Pubmed Search

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

5. Advanced searches

Support these query patterns:

• "CRISPR"[Title] AND "delivery"[Title] — title-specific
• "2026"[Date - Publication] — date filter
• "Nature"[Journal] — journal filter
• review[Publication Type] — type filter

6. Follow-up suggestions

After showing results, suggest:

• "Want me to summarize any of these papers?"
• "Should I search with different keywords?"
• "Want me to find related papers to any of these?"

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: cheatthegod
• Source: cheatthegod/BioHermes
• License: MIT

Install and usage instructions live in the source repository linked above.