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)#

python

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)#

python

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:

FieldDescriptiontitlePaper titleauthorsAuthor listabstractFull abstractdoiDOI identifierpmidPubMed IDdatePublication datelinkPubMed URL

bioRxiv Results#

Returns list of papers with:

FieldDescriptiontitlePaper titleauthorsAuthor listabstractFull abstractdoiDOI identifierdatePublication datecategorySubject categorylinkbioRxiv URL

Category Filters for bioRxiv#

CategoryDescriptioncancer_biologyCancer researchimmunologyImmune system studiescell_biologyCellular processesbioinformaticsComputational biologyneuroscienceNervous system researchmicrobiologyMicrobial studiesgenomicsGenome analysis

Error Handling#

ErrorSolutionNo PubMed resultsBroaden search terms, check spellingbioRxiv timeoutReduce date range, retryEmpty abstractPaper may not have abstract availableRate limitingAdd 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.