Life-Science Remote MCP Server List (Audit Update)

Verified: 2026-09-18 This is a differential update of the previous version (https://hackmd.io/zTFMecEjQzSx2WY-IQrIXw ). Not every endpoint in the main table was re-probed each cycle (most are not directly reachable from this environment and were checked via web sources). Completeness is not claimed; open items are listed at the end.

Subject areas have been normalized to English controlled/established vocabulary (previous mixed Japanese/English values replaced after confirming meaning).

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A. Public hosted remote MCP

MCP server	Subject area	Public remote endpoint	Provider	Remote type	Auth / notes
Ask Helena Public Knowledge	genomics; biomedical knowledge; information retrieval	https://api.helena.bio/ask/v1/mcp	Helena Bioinformatics	official-public	No auth, read-only. Search with source citations. Sources: Helena llms resource, MCPBeat: Ask Helena
EMBL-EBI Ontology Lookup Service (OLS) MCP	biomedical ontologies; ontology search; semantic search	https://www.ebi.ac.uk/ols4/api/mcp	EMBL-EBI	official-public	Streamable HTTP, no auth. GO/EFO/HPO/MONDO/ChEBI etc. Sources: EMBL-EBI OLS MCP, OLS4 GitHub
Expasy SPARQL Assistant MCP	RDF data integration; SPARQL query generation; proteins	https://chat.expasy.org/mcp	SIB Swiss Institute of Bioinformatics	official-public	Official repo states the public server URL explicitly. Assists SPARQL query generation/execution over SIB endpoints (UniProt/Bgee/OMA/SwissLipids/Cellosaurus etc.). No auth. Public endpoint confirmed in official repo on 2026-09-18. Source: sib-swiss/sparql-llm
fanta.bio MCP	functional genomics; cis-regulatory elements; transcription factor binding; gene expression	https://mcp.fanta.bio/mcp	fanta.bio	official-public	Streamable HTTP (JSON-RPC 2.0), no auth (per-endpoint hourly rate limits: 500/hr lookups, 100/hr full-text, 50/hr batch). CREs, genes, SNPs and TF binding for human (hg38) / mouse (mm10), cross-referenced with SCREEN cCRE / ChIP-Atlas / Ensembl / GWAS. 19 tools, 5 prompts, 2 resources. Docs at docs.fanta.bio/mcp/; transport endpoint mcp.fanta.bio/mcp. Source: fanta.bio MCP docs
Folklore Variant Evidence MCP	genetic variation; variant interpretation; human genome	https://api.helena.bio/folklore/v1/mcp	Helena Bioinformatics	official-public	Read-only, no auth. GRCh38 germline variant evidence. Source: Folklore integrations
GWAS Catalog MCP	genome-wide association study; genetic variation; phenotypes	https://ebi.ac.uk/gwas/mcp	GWAS Catalog / EMBL-EBI	official-public	Official hosted version, no install required. Source: GWAS Catalog MCP
Open Targets Platform MCP	target–disease associations; drug discovery	https://mcp.platform.opentargets.org/mcp	Open Targets	official-public	Official, no auth. Source: Open Targets Platform MCP
PubMed MCP — Anthropic life-sciences	literature search	https://pubmed.mcp.claude.com/mcp	Anthropic	official-public	No auth. Source: Anthropic life-sciences
STRING MCP	protein interactions; functional enrichment; sequence similarity	https://mcp.string-db.org/	STRING (meringlab)	official-public	Updated: previously "in development" → now documented as a production service. Streamable HTTP. STRING Chat (https://string-db.org/cgi/chat) is a working example that uses this MCP. Third-party health check reported "Healthy" on 2026-09-13. Repo: meringlab/string-mcp. Sources: STRING Help: MCP, mcp.string-db.org, Glama health check
TogoMCP	life-science data integration; RDF/SPARQL; identifier mapping	https://togomcp.rdfportal.org/mcp	DBCLS	official-public	Confirmed live via initialize probe on 2026-09-18 (serverInfo TogoMCP: RDF Portal MCP Server v2.19.0, no auth). Integrates 20+ DBs/APIs. Sources: TogoMCP, 2026-09-18 endpoint probe
Synapse MCP	research data management; data sharing	https://mcp.synapse.org/mcp	Sage Bionetworks	official-auth	OAuth2. Source: Synapse MCP
