pubmed-search
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".
Best use case
pubmed-search is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
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".
Teams using pubmed-search should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/pubmed-search/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How pubmed-search Compares
| Feature / Agent | pubmed-search | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
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".
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# 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?"Related Skills
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