| name | biomedical-literature-search |
| description | Search biomedical literature from PubMed and bioRxiv for research papers. Use this skill when: (1) Finding research papers on a specific topic or disease, (2) Retrieving recent preprints from bioRxiv, (3) Getting paper titles, abstracts, and metadata, (4) Literature review for drug discovery or biomedical research.
|
| license | MIT |
| category | knowledge-retrieval |
| tags | ["literature-search","pubmed","biorxiv","preprints","research-papers"] |
Biomedical Literature Search
Search PubMed and bioRxiv for biomedical research papers with titles and abstracts.
When to Use
- Find research papers on a specific biomedical topic
- Retrieve recent preprints from bioRxiv
- Get paper titles, abstracts, authors, and links
- Literature review for drug discovery or biomedical research
Workflow
PubMed Search (Keyword-based)
import requests
import xml.etree.ElementTree as ET
search_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
params = {"db": "pubmed", "term": "PD-1 inhibitor cancer", "retmax": 10, "retmode": "json"}
response = requests.get(search_url, params=params)
pmids = response.json()["esearchresult"]["idlist"]
fetch_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
response = requests.get(fetch_url, params={"db": "pubmed", "id": ",".join(pmids), "rettype": "abstract", "retmode": "xml"})
bioRxiv Fetch (Date-range based)
import requests
url = "https://api.biorxiv.org/details/biorxiv/2026-02-01/2026-03-01"
response = requests.get(url)
papers = response.json()["collection"]
for paper in papers[:5]:
print(f"Title: {paper['title']}")
print(f"Abstract: {paper['abstract'][:200]}...")
Expected Outputs
PubMed Results
Returns list of papers with:
| Field | Description |
|---|
title | Paper title |
authors | Author list |
abstract | Full abstract |
doi | DOI identifier |
pmid | PubMed ID |
date | Publication date |
link | PubMed URL |
bioRxiv Results
Returns list of papers with:
| Field | Description |
|---|
title | Paper title |
authors | Author list |
abstract | Full abstract |
doi | DOI identifier |
date | Publication date |
category | Subject category |
link | bioRxiv URL |
Category Filters for bioRxiv
| Category | Description |
|---|
cancer_biology | Cancer research |
immunology | Immune system studies |
cell_biology | Cellular processes |
bioinformatics | Computational biology |
neuroscience | Nervous system research |
microbiology | Microbial studies |
genomics | Genome analysis |
Error Handling
| Error | Solution |
|---|
| No PubMed results | Broaden search terms, check spelling |
| bioRxiv timeout | Reduce date range, retry |
| Empty abstract | Paper may not have abstract available |
| Rate limiting | Add delay between requests (NCBI: 3 req/sec) |
API References
Notes
- PubMed: Keyword search via NCBI E-utilities API
- bioRxiv: Date-range or category-based fetch via bioRxiv API
- bioRxiv does not support direct keyword search
- For comprehensive search, use both sources together
See examples/basic_example.py for complete runnable examples.
