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

pubmed-search

GitHub

用于在PubMed中搜索科学文献，支持按主题查找论文、获取最新出版物及引用信息。提供详细的执行步骤，包括设置Entrez、搜索、获取文章详情（标题、作者、摘要等）及格式化输出，并支持高级查询模式。

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

Trigger Scenarios

查找特定主题的论文获取某领域的最新出版物查询参考文献或引用了解某话题的研究现状

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