e87858ec2e5c2cd9552e93c3633897f78345e"
  )

5. Air-gapped clinical workflow with sealed cache.

# Day 1, online: cache populates as queries run.
export UNIPROT_MCP_CACHE_DIR=~/sealed-cache
# … every uniprot-mcp tool call writes to ~/sealed-cache/<sha>.json
# Day N, offline: replay any prior answer.
> uniprot_replay_from_cache("https://rest.uniprot.org/uniprotkb/P04637")

---

Testing

Layer	Path	What
Unit	tests/unit/	Behaviour of every public function.
Property	tests/property/	Hypothesis-driven invariants on regexes + query construction.
Contract	tests/contract/	Manifest / pyproject / docs / incident-policy / benchmark drift prevention.
Client	tests/client/	Retry / back-off / id-mapping polling against respx-mocked HTTP.
Integration	tests/integration/	Live UniProt + AlphaFold; opt-in via --integration.
Benchmark	tests/benchmark/	30 SHA-256-committed prompts + reproducible verifier.

446 offline + 42 live integration tests, all green (real counts via pytest --collect-only on commit 01ab7a8). Mypy (strict), ruff (check + format), bandit (0 issues at any severity), pip-audit (--strict, no known vulnerabilities) all clean. Mutation testing (mutmut) gate ≥ 95 % kill, populated post-billing-reset.

# Fast, offline (CI on every push):
pytest tests/unit tests/property tests/client tests/contract -v

# Live UniProt (opt-in, nightly in CI):
pytest --integration tests/integration -v

# Lint / type-check / security / SCA:
ruff check . && ruff format --check . && mypy src/uniprot_mcp
bandit -r src/uniprot_mcp && pip-audit --strict

---

Architecture & threat model

• docs/THREAT_MODEL.md — twelve STRIDE-shaped threats, each receipt-anchored to a code path or commit SHA, plus the cross-origin allowlist policy (§T3b).
• docs/INCIDENT_POLICY.md + docs/POSTMORTEM_TEMPLATE.md + docs/INCIDENT_LOG.md — every nightly integration breakage triggers a postmortem entry.
• AUDIT.md — pre-1.0.1 professional audit, P0/P1 remediations recorded.
• docs/MERGE_PLAN.md — five-phase merge → tag → flip operational plan with rollback policy.
• docs/PENDING_V1.md — the binary punch list to v1.0.1.
• mkdocs.yml — Material-themed docs site, deployable to gh-pages via .github/workflows/docs.yml. Build locally with pip install -e ".[docs]" && mkdocs serve.

---

Citation

Cite via CITATION.cff (GitHub renders a "Cite this repository" button). Always also cite the UniProt Consortium:

The UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Research (2025). doi:10.1093/nar/gkae1010

---

License

Apache-2.0 — see LICENSE and NOTICE.

This project is the gateway layer of the Topologica Bio MCP suite. Multi-source orchestration and tamper-evident provenance ledgers live in the companion topologica-bio repository under BUSL-1.1 (Change Date 2030-04-19, auto-reverts to Apache-2.0). uniprot-mcp itself is and will remain permissively Apache-2.0.

Copyright © 2026 Santiago Maniches. TOPOLOGICA LLC.