biomedical-literature-search

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

# Step 1: Search for PMIDs
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"]

# Step 2: Fetch paper details
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

# Fetch papers by date range
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

• PubMed E-utilities: https://www.ncbi.nlm.nih.gov/books/NBK25500/
• bioRxiv API: https://api.biorxiv.org/

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.