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

pubmed-search

GitHub

通过 BioPython 调用 NCBI PubMed API 搜索科学文献，提取论文标题、作者、摘要等详细信息，并支持高级查询过滤。

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

触发场景

查找特定主题的论文检索最新发表的研究成果获取参考文献或引用信息了解某领域的研究现状

安装

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

更多选项

非标准路径

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

不安装直接使用

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