Skip to content
Agentmart
Submit a tool

pubmed-stream

Search PubMed and PMC, read full texts, map evidence and build Obsidian knowledge graphs

Connector by melhzy · GitHub account verified by the MCP Registry

IndexedMITLocal (stdio)
Write a review

Chalk Labs

Need help deploying pubmed-stream?

Chalk Labs sets up agents like this inside real teams: connected to your tools, tested on your data, with a human in the loop where it matters.

Book a call

Install

Works with Claude Code, Codex, VS Code, Cursor, Windsurf, Claude Desktop. Read the repository before you give any tool access to your data.

npx agentmarket install connector/melhzy-pubmed-stream

Asks which of your tools to add it to (Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI, Claude Desktop) and shows the change first. See https://agentmart.dev/cli.

Get the weekly diff

The weekly diff: one email a week with new agent tools, notable updates and grade changes, plus security alerts for tools you follow. Double opt-in, one-click unsubscribe.

We use your email only for this newsletter. Privacy

About

Search PubMed and PMC, read full texts, map evidence and build Obsidian knowledge graphs

Reviews

Write a review

No reviews yet. Installed it? Reviews come from verified installers only. How reviews work

Permissions

What this server can do and what it asks for, from its tool list, install config and code. Checked Oct 25, 2026.

Tools
2 read · 3 write · 0 delete · 4 not yet classified
Secrets
1 (API keys, tokens or passwords)
Install scripts
None found
Runs as
Python package

Tools by what they do 9

Read from the source code; the running server may list different tools.

Read 2 · Look things up without changing anything.

  • read_article
  • search_pmc

Write 3 · Create, change, send or run things.

  • build_knowledge_graph
  • download
  • export_citations

Not yet classified 4 · We could not tell from the name and description.

  • fetch_abstracts
  • list_articles
  • most_cited
  • neighborhood

Secrets and settings it asks for

Secrets: values you paste in that let it act as you.

  • NCBI_API_KEY

Other settings (environment variables or headers).

  • NCBI_EMAIL

Network hosts it talks to 15

  • account.ncbi.nlm.nih.gov · found in code
  • api.infini-gram.io · found in code
  • api.semanticscholar.org · found in code
  • doi.org · found in code
  • eutils.ncbi.nlm.nih.gov · found in code
  • github.com · found in code
  • infini-gram.io · found in code
  • linkeddiscoveries.ncbi.nlm.nih.gov · found in code
  • melhzy.github.io · found in code
  • meshb.nlm.nih.gov · found in code
  • obsidian.md · found in code
  • ollama.com · found in code
  • pmc.ncbi.nlm.nih.gov · found in code
  • pubmed.ncbi.nlm.nih.gov · found in code
  • semanticscholar.org · found in code

Files it touches

  • Your home directory (~)
  • ~/.pubmed-stream.json
  • Any path the agent passes to its tools

Tools (9)

Read from the source code; the running server may differ. Descriptions are the server’s own words; hidden characters are shown as [U+…].

  • build_knowledge_graph

    Link a study's searches and key papers into an Obsidian vault, kg_<topic>, with notes for papers, MeSH concepts and searches. Later calls with the same topic add to it; refresh reruns every recorded search and key paper.

  • download

    Download the newest matches of a PMC search as JSON files, one per article, into <output_dir>/<folder named after the search>. Existing files are skipped. Articles whose publishers forbid downloading are counted as unavailable.

  • export_citations

    Write the downloaded articles, or chosen ones, as a BibTeX or RIS file that Zotero, EndNote or Mendeley imports. Give the researcher the file's path.

  • fetch_abstracts

    Save the abstracts of a PubMed search's newest matches, including articles whose full text is not free in PMC, into the same folder download uses. list_articles then shows them marked [abstract only]. Use it when search_pmc reports many more articles in PubMed than in PMC.

  • list_articles

    Downloaded articles, newest first, each once: identifiers, year, journal, title and length. With ids, only those articles; with abstracts, their abstracts too. Scan titles first, then read the abstracts of the articles that bear on the question.

  • most_cited

    The works the downloaded articles cite most: the field's foundations, and good key papers for the neighborhood tool.

  • neighborhood

    Similar, citing and cited papers of one PubMed article, with counts of reviews, retractions and NIH funding, and the retracted papers named. Saved as <output_dir>/neighborhood_<pmid>/neighborhood.json.

  • read_article

    The full text of one downloaded article. With find, only the paragraphs that contain the term, numbered, which is usually enough; without it, the text up to max_chars.

  • search_pmc

    Count a PubMed Central search and list its newest matches, without downloading. Use PubMed field tags: [Title], [Title/Abstract], [mh] for MeSH, "open access"[filter]. Plain words match anywhere in the full text, so most results are off topic.

Compare and alternatives

    Featured in

    Signals

    Stars
    0
    Forks
    0
    Open issues
    2
    Weekly downloads
    780
    Last commit
    Oct 23, 2026 (7 days ago)
    Last release
    Oct 23, 2026 (7 days ago)
    Last package publish
    Oct 23, 2026 (7 days ago)

    From GitHub (fetched Oct 24, 2026) and the package registry.

    Details

    Registry name
    io.github.melhzy/pubmed-stream
    Version
    0.4.4
    Auth
    API key
    Packages
    pypi pubmed-stream
    License
    MIT
    Repository
    github.com/melhzy/pubmed-stream
    Website
    melhzy.github.io/pubmed-stream/
    First seen
    Oct 24, 2026
    Last checked
    Oct 24, 2026
    Source
    Official MCP Registrygithub-graphql

    Done for you

    Rather not set it up yourself?

    Chalk Labs scopes, builds and runs agents for your team: the task audit, the eval harness, the integrations and the weekly ops report. Fixed scope, priced before we start.

    See how we build AI agents →Read the case studies

    Chalk Labs is a two-founder AI and growth studio. We build AI agents, CRMs and MVPs for Web3 and AI companies, and have shipped 50+ product and token launches.

    launches shipped
    50+
    launches shipped
    media placements
    500+
    media placements
    founders on every account
    2
    founders on every account

    Press we've placed: Forbes · CoinDesk · Decrypt · Cointelegraph · The Block

    Rahil Jain, Co-founder, Chalk Labs. Ex-Goldman Sachs engineer. You talk to the person who builds it.

    Get pubmed-stream running in your business

    Tell us what you want to automate. A founder replies within one working day with a plan, not a pitch deck.

    Goes to the Chalk Labs founders, not the newsletter. Privacy

    Need help deploying pubmed-stream?

    CallGet help
    Cite this page

    pubmed-stream MCP server. Agent Mart. https://agentmart.dev/connectors/melhzy-pubmed-stream (last updated 2026-10-24)