Find scientific papers in PubMed by turning a research question into targeted search terms and synonyms. Collect titles, authors, abstracts, and identifiers into a structured paper list ready for relevance evaluation.
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PubMed search with keyword optimization, result parsing, and metadata extraction
实测评分 未实测
查看安装方法安装前可以查看交给 AI 代理的指令内容。
Search PubMed for scientific literature using optimized queries. Extract metadata and prepare papers for relevance evaluation.
Core principle: Cast a wide enough net to find relevant papers, but use targeted keywords to keep results manageable.
Use this skill when:
Extract:
Boolean operators:
Example queries:
"BTK inhibitor"[Title/Abstract] AND selectivity[Title/Abstract]
("kinase inhibitor" OR "protein kinase") AND (selectivity OR "off-target")
"ibrutinib"[Title/Abstract] AND ("IC50" OR "inhibitory concentration")
Field tags:
[Title/Abstract] - search title and abstract only[Title] - title only (more precise)[Author] - specific author[Journal] - specific journal[Date] - date rangeAPI endpoint:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?\
db=pubmed&\
term=YOUR_QUERY&\
retmax=100&\
retmode=json&\
sort=relevance
Parameters:
db=pubmed - search PubMed databaseterm= - your query (URL encode spaces and special chars)retmax=100 - max results (start with 100)retmode=json - return JSONsort=relevance - most relevant first (or pub_date for newest)Example bash:
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=BTK+inhibitor+selectivity&retmax=100&retmode=json&sort=relevance"
Response format:
{
"esearchresult": {
"count": "156",
"retmax": "100",
"idlist": ["12345678", "87654321", ...]
}
}
API endpoint:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?\
db=pubmed&\
id=12345678,87654321&\
retmode=json
Extract from response:
articleids)Getting DOI from PMID:
"articleids": [
{"idtype": "pubmed", "value": "12345678"},
{"idtype": "doi", "value": "10.1234/example.2023"}
]
If DOI missing:
Create list of paper objects:
[
{
"pmid": "12345678",
"doi": "10.1234/example.2023",
"title": "Selective BTK inhibitors for autoimmune diseases",
"authors": ["Smith J", "Doe A", "Johnson B"],
"journal": "Nature Chemical Biology",
"year": "2023",
"abstract": "We developed a series of...",
"source": "pubmed_search"
}
]
Rate limits (CRITICAL - shared across all processes/subagents):
delay_seconds = (num_parallel / rate_limit) + safety_marginEmpty results:
Too many results (>500):
After search completes:
initial-search-results.jsonevaluating-paper-relevance skillpapers-reviewed.json (use DOI as key, fallback to PMID)| Task | Command |
|---|---|
| Search PubMed | curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=QUERY&retmax=100&retmode=json" |
| Get metadata | curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=PMID1,PMID2&retmode=json" |
| URL encode query | Replace spaces with +, special chars with %XX |
| Narrow results | Use AND, add field tags, more specific terms |
| Broaden results | Use OR, remove field tags, add synonyms |
Too narrow: Only 5 results → Use OR, remove constraints Too broad: 5000 results → Add AND terms, use field tags Missing abstracts: Use efetch instead of esummary for full abstract text DOI not found: Many older papers lack DOI - use PMID as fallback Rate limiting: Add 500ms delays (single agent) or longer (parallel subagents sharing rate limit)
After completing search:
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Turn a broad research idea into clear, testable questions. Compare familiar and less conventional approaches, structure the selected question around its population and methods, and assess variables, feasibility, and potential theoretical contributions.
中文简介正在准备中。当前显示英语简介。
Helps build a research framework by comparing theories, mapping relationships between variables, and deriving testable hypotheses. Explores less conventional options, examines weaknesses and competing explanations, and produces diagrams with anticipated reviewer objections.
中文简介正在准备中。当前显示英语简介。
Clarify the philosophical assumptions behind a research project and check whether they fit the proposed methods. Get a reasoned research stance, draft proposal wording, and guidance for explaining how the researcher's background and values shape the study.
中文简介正在准备中。当前显示英语简介。
Plan and draft academic papers through specialized agent roles covering literature, arguments, citations, and review. Get chapter guidance, revision roadmaps, Traditional Chinese and English abstracts, and documents formatted as LaTeX, DOCX, PDF, or Markdown.
中文简介正在准备中。当前显示英语简介。
Turn a detailed outline into a philosophy or interdisciplinary manuscript. Draft chapters with repeated quality reviews, check terminology and arguments across sections, and prepare the manuscript, evaluation reports, abstract, and metadata for submission.
中文简介正在准备中。当前显示英语简介。
Simulate academic peer review through five reviewer roles tailored to the paper's field. Receive separate critiques, an editorial decision, and a prioritized revision roadmap, or check whether a revised manuscript addresses earlier comments.
中文简介正在准备中。当前显示英语简介。