pm-search

name	pm-search
description	Search PubMed for biomedical literature by keywords. Returns structured results with PMID, title, authors, journal, date, DOI. Use when the user wants to find papers on a topic.
argument-hint	[search keywords]

PubMed Basic Search

Search PubMed for papers using keyword(s). Returns result count and structured result list via NCBI E-utilities API.

Arguments

$ARGUMENTS contains the search keyword(s) in English or Chinese.

Steps

1. Navigate

Use mcp__chrome-devtools__navigate_page:

• url: https://pubmed.ncbi.nlm.nih.gov/?term={URL_ENCODED_KEYWORDS}&size=20
• This shows the search results page to the user in the browser.

2. Search + extract results (single evaluate_script)

Replace YOUR_KEYWORDS with the actual search terms from $ARGUMENTS:

async () => {
  const query = "YOUR_KEYWORDS";
  const page = 1, size = 20;
  const retstart = (page - 1) * size;

  // E-utilities esearch: get PMID list
  const searchResp = await fetch(
    `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=${encodeURIComponent(query)}&retmax=${size}&retstart=${retstart}&retmode=json&sort=relevance`
  );
  const searchData = await searchResp.json();
  const ids = searchData.esearchresult?.idlist || [];
  const total = parseInt(searchData.esearchresult?.count || '0');
  const queryTranslation = searchData.esearchresult?.querytranslation || '';

  if (ids.length === 0) return { query, total: 0, results: [] };

  // E-utilities esummary: batch get metadata
  const sumResp = await fetch(
    `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=${ids.join(',')}&retmode=json`
  );
  const sumData = await sumResp.json();

  const results = ids.map((id, i) => {
    const r = sumData.result?.[id] || {};
    const doi = (r.articleids || []).find(a => a.idtype === 'doi')?.value || '';
    return {
      n: retstart + i + 1,
      pmid: id,
      title: r.title || '',
      authors: (r.authors || []).map(a => a.name).join(', '),
      journal: r.fulljournalname || '',
      source: r.source || '',
      pubdate: r.pubdate || '',
      volume: r.volume || '',
      issue: r.issue || '',
      pages: r.pages || '',
      doi,
      pubtype: (r.pubtype || []).join(', ')
    };
  });

  return { query, queryTranslation, total, page, size, results };
}

3. Report

Present results as a numbered list:

Searched PubMed for "$ARGUMENTS": found {total} results (page {page}, showing {size} per page).

1. {title}
   PMID: {pmid} | DOI: {doi}
   Authors: {authors}
   Journal: {journal} ({pubdate}) | Vol {volume}({issue}):{pages}

2. ...

4. Follow-up

When the user wants to:

• Open a paper: use pm-paper-detail with the PMID
• See more results: use pm-navigate-pages to go to next page
• Get full text: use pm-fulltext with the PMID
• Export to Zotero: use pm-export with the PMID(s)

Sort options

The sort parameter in esearch accepts:

• relevance (default, best match)
• date (most recent first)
• pub_date (publication date)
• first_author (alphabetical by first author)
• journal (alphabetical by journal)

To change sort, modify the sort= parameter in the esearch URL.

Pagination

• retstart: 0-indexed offset (page 1 = 0, page 2 = 20, page 3 = 40, ...)
• retmax: results per page (default 20, max 10000)
• Total pages: ceil(total / size)

Notes

• This skill uses 2 tool calls: navigate_page + evaluate_script
• E-utilities API is public, no authentication needed
• Results are fetched via API, not DOM scraping, for reliability