MCP.Market

PubMed Search MCP server

by u9401066·io.github.u9401066/pubmed-search-mcp·v0.8.0·28 stars
No reviews yet

Multi-source biomedical literature search: PubMed, Europe PMC, OpenAlex, full text, citations

B75/100grade B
Write a reviewInstall
What users say
No reviews yet
Be the first
Safety scan
B75/100

full report

Adoption
Established

28 stars454 downloads/wk

Reviews

Write one

Nobody has reviewed PubMed Search yet.

If you have run it, two minutes of your experience saves the next person an afternoon.

PubMed Search tools (41, 2 write)

write = sends, deletes, buys or posts

Read from the package source without running it. The installed server may list more.

  • analyze_search_query

    Analyze a search query without executing the search.

  • build_citation_tree
  • build_research_chronicle
  • configure_institutional_access
  • convert_icd_mesh

    Query the curated ICD/MeSH crosswalk in one explicit direction.

  • delete_pipelinewrite action

    Permanently delete a saved pipeline configuration and execution history.

  • diagnose_institutional_access

    Diagnose why institutional fulltext access succeeds or fails for an article.

  • fetch_article_details

    Fetch detailed information for one or more PubMed articles.

  • find_citing_articles

    Find articles that cite a given PubMed article. Uses PubMed Central's citation data to find papers that reference this article.

  • find_related_articles

    Find articles related to a given PubMed article. Uses PubMed's "Related Articles" feature to find similar papers.

  • generate_search_queries
  • get_article_figures

    Get structured figure metadata (label, caption, image URL) and PDF links from a PMC Open Access article.

  • get_article_references

    Get the references (bibliography) of a PubMed article.

  • get_citation_metrics

    Get citation metrics from NIH iCite for articles.

  • get_compound_details

    Get detailed information about a compound by PubChem CID.

  • get_compound_literature

    Get PubMed articles linked to a compound.

  • get_fulltext

    🔥 Enhanced multi-source fulltext retrieval.

  • get_gene_details

    Get detailed information about a gene by NCBI Gene ID.

  • get_gene_literature

    Get PubMed articles linked to a gene.

  • get_institutional_link

    Generate institutional access link (OpenURL) for an article.

  • get_pipeline_history

    Get execution history for a saved pipeline.

  • get_text_mined_terms

    Get text-mined annotations from Europe PMC.

  • list_pipelines

    List all saved pipeline configurations.

  • list_resolver_presets

    List available institutional link resolver presets.

  • load_pipeline

    Load a pipeline configuration for review or editing.

  • prepare_export

    Export citations to reference manager formats.

  • prepare_figure_search
  • read_research_chronicle

    Read stored Research Chronicles: load, list, diff, narrate, analyze, compare.

  • read_session

    Read session data through one schema-exact discriminated request.

  • save_literature_notes

    Save searched articles as guided local wiki/Foam/Markdown notes.

  • save_pipeline

    Save a pipeline configuration for later reuse.

  • schedule_pipeline

    Schedule a saved pipeline for periodic execution.

  • search_biomedical_images
  • search_clinvar

    Search ClinVar for clinical variants.

  • search_compound

    Search PubChem for chemical compounds.

  • search_gene

    Search NCBI Gene database for gene information.

  • test_institutional_access

    Test your institutional link resolver configuration.

  • unified_search
  • unschedule_pipelinewrite action

    Remove the active schedule for a saved pipeline.

  • validate_pico_plan

    Validate agent-provided P/I/C/O and return a runnable PICO pipeline.

  • verify_reference_list

    Verify a plain-text reference list against PubMed evidence.

Public scan report

scanner v0.1.10 · 2026-10-27 · same rubric, same numbers if you re-run it

1 medium
  • Code scan230 source files scanned20/25
  • –Live reliabilityno gateway calls yet and no remote to proben/a
  • –Tool poisoningtools not inspected (local package is not executed); not countedn/a
  • Auth qualitystatic API keys via environment variables6/15
  • Maintenancelast push 7 days ago15/15
  • Maintainer identityregistry namespace matches repository owner; GitHub account older than a year8/10

Findings (1)

  • mediumsubprocess with shell=Trueexec.shell-true
    pubmed_search_mcp-0.8.0/pyproject.toml: …d it "B603", # subprocess without shell=True — scripts intentional "B311", # p…
Overall 75/100. Components that don't apply are left out of the denominator. Any critical finding is an F.RubricAppeal a findingJSON

How PubMed Search compares

Against every graded Web search MCP server, from our own scans and uptime checks. Updated after each scan run.

