Pubtator
PubTator 3 MCP — biomedical entity search, literature search with entity
MCP server · by pipeworx-io
About
Pubtator is an MCP server published by pipeworx-io. Marketplaces we read that list it: 1 (Official MCP Registry). We first saw it on 2026-10-11 and have recorded no change since. As of our marketplace pass on 2026-10-14.
What it asks for
- Runs remotely
None of the marketplaces we read publishes its tools or the settings it asks for.
What it declares, asks for and runs, in full
Only install plugins from developers you trust. We list what marketplaces publish and do not test plugins.
Works with
- Claude Code
- Codex
- Cursor
- VS Code
- Copilot CLI
A one-click link opens the client, which asks you to confirm before it adds the server.
From the marketplaces that list it and the MCP transport it declares, as each client documents them. We do not test plugins.
Connect
Commands and configs built only from what its marketplaces declare. We do not run them for you and do not test plugins.
As a remote MCP server
Built from what Official MCP Registry declares.
claude mcp add --transport http pubtator https://gateway.pipeworx.io/pubtator/mcp[mcp_servers.pubtator]
url = "https://gateway.pipeworx.io/pubtator/mcp"{
"mcpServers": {
"pubtator": {
"url": "https://gateway.pipeworx.io/pubtator/mcp"
}
}
}Where it is published
| Marketplace | Status | Version | Figures | Verified | First seen |
|---|---|---|---|---|---|
| Official MCP Registry (Open the registry record) | Listed | 0.1.0 | Forks (GitHub): 0 Stars (GitHub): 0 |
Not marked |
Each figure is the marketplace's own and is never added up across marketplaces. A marketplace that publishes no figure shows none: no number is not zero.
What changed
Nothing has moved on this plugin since we started watching it.
Similar plugins
Products whose own names, descriptions, tools and skills are closest in meaning to this one, on every marketplace we read. Closeness is ranked within this list only.
-
pubcrawl io.github.nickjlamb/pubcrawl
PubMed & Europe PMC literature search, US/UK drug labelling, and clinical trials for AI assistants.
-
pubmed-mcp-server io.github.cyanheads/pubmed-mcp-server
Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms.
-
50+ biomedical data sources in one MCP server — PubMed, ClinVar, gnomAD, KEGG, and more
-
Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.
-
arXiv, PubMed, Crossref and OpenAlex scholarly metadata.
-
biolit io.github.rachadele/biolit
LLM-assisted biomedical literature screening and extraction for PubMed, GEO, and preprints.
-
Auditable MCP server for PubMed, Europe PMC, ClinicalTrials.gov, and bioRxiv/medRxiv queries
-
mcp-scholaris io.github.penny4nonsense/mcp-scholaris
Academic paper search and retrieval via arXiv, Semantic Scholar, PubMed, Unpaywall.
-
ebi-search-mcp io.github.mrfentmen/ebi-search-mcp
EBI Search API: search EMBL-EBI biomedical databases.
-
lit-mcp io.github.gauravfs-14/lit-mcp
MCP server for academic literature databases (arXiv, DBLP) to accelerate research using LLMs.
Similar plugins by marketplace
The same question asked of one marketplace at a time: is there an analog of this plugin there?
Has a listing on Claude Code: claude-plugins-community (5)
-
Forensic-grade PubMed research engine for Claude Code. Search 36M+ biomedical articles with PICO-structured queries, synthesize evidence with GRADE confidence ratings, critically…
-
197 ready-to-use life sciences skills that turn Claude into a domain expert for genomics, proteomics, drug discovery, biostatistics, scientific computing, and scientific writing…
-
nodebench io.github.HomenShum/nodebench
260 MCP tools across 49 domains. AI Flywheel, quality gates, research, web scraping.
-
Zero-config MCP server for searchable documentation. SQLite or PostgreSQL.
-
mcp-server io.github.cap-js/mcp-server
Model Context Protocol (MCP) server for AI-assisted development of CAP applications.
Has a listing on Claude Code: claude-plugins-official (5)
-
mcp-server io.github.cap-js/mcp-server
Model Context Protocol (MCP) server for AI-assisted development of CAP applications.
-
mdk-mcp-server io.github.SAP/mdk-mcp-server
Model Context Protocol (MCP) server for AI-assisted development of MDK applications.
-
MCP server for terminal commands, file operations, and process management
-
Connect Claude to a private MCP server through an Anthropic MCP tunnel. The /create-docker-mcp-tunnel command drives the Docker Compose quickstart end to end: certificates, proxy…
-
Search companies and contacts, enrich leads, find lookalikes, and get AI-ranked contact recommendations. Pre-built skills chain multiple ZoomInfo tools into complete B2B sales…
Has a listing on Claude: knowledge-work-plugins (5)
-
Connect to preclinical research tools and databases (literature search, genomics analysis, target prioritization) to accelerate early-stage life sciences R&D
-
Evidence-backed BioPharma research workflows over Maven Bio's drug, trial, company, and deal knowledge graph. Skills for competitive pipelines, indication landscapes, asset…
-
MCP server for terminal commands, file operations, and process management
-
Search companies and contacts, enrich leads, find lookalikes, and get AI-ranked contact recommendations. Pre-built skills chain multiple ZoomInfo tools into complete B2B sales…
-
Figma design platform integration. Access design files, extract component information, read design tokens, and translate designs into code. Bridge the gap between design and…
Has a listing on Codex: openai-curated (openai/plugins) (5)
-
General life-sciences research workflows with query routing, evidence synthesis, and optional parallel subagent analysis across genetics, omics, biology, chemistry, structure…
-
Consensus is the go-to MCP for academic research. Connect directly to 220M+ peer-reviewed papers to search, synthesize, and build structured research outputs from within your…
-
Predict structures, screen molecules and proteins, and design binders.