BioContextAI Knowledgebase MCP	data integration; proteins; pathways; protein interactions	https://mcp.biocontext.ai/mcp/	BioContextAI	community-public	Public remote service, fair-use limits. Integrates UniProt/Reactome/STRING/InterPro/PRIDE/Open Targets etc. Source: BioContextAI Knowledgebase
Cellosaurus MCP — QuentinCody	cell lines; cross-references	https://cellosaurus-mcp-server.quentincody.workers.dev/mcp	QuentinCody / community	community-public-likely	Community implementation of the SIB Cellosaurus API. Cloudflare Workers deployment domain is stated, but a deployed and ready claim is weaker, so treated at lower confidence. Not the official Cellosaurus MCP. Source: Cellosaurus MCP GitHub
ClinPGx MCP — QuentinCody	pharmacogenomics; drug–gene interactions; clinical guidelines	https://clinpgx-mcp-server.quentincody.workers.dev/mcp	QuentinCody	community-public	README states a deployed remote endpoint. CPIC/DPWG guidelines. Not the official ClinPGx MCP. Source: ClinPGx MCP GitHub
Ensembl MCP — cyanheads	genomics; sequence analysis; variant effect prediction; orthologs	https://ensembl.caseyjhand.com/mcp	cyanheads	community-public	Public hosted instance. Source: cyanheads/ensembl-mcp-server
Europe PMC MCP — QuentinCody	literature search; full-text mining; citations	https://europepmc-mcp-server.quentincody.workers.dev/mcp	QuentinCody	community-public	README states a public remote endpoint. Not the official Europe PMC MCP. Source: Europe PMC MCP GitHub
FDA Purple Book MCP — QuentinCody	biologics; biosimilars; drug regulation	https://fda-purple-book-mcp-server.quentincody.workers.dev/mcp	QuentinCody	community-public	README states a public remote endpoint. Not an official FDA MCP. Source: FDA Purple Book MCP GitHub
IEDB MCP — QuentinCody	immunology; immune epitopes; MHC binding	https://iedb-mcp-server.quentincody.workers.dev/mcp	QuentinCody	community-public	README states a deployed remote endpoint. Not the official IEDB MCP. Source: IEDB MCP GitHub
PubMed MCP — cyanheads	literature search; information retrieval	https://pubmed.caseyjhand.com/mcp	cyanheads	community-public	Public hosted instance. PubMed / Europe PMC / PMC / Unpaywall. Source: cyanheads/pubmed-mcp-server
UniProt MCP — cyanheads	proteins; sequence analysis; taxonomy; identifier mapping	https://uniprot.caseyjhand.com/mcp	cyanheads	community-public	Public hosted instance. Uses the UniProt REST API. Source: cyanheads/uniprot-mcp-server
BioStudies MCP — Pipeworx	research data; information retrieval	https://gateway.pipeworx.io/biostudies/mcp	Pipeworx	gateway	Hosted MCP on the Pipeworx gateway. EMBL-EBI BioStudies search and study metadata. Not the official EMBL-EBI MCP. Source: Pipeworx BioStudies documentation
GWAS Catalog MCP — Pipeworx	genome-wide association study; genetic variation; phenotypes	https://gateway.pipeworx.io/gwas-catalog/mcp	Pipeworx	gateway	Separate implementation from the EBI official version. Source: Pipeworx GWAS Catalog MCP
Genomic Intelligence MCP	regulatory genomics; gene expression; sequence analysis	https://mcp.genomicintelligence.ai/mcp	Genomic Intelligence	commercial-public	Public demo available; API key extends quota. Predicts promoter/splice/enhancer/chromatin/expression. Source: Genomic Intelligence MCP
AdisInsight MCP	drug pipeline intelligence; clinical trials; pharmacovigilance	https://adisinsight-mcp.springer.com/mcp	Springer Nature	commercial-auth	OAuth 2.0, for AdisInsight subscribers. Sources: AdisInsight MCP, AdisInsight
BioRender MCP	scientific illustration; figure generation	https://mcp.services.biorender.com/mcp	BioRender	commercial-auth	Official MCP connector. Authenticate with a BioRender account. Template/icon search, figure generation. Sources: BioRender MCP connector, Claude Connector Directory
Consensus MCP	literature search; systematic review; evidence synthesis	https://mcp.consensus.app/mcp	Consensus	commercial-auth	OAuth or Bearer token. Sources: Consensus MCP documentation, Consensus MCP