Safety score
75/100
higher than 45% of 3,472 Web search servers
Tools
41
the typical Web search server has 5
Tools that change things
5%
typical: 0%. Fewer write tools means less an agent can break
GitHub stars
28
more than 90% of 1,783 Web search servers
Downloads a week
454
more than 84% of 816 Web search servers with a package

What its tools let an agent do: 36 read · 3 create · 1 change · 1 delete

Install PubMed Search in Claude Code, Cursor or VS Code

claude mcp add pubmed-search-mcp -- uvx pubmed-search-mcp
Add to Cursor

What the publisher says

From the PubMed Search repository's README, as published. We do not edit it. Read it on GitHub

PubMed Search MCP

<!-- mcp-name: io.github.u9401066/pubmed-search-mcp -->

Professional Literature Research Assistant for AI Agents - More than just an API wrapper

A Domain-Driven Design (DDD) based MCP server that serves as an intelligent research assistant for AI agents, providing task-oriented literature search and analysis capabilities.

✨ What's Included:

  • 🔧 41 MCP Tools - Streamlined PubMed, Europe PMC, CORE, NCBI database access, and the versioned Research Chronicle
  • 🛡️ Multi-Agent Service Mode - Deploy once and serve many agents: per-tenant sessions, caches, and artifacts, bearer-token auth, and per-tenant fair-share limits. See DEPLOYMENT.md
  • 🖼️ OA Figure Extraction - Pull figure captions, direct image URLs, and PDF links from PMC Open Access articles
  • 📘 Docs Site - Browse the complete language-switchable handbook: user workflows, architecture, 41-tool reference, pipeline tutorials, source/broker contracts, integrations and operations, security, and deployment at u9401066.github.io/pubmed-search-mcp
  • 📖 GitHub Wiki - GitHub-native mirror of the same canonical documentation at github.com/u9401066/pubmed-search-mcp/wiki
  • 📚 26 Claude Skills - Ready-to-use workflow guides for AI agents (Claude Code-specific)
  • 📖 Copilot Instructions - VS Code GitHub Copilot integration guide
  • Research automation - Scheduled pipeline diffs/local notifications, Chronicle rebuild summaries, multi-seed citation snowballing, and opt-in session deduplication with options="exclude_seen".

🌐 Language: English | 繁體中文

📘 Documentation Map: README is the quick project entry point. Use the Docs Site for the best reading experience, the GitHub Wiki for GitHub-native navigation, and source docs for edits: User guide | Advanced workflows | Capability-first guide | Unified Search architecture | 41-tool quality audit | 60-repository academic retrieval landscape | Provider data planes | BioMCP architecture analysis | Developer guide | Complete index

Documentation map · Maintenance scripts

Research automation and portable installation — v0.8.0

Shortened. The full README is on GitHub.

Nothing above is checked by us. What we check is on the safety report.

PubMed Search: common questions

Is PubMed Search MCP server safe?
Mostly: it is graded B (75/100). Read the PubMed Search safety report
How do I install PubMed Search?
It runs on your machine. Copy the Claude Code, Cursor, VS Code or Claude Desktop config from the install section.
Does PubMed Search need an API key?
Yes. The registry entry asks for NCBI_API_KEY.
Is PubMed Search maintained?
The last commit was 13 days ago (2026-10-20). The latest release is v0.8.0.
What can I use instead of PubMed Search?
Servers from other publishers that do the same job: Pubmed MCP server, Arxiv MCP server and obsei MCP server.
How does PubMed Search compare with other Web search MCP servers?
safety score 75/100 (higher than 45% of 3,472 Web search servers); tools 41 (the typical Web search server has 5); tools that change things 5% (typical: 0%. Fewer write tools means less an agent can break). Full comparison.

Alternatives to PubMed Search

Same job from other publishers: the closest match first, then the best rated.

  • Pubmed
    Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms.
    More from cyanheads →
    A
  • Arxiv
    Search arXiv papers, download full text, semantic search, citation graphs, and alerts via MCP.
    A
  • obsei
    Self-hosted customer feedback with PII stripped at ingest: search, stats and themes with citations.
    A
  • Zoteus
    Zotero MCP server for Claude and ChatGPT: search, citations, safe writes, PDF passages and pages.
    A
  • Misakanet
    Failure-memory layer for coding agents: search evidence-rated failure lessons by error text.
    A
PubMed Search vs PubmedPubMed Search vs Arxiv