pubmed-search

by FreedomIntelligence

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SKILL.md About

---
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

```python
from Bio import Entrez
Entrez.email = "medclaw@freedomai.com"
```

### 2. Search PubMed

```python
# 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

```python
# 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?"