Cortellis Regulatory Intelligence MCP	regulatory intelligence; drug regulation; medical devices	https://api.clarivate.com/lifesciences/mcp-regulatory/mcp	Clarivate	commercial-auth	Streamable HTTP, OAuth 2.0. Requires a Cortellis Regulatory Intelligence subscription. Sources: Clarivate MCP documentation, Clarivate announcement
Medidata MCP	clinical trials; clinical research; site selection	https://mcp.imedidata.com/mcp	Medidata Solutions	commercial-auth	Official MCP. Platform Help and Intelligent/Predictive Site Ranking etc. Requires Medidata credentials. Sources: Medidata + Anthropic MCP, Claude Connector Directory
Owkin MCP	digital pathology; histopathology; survival analysis	https://mcp.k.owkin.com/mcp	Owkin	commercial-auth	Requires Owkin credentials. Sources: Owkin announcement, Claude Connector Directory
PatSnap Biology Modality MCP	biological sequences; antibodies; proteins; patent search	https://connect.patsnap.com/06e741/logic-mcp?apikey=<API_KEY>	PatSnap	commercial-auth	Official remote MCP. API key required. Source: PatSnap Biology Modality MCP
PatSnap Chemical Molecular MCP	cheminformatics; small molecules; ADMET	https://connect.patsnap.com/713886/logic-mcp?apikey=<API_KEY>	PatSnap	commercial-auth	Official remote MCP. API key required. Source: PatSnap Chemical Molecular MCP
PatSnap Clinical Trials MCP	clinical trials; drug development; competitive intelligence	https://connect.patsnap.com/051cd3/logic-mcp?apikey=<API_KEY>	PatSnap	commercial-auth	Official remote MCP. API key required. Source: PatSnap Clinical Trials MCP
PatSnap Company & Deal Intelligence MCP	business intelligence; licensing; mergers and acquisitions	https://connect.patsnap.com/1f8934/logic-mcp?apikey=<API_KEY>	PatSnap	commercial-auth	Official remote MCP. API key required. Source: PatSnap Company & Deal Intelligence MCP
PatSnap Drug & Asset MCP	drug assets; drug development; targets	https://connect.patsnap.com/30cd71/logic-mcp?apikey=<API_KEY>	PatSnap	commercial-auth	Official remote MCP. API key required. Source: PatSnap Drug & Asset MCP
PatSnap Pharma Intelligence MCP	drug pipeline intelligence; drug development; competitive intelligence	https://connect.patsnap.com/096456/logic-mcp?apikey=<API_KEY>	PatSnap	commercial-auth	Official remote MCP. API key required. Source: PatSnap Pharma Intelligence MCP
PatSnap Regulatory & Guidelines MCP	drug regulation; clinical guidelines	https://connect.patsnap.com/6415c2/logic-mcp?apikey=<API_KEY>	PatSnap	commercial-auth	Official remote MCP. API key required. Source: PatSnap Regulatory & Guidelines MCP
PatSnap Scientific & Translational Evidence MCP	translational research; target validation; clinical evidence	https://connect.patsnap.com/9c333c/logic-mcp?apikey=<API_KEY>	PatSnap	commercial-auth	Official remote MCP. API key required. Source: PatSnap Scientific & Translational Evidence MCP
PatSnap Target & Disease MCP	target biology; disease; epidemiology	https://connect.patsnap.com/2a2645/logic-mcp?apikey=<API_KEY>	PatSnap	commercial-auth	Official remote MCP. API key required. Source: PatSnap Target & Disease MCP
Seqera MCP	bioinformatics workflows; workflow execution; sequence data retrieval	https://mcp.seqera.io/mcp	Seqera	commercial-auth	OAuth 2.1 / PAT. Nextflow/nf-core, SRA/ENA/GEO. Source: Seqera MCP documentation
Wiley Scholar Gateway MCP	literature search; information retrieval; evidence synthesis	https://connector.scholargateway.ai/mcp	Wiley / Scholar Gateway	commercial-auth	OAuth 2.1, CONNECT SSO. Institutional subscription or trial. Sources: Wiley Scholar Gateway documentation, Wiley AI Solutions
Benchling MCP	electronic laboratory notebook; research data management	https://<tenant>.mcp.benchling.com/mcp	Benchling	tenant-specific	Tenant-specific, OAuth 2.1. Source: Benchling MCP configuration
SHARP-on-MCP .NET	health data interoperability; FHIR	https://dotnet.fhir-mcp.promptopinion.ai/mcp	SHARP-on-MCP	test	Public test environment. Source: SHARP-on-MCP
SHARP-on-MCP TypeScript	health data interoperability; FHIR	https://ts.fhir-mcp.promptopinion.ai/mcp	SHARP-on-MCP	test	Public test environment. Source: SHARP-on-MCP

