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PubMed & PubTator3

Search 35M+ biomedical articles and preprints. Find literature by gene, disease, chemical, keyword, or variant.

Key Tools

pubmed_search_articles — Search literature

{
  "name": "pubmed_search_articles",
  "arguments": {
    "query": "myasthenia gravis treatment",
    "genes": ["CHRNE", "RAPSN"],
    "diseases": ["myasthenia gravis"],
    "chemicals": ["immunoglobulin"],
    "keywords": ["autoimmune"],
    "max_results": 20
  }
}

Arguments:

  • query (str): Free-text search term
  • genes (list, optional): Filter by NCBI gene symbols (AND logic)
  • diseases (list, optional): Filter by disease names
  • chemicals (list, optional): Filter by chemical/drug names
  • keywords (list, optional): Filter by subject headings
  • max_results (int, default 20): Results to return

Returns: Array of articles with PMID, title, abstract, authors, publication year, DOI

pubmed_get_article — Get full article details

{
  "name": "pubmed_get_article",
  "arguments": {
    "pmid": "35641234",
    "include_full_text": true
  }
}

Arguments:

  • pmid (str): PubMed ID
  • include_full_text (bool, optional): Fetch full article text if available

Returns: Article metadata including abstract, full text, MeSH terms, authors, affiliations

pubmed_search_preprints — Search bioRxiv/medRxiv

{
  "name": "pubmed_search_preprints",
  "arguments": {
    "query": "SARS-CoV-2 immune response",
    "max_results": 10
  }
}

Returns: Preprints from bioRxiv and medRxiv (peer-review pending)

Use Cases

Literature Review by Gene

Find all papers mentioning TP53 in cancer:

{
  "name": "pubmed_search_articles",
  "arguments": {
    "genes": ["TP53"],
    "diseases": ["cancer"],
    "max_results": 50
  }
}

Mechanistic Deep Dive

Find papers on immune tolerance mechanisms in autoimmune disease:

{
  "name": "pubmed_search_articles",
  "arguments": {
    "query": "immune tolerance regulatory T cells",
    "diseases": ["autoimmune"],
    "max_results": 30
  }
}

Safety Signals

Find adverse event reports for a drug:

{
  "name": "pubmed_search_articles",
  "arguments": {
    "chemicals": ["your-drug-name"],
    "keywords": ["adverse effect", "toxicity"],
    "max_results": 20
  }
}

Recent Developments

Get latest papers on a topic (combine with OpenTargets for targets):

{
  "name": "pubmed_search_articles",
  "arguments": {
    "query": "complement inhibitor immunotherapy 2025",
    "max_results": 20
  }
}

Workflow: Full Literature Review

  1. Find target papers (search by gene + disease)
  2. Get full text (use pmid to fetch complete article)
  3. Extract key data (mechanisms, results, conclusions)
  4. Cross-reference citations (follow citation trails)
  5. Identify gaps (what's NOT being studied?)

Notes

  • Coverage: 1966–present (MEDLINE indexed articles)
  • Preprints: bioRxiv (life sciences), medRxiv (medicine) — not yet peer-reviewed
  • MeSH tagging: Automated by NLM (consistent vocabularies)
  • Full text availability: ~30% of articles; depends on publisher + open access
  • Citation linking: Search results include citation counts and related articles

Rate Limits

  • No API key required
  • Generous public limits (1,000+ req/day)
  • Results cached (30-day TTL)

Examples

Example 1: Find papers on Myasthenia Gravis immunotherapy

{
  "method": "tools/call",
  "params": {
    "name": "pubmed_search_articles",
    "arguments": {
      "query": "",
      "diseases": ["myasthenia gravis"],
      "keywords": ["immunotherapy", "treatment"],
      "max_results": 15
    }
  }
}

Example 2: Get full article details for mechanistic understanding

{
  "method": "tools/call",
  "params": {
    "name": "pubmed_get_article",
    "arguments": {
      "pmid": "35641234",
      "include_full_text": true
    }
  }
}

Example 3: Find recent preprints on novel therapeutic targets

{
  "method": "tools/call",
  "params": {
    "name": "pubmed_search_preprints",
    "arguments": {
      "query": "novel drug target autoimmune disease 2025",
      "max_results": 20
    }
  }
}