-
Work with Zotero from Codex: search your library, export BibTeX, insert citations, and import references through the Zotero desktop app.
-
Guided NGS intake, local execution, and public-pipeline routing for BCL, FASTQ, DNA variant, RNA-seq, single-cell, epigenomics, amplicon, and metagenomics analyses, with deeper…
Has a listing on Community GitHub marketplaces (5)
-
Scopus and more: search, full text, citation networks, journal quality, bibliometrics.
-
tooluniverse io.github.mims-harvard/tooluniverse
2,700+ scientific tools for AI scientists: life science, research, literature, and more.
-
arxiv-mcp-server io.github.blazickjp/arxiv-mcp-server
Search arXiv papers, download full text, semantic search, citation graphs, and alerts via MCP.
-
Literature, Zotero, PDF, citation, materials, and scientific image tools for research agents.
-
Section-level doc search for .md, .rst, .adoc, .ipynb, .html, .yaml, .json, and OpenAPI specs.
Has a listing on Copilot CLI: github/awesome-copilot (5)
-
Complete toolkit for building Model Context Protocol (MCP) servers in Go using the official github.com/modelcontextprotocol/go-sdk. Includes instructions for best practices, a…
-
Complete toolkit for building Model Context Protocol (MCP) servers in TypeScript/Node.js using the official SDK. Includes instructions for best practices, a prompt for generating…
-
Safe BLE diagnostics, evidence workflows, and guarded automation for AI agents.
-
Complete toolkit for building Model Context Protocol (MCP) servers in Kotlin using the official io.modelcontextprotocol:kotlin-sdk library. Includes instructions for best…
-
Figma design platform integration. Access design files, extract component information, read design tokens, and translate designs into code. Bridge the gap between design and…
Has a listing on Copilot CLI: github/copilot-plugins (5)
-
mcp-apps
Generate MCP App widgets for MCP tools. Produces self-contained HTML widgets using the MCP Apps protocol.
-
Toolkit for building Microsoft 365 Copilot declarative agents — scaffolding, JSON manifest development, and capability configuration.
-
Build Power Apps Canvas Apps using the Canvas Authoring MCP server.
-
model-apps
Build and deploy Power Apps generative pages for model-driven apps with specialist agents for planning, entity creation, and parallel code generation. Requires PAC CLI >= 2.7.0…
-
workiq
Query Microsoft 365 data with natural language — emails, meetings, documents, Teams messages, and more.
Has a listing on Cursor: cursor/plugins (5)
-
Let Grok Bot reach MCP servers on your private Tailscale network. Sign in to Tailscale to connect your tailnet; Grok Bot joins it as one tagged device and only reaches the hosts…
-
playwright-mcp io.github.microsoft/playwright-mcp
Playwright Tools for MCP
-
Track AI visibility, sentiment, and citations.
-
Search media and social mentions and pull analytics.
-
Capture, search, and organize notes and collections.
Has a listing on Docker MCP Catalog (5)
-
The Official Model Context Protocol (MCP) server for Kagi Search & other tools.
-
Dynatrace-mcp io.github.dynatrace-oss/Dynatrace-mcp
[DEPRECATED] Dynatrace MCP Server. Migrate to dynatrace-for-ai or Dynatrace Remote MCP Server.
-
MCP server providing Prometheus metrics access and PromQL query execution for AI assistants
-
Access to Rube's catalog of remote MCP servers.
-
MCP, CLI, Skills for searching and downloading academic papers from multiple sources like arXiv, PubMed, bioRxiv, etc.
Has a listing on Official MCP Registry (5)
-
pubcrawl io.github.nickjlamb/pubcrawl
PubMed & Europe PMC literature search, US/UK drug labelling, and clinical trials for AI assistants.
-
pubmed-mcp-server io.github.cyanheads/pubmed-mcp-server
Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms.
-
50+ biomedical data sources in one MCP server — PubMed, ClinVar, gnomAD, KEGG, and more
-
Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.
-
arXiv, PubMed, Crossref and OpenAlex scholarly metadata.
Found by meaning, not by shared code or a shared repository: similar plugins stay separate products, and this is not a review or a recommendation.
Is this your plugin?
Add it to your projects and prove you maintain it with a file in its repository, a file on your domain or a DNS record. You get alerts when a marketplace lists it, drops it, changes its verified mark or what it asks for, and its remote endpoint goes on monitoring as a web service.
Data comes from the Official MCP Registry (registry.modelcontextprotocol.io), CC0 1.0. Figures come from our own regular passes over the marketplaces, last read on . We publish no contact details for plugin publishers.