PubMed Advanced Search

Construct and execute a PubMed query using field qualifiers, boolean operators, and filters based on the user's natural language description.

Arguments

$ARGUMENTS is a natural language description of the search criteria, e.g.:

• "搜索 Zhang Wei 在 Nature 上发表的关于 CRISPR 的综述"
• "Find reviews about CAR-T therapy published after 2020 with IF>10"
• "Search for clinical trials on COVID-19 vaccines in 2023-2024"

Step 1: Parse search criteria into PubMed query syntax

Map the user's intent to PubMed field tags:

| Field | Tag | Example | |-------|-----|---------| | Author | [AU] | Zhang W[AU] | | First Author | [1AU] | Smith J[1AU] | | Title words | [TI] | CRISPR[TI] | | Title/Abstract | [TIAB] | machine learning[TIAB] | | Journal | [TA] | Nature[TA] | | MeSH term | [MESH] | Neoplasms[MESH] | | Date range | [DP] | 2020/01:2025/12[DP] | | Publication type | [PT] | Review[PT], Clinical Trial[PT], Meta-Analysis[PT], Systematic Review[PT], Randomized Controlled Trial[PT] | | Affiliation | [AD] | Harvard[AD] | | Language | [LA] | English[LA] | | All fields | [ALL] | cancer[ALL] |

Boolean operators: AND, OR, NOT (must be uppercase).

Examples:

• "Zhang Wei 在 Nature 上的 CRISPR 综述" → Zhang W[AU] AND CRISPR[TI] AND Nature[TA] AND Review[PT]
• "2020年以后关于 COVID-19 疫苗的临床试验" → COVID-19 vaccine[TIAB] AND Clinical Trial[PT] AND 2020:2026[DP]
• "IF>10 的癌症免疫治疗系统综述" → cancer immunotherapy[TIAB] AND Systematic Review[PT]

Note: PubMed does not have a built-in impact factor filter. For IF filtering, search first and then the user can check journal IF manually.

Step 2: Navigate

Use mcp__chrome-devtools__navigate_page:

• url: https://pubmed.ncbi.nlm.nih.gov/?term={URL_ENCODED_QUERY}&size=20

Replace {URL_ENCODED_QUERY} with the constructed query string, URL-encoded.

Step 3: Search + extract (evaluate_script)

Same pattern as pm-search, using the constructed query:

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

  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, queryTranslation, total: 0, results: [] };

  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 || '',
      doi,
      pubtype: (r.pubtype || []).join(', ')
    };
  });

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

Step 4: Report

Advanced search: {query}
PubMed translated query: {queryTranslation}
Found {total} results (page {page}):

1. {title}
   PMID: {pmid} | DOI: {doi}
   Authors: {authors}
   Journal: {journal} ({pubdate}) | Type: {pubtype}

2. ...

Always show the queryTranslation so the user can see how PubMed interpreted the query.

Common Publication Types

| Chinese | English | PubMed tag | |---------|---------|------------| | 综述 | Review | Review[PT] | | 系统综述 | Systematic Review | Systematic Review[PT] | | Meta分析 | Meta-Analysis | Meta-Analysis[PT] | | 临床试验 | Clinical Trial | Clinical Trial[PT] | | 随机对照试验 | RCT | Randomized Controlled Trial[PT] | | 病例报告 | Case Report | Case Reports[PT] |

Notes

• This skill uses 2 tool calls: navigate_page + evaluate_script
• The key difference from pm-search is query construction — this skill translates natural language to PubMed syntax
• queryTranslation in the response shows how PubMed actually interprets the query (MeSH expansion, etc.)