pubmed

name: pubmed description: PubMed — NCBI's biomedical literature database (>35M citations). Keyword search inline, or batch-fetch full title + structured abstract + authors + DOI for a known list of PMIDs. Use for medical / biological literature lookup, citation resolution, or building an abstract corpus for downstream NLP. Honors NCBI_API_KEY env var. license: Unknown metadata: skill-author: VenusFactory2 (download_pubmed_abstracts_by_pmids adapted from Google DeepMind).

Overview

Two complementary tools: existing query_pubmed_tool (keyword search, returns small JSON inline) + new download_pubmed_abstracts_by_pmids (batch-fetch full abstracts by PMID list, one efetch XML call, saves normalized JSON to disk).

Project Tools (VenusFactory2)

Tool	Args	Returns	Description
query_pubmed	`query` (text), `max_results` (default 5, max 50), `max_content_length`	JSON list of paper records inline	Keyword search; small payload to agent.
download_pubmed_abstracts_by_pmids	`pmids` (list of PMID strings, max 200 per call), `out_path` (JSON file path), `timeout` (default 60s)	rich JSON envelope; saved file is `{requested_pmids, articles[]}` where each article has `pmid, title, authors, journal, year, doi, abstract` (structured abstracts join `Label: body` segments with newlines)	Batch-fetch full abstracts + metadata by PMID via efetch.

When to Use Each

Goal	Tool
"Find papers about X"	`query_pubmed`
"Get me the full abstracts for these 50 PMIDs"	`download_pubmed_abstracts_by_pmids`
Build a corpus for fine-tuning a biomedical NLP model	`query_pubmed` → collect PMIDs → batch fetch via `download_pubmed_abstracts_by_pmids`
Resolve a citation string to a PMID	(out of scope here — use the search tool with the citation text, parse hits)

Output Schema for `download_pubmed_abstracts_by_pmids`

{
  "requested_pmids": ["34265844", "37962427", ...],
  "articles": [
    {
      "pmid": "34265844",
      "title": "Highly accurate protein structure prediction with AlphaFold",
      "authors": ["Jumper J", "Evans R", ...],
      "journal": "Nature",
      "year": "2021",
      "doi": "10.1038/s41586-021-03819-2",
      "abstract": "Proteins are essential to life..."
    },
    ...
  ]
}

Structured abstracts (with BACKGROUND:/METHODS:/RESULTS:/CONCLUSIONS: sections) are joined with \n and each section is prefixed by its label.

Rate Limiting

Without NCBI_API_KEY: 3 req/s.
With NCBI_API_KEY (free; get at https://www.ncbi.nlm.nih.gov/account/settings/): 10 req/s.
download_pubmed_abstracts_by_pmids does ONE efetch for the whole batch — much friendlier than N individual fetches.
Hard cap: 200 PMIDs per call (split into chunks if you need more).

Common Mistakes

PMID as int: the tool accepts strings; pass "34265844", not 34265844. (Int is coerced to str internally but use string defensively.)
>200 PMIDs in one call: returns ValidationError. Split into chunks of ≤200.
Missing abstract: not all PubMed records have abstracts (older / non-research / book chapters). The abstract field will be null for those.
Confusing PMID with PMCID: PMID is a number (e.g. 34265844); PMCID is PMC<number> (e.g. PMC8371605). This tool uses PMIDs.