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B. Held / needs re-confirmation

Candidate	Subject area	Candidate endpoint	Provider	Reason held	Next to confirm	Source
CIViC MCP	cancer genomics; somatic variants; clinical interpretation	https://civic-mcp-server.quentincody.workers.dev/mcp	Griffith Lab / QuentinCody	Paper now peer-reviewed and published (updated). The official chat https://civicdb.org/mcp-chat is a web UI, not an MCP transport endpoint. The Workers URL is presented in README/Glama as "replace with your own subdomain" = a deployment template, so a permanent public endpoint cannot be confirmed.	Whether civicdb.org exposes a hosted transport endpoint reachable by a standard MCP client, or whether the Workers URL is an author-operated permanent service	griffithlab/civic-mcp-server, Schimmelpfennig et al. 2026, Bioinform Adv
Identifiers.org MCP	identifier resolution; compact identifiers; data integration	https://resolver.api.identifiers.org/sse	EMBL-EBI (Identifiers.org)	Exists as a Claude connector (has connection history, SSE transport), but no primary-source MCP documentation could be confirmed, and the endpoint could not be probed from this environment (domain reachability limits).	Official Identifiers.org / EMBL-EBI MCP page; endpoint probe	Claude connector directory (connection history)
PubDictionaries MCP	text annotation; dictionaries; named entity recognition	https://pubdictionaries.org/mcp	DBCLS (PubDictionaries)	Exists as a Claude connector (has connection history), but no primary-source MCP documentation could be confirmed, and the endpoint could not be probed from this environment.	Official PubDictionaries MCP page; endpoint probe; whether auth is required	Claude connector directory (connection history)
GrEBI (Graphs@EBI) MCP	biomedical knowledge graph; data integration	https://www.dev.ebi.ac.uk/kg	EMBL-EBI (EBISPOT)	The paper states a publicly accessible MCP server, but the URL is given as an API/MCP base URL and it is unclear whether it is the transport endpoint itself. Not re-verified this round (carried forward as-is).	Exact MCP transport path; permanence of the dev domain	GrEBI GitHub, McLaughlin et al. 2026

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C. Remote-capable / self-hosted MCP implementations

No changes this round (carried forward as-is; individual items not re-verified).

MCP	Subject area	Remote use / status
BioMCP	cancer genomics; genetic variation; clinical trials; literature search	Streamable HTTP supported; no official public hosted endpoint confirmed
Galaxy MCP	bioinformatics workflows; tool execution	/api/mcp supported; enablement on public Galaxy instances is instance-dependent
GEOmcp	gene expression; sequence data retrieval	HTTP server supported; no public standing endpoint confirmed
PLSDB MCP	plasmids; sequence databases	Primarily stdio/self-hosted
UCSC Cell Browser MCP	single-cell transcriptomics	Primarily stdio/self-hosted
scmcp	single-cell transcriptomics; data analysis	Streamable HTTP supported; self-hosted
CellRank MCP	single-cell transcriptomics; trajectory inference	Streamable HTTP supported; self-hosted
BioinfoMCP	bioinformatics; command-line tool integration	local/Docker deployment
ProteinMCP	protein engineering	MCP framework/tool ecosystem
Coala	workflow conversion (CWL → MCP)	generic self-hosted MCP server
Holy Bio MCP	bioinformatics (collection)	Primarily local/stdio
10x Genomics MCP	single-cell transcriptomics; spatial transcriptomics	MCPB/local distribution
ToolUniverse	scientific tools (collection)	MCPB/local distribution

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Changes this round (2026-09-18)

• Added (main table):
  • Expasy SPARQL Assistant MCP (SIB, official-public) — public endpoint confirmed in official repo
• Updated:
  • STRING MCP — previously "in development" → now documented as a production service; source changed to string-db.org/help/mcp/; repo and health check added
  • TogoMCP — re-confirmed live on 2026-09-18 (v2.19.0)
  • Normalized the Subject area column across the whole main table to English controlled/established vocabulary (resolved Japanese/English mixing)
• Added to / updated in the held table:
  • CIViC MCP — reflected the peer-reviewed publication and official chat, but held pending an unconfirmed MCP transport endpoint
  • Identifiers.org MCP, PubDictionaries MCP
• Removed: none
• Evidence-only updates: STRING source URL
• Confirmed unchanged: self-hosted table, 13 entries (individual items not re-verified; previous state retained)

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Considered but not added to the main table

• Wikidata MCP (https://wd-mcp.wmcloud.org/mcp) — a general-purpose knowledge base without a primarily life-science-specific function; out of scope.
• Apify-hosted EBI scrapers (OLS/Proteins/BioStudies etc., mcp.apify.com) — Actor wrappers hosted by Apify that require an Apify account/OAuth; a gateway type. Not EMBL-EBI official and are scraper implementations, so not added this round (can be listed separately in a gateway table if needed).
• cBioPortal MCP (docs.cbioportal.org/ai-integrations/mcp) — cancer genomics. Official docs state "prototypes / work in progress" and no hosted remote endpoint is confirmed, so treated as self-hosted/in-development (re-check next round).

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Open items / caveats

1. Many of the commercial/community endpoints in this table are not directly reachable from this environment and were confirmed only via web information (official docs/repos/third-party health checks).
2. Identifiers.org and PubDictionaries have Claude connector connection history, but their MCP endpoints are not yet confirmed against primary sources and are therefore held.
3. GrEBI and the self-hosted table were not individually re-verified this round; their previous state is retained. Endpoint probing and official-path confirmation are recommended next round.
4. No claim of covering "all MCPs worldwide." Discovery sources: official docs/repos, papers (PMC/bioRxiv), Glama/mcpservers.org/MCPBeat, Claude connector directory, GitHub.