Agent Skills › Runchuan-BU/BioClaw › pubmed-search

pubmed-search

GitHub

通过BioPython调用NCBI PubMed接口，搜索并提取科学文献信息。支持按关键词、日期、期刊等高级过滤，返回标题、作者、摘要及链接，适用于查找论文和研究现状。

container/skills/pubmed-search/SKILL.md Runchuan-BU/BioClaw

Trigger Scenarios

用户要求查找特定主题的论文或出版物询问某领域的最新研究进展请求获取参考文献或引用信息提及PubMed、papers、literature、research on等关键词

Install

npx skills add Runchuan-BU/BioClaw --skill pubmed-search -g -y

More Options

Non-standard path

npx skills add https://github.com/Runchuan-BU/BioClaw/tree/main/container/skills/pubmed-search -g -y

Use without installing

npx skills use Runchuan-BU/BioClaw@pubmed-search

指定 Agent (Claude Code)

npx skills add Runchuan-BU/BioClaw --skill pubmed-search -a claude-code -g -y

安装 repo 全部 skill

npx skills add Runchuan-BU/BioClaw --all -g -y

预览 repo 内 skill

npx skills add Runchuan-BU/BioClaw --list

SKILL.md

Frontmatter

{
    "name": "pubmed-search",
    "description": "Search PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or asks about recent studies. Triggers on \"pubmed\", \"papers\", \"literature\", \"publications\", \"research on\", \"studies about\"."
}

PubMed Search

Search NCBI PubMed for scientific literature using BioPython's Entrez module.

When to Use

User asks to find papers on a topic
User wants recent publications in a field
User asks for references or citations
User wants to know the state of research on a topic

How to Execute

1. Set up Entrez

from Bio import Entrez
Entrez.email = "bioclaw@example.com"

2. Search PubMed

# Search
handle = Entrez.esearch(db="pubmed", term="CRISPR delivery methods", retmax=20, sort="date")
record = Entrez.read(handle)
handle.close()

id_list = record["IdList"]
print(f"Found {record['Count']} results, showing top {len(id_list)}")

3. Fetch article details

# Fetch details
handle = Entrez.efetch(db="pubmed", id=id_list, rettype="xml")
records = Entrez.read(handle)
handle.close()

for article in records['PubmedArticle']:
    medline = article['MedlineCitation']
    pmid = str(medline['PMID'])
    title = medline['Article']['ArticleTitle']
    
    # Get authors
    authors = medline['Article'].get('AuthorList', [])
    first_author = f"{authors[0].get('LastName', '')} {authors[0].get('Initials', '')}" if authors else "Unknown"
    
    # Get journal and year
    journal = medline['Article']['Journal']['Title']
    pub_date = medline['Article']['Journal']['JournalIssue'].get('PubDate', {})
    year = pub_date.get('Year', 'N/A')
    
    # Get abstract
    abstract_parts = medline['Article'].get('Abstract', {}).get('AbstractText', [])
    abstract = ' '.join(str(a) for a in abstract_parts)[:300]
    
    print(f"PMID: {pmid}")
    print(f"Title: {title}")
    print(f"Authors: {first_author} et al.")
    print(f"Journal: {journal} ({year})")
    print(f"Abstract: {abstract}...")
    print(f"Link: https://pubmed.ncbi.nlm.nih.gov/{pmid}/")
    print()

4. Output format for WhatsApp

*PubMed Search: "CRISPR delivery methods"*
_Found 1,234 results. Top 5:_

*1.* Lipid nanoparticle-mediated CRISPR delivery...
   _Smith J et al. — Nature (2026)_
   PMID: 12345678
   pubmed.ncbi.nlm.nih.gov/12345678

*2.* AAV-based CRISPR therapeutics: advances and challenges
   _Chen L et al. — Cell (2026)_
   PMID: 12345679
   pubmed.ncbi.nlm.nih.gov/12345679