pyEuropePMC

Frequently Asked Questions

General Questions

What is PyEuropePMC?

PyEuropePMC is a Python library for searching and retrieving scientific literature from the Europe PMC database. It provides a simple, robust interface to access millions of research articles, preprints, and other scholarly content.

Who should use PyEuropePMC?

Installation & Setup

How do I install PyEuropePMC?

pip install pyeuropepmc

For development:

pip install -e ".[dev]"

What Python versions are supported?

Python 3.10 and newer versions are supported.

Do I need an API key?

No, Europe PMC provides open access to their search API without requiring registration or API keys.

Usage Questions

from pyeuropepmc.search import SearchClient

with SearchClient() as client:
    results = client.search("CRISPR", pageSize=10)
    for paper in results["resultList"]["result"]:
        print(paper["title"])

How can I search for specific authors?

# Search by author
results = client.search('AUTH:"Smith J"')

# Search by author and topic
results = client.search('AUTH:"Smith J" AND cancer')

How do I handle large result sets?

Use the pagination features:

# Automatic pagination
all_results = client.fetch_all_pages("machine learning", max_results=1000)

# Manual pagination
page1 = client.search("query", pageSize=100, offset=0)
page2 = client.search("query", pageSize=100, offset=100)

What output formats are available?

Note: RIS and BibTeX support has been removed as of vX.Y.Z. Please use JSON, XML, or Dublin Core formats.

json_results = client.search("query", format="json")
xml_results = client.search("query", format="xml")
dc_results = client.search("query", format="dc")

How do I filter by publication date?

# Specific year
results = client.search("cancer AND PUB_YEAR:2023")

# Date range
results = client.search("cancer AND PUB_YEAR:[2020 TO 2023]")

# Recent articles (last 5 years)
from datetime import datetime
current_year = datetime.now().year
results = client.search(f"cancer AND PUB_YEAR:[{current_year-5} TO {current_year}]")

Advanced Usage

How do I implement rate limiting?

# Built-in rate limiting
client = SearchClient(rate_limit_delay=2.0)  # 2 seconds between requests

# Custom throttling
import time
for query in queries:
    results = client.search(query)
    time.sleep(1)  # Additional delay

Can I search multiple databases simultaneously?

# Search specific sources
results_pubmed = client.search("query", source="MED")
results_pmc = client.search("query", source="PMC")
results_preprints = client.search("query", source="PPR")

# Combine results
all_results = results_pubmed + results_pmc + results_preprints

How do I handle errors and retries?

from pyeuropepmc.search import SearchClient, EuropePMCError

try:
    with SearchClient() as client:
        results = client.search("complex query")
except EuropePMCError as e:
    print(f"Search failed: {e}")
except Exception as e:
    print(f"Unexpected error: {e}")

The client includes built-in retry logic for network errors.

Performance & Limits

Are there API rate limits?

Europe PMC doesn’t publish specific rate limits, but we recommend:

How many results can I retrieve?

How can I optimize performance?

# Use appropriate page sizes
results = client.search("query", pageSize=100)  # vs. pageSize=10

# Request only needed fields
results = client.search("query", resultType="lite")  # vs. "core"

# Use caching for repeated queries
# (implement your own caching layer)

Data & Results

What information is included in search results?

Standard fields include:

How do I access full-text articles?

for paper in results["resultList"]["result"]:
    # Check if full text is available
    if paper.get("isOpenAccess") == "Y":
        print(f"Open access: {paper.get('fullTextUrlList')}")

    # PMC articles may have full text
    if paper.get("pmcid"):
        print(f"PMC ID: {paper['pmcid']}")

How accurate are citation counts?

Citation counts are updated regularly but may not be real-time. They include:

Troubleshooting

Why am I getting no results?

  1. Check query syntax: Ensure proper quoting and operators
  2. Verify field names: Use AUTH: not AUTHOR:
  3. Check spelling: Try variations and synonyms
  4. Broaden search: Remove restrictive filters
# Debug: Check hit count
hit_count = client.get_hit_count("your query")
print(f"Total matches: {hit_count}")

Why am I getting timeout errors?

# Increase timeout
client = SearchClient(timeout=60)  # Default is 30 seconds

# Check network connectivity
# Try simpler queries first

Why are some fields missing?

Not all articles have complete metadata:

Use safe access:

title = paper.get("title", "No title available")
authors = paper.get("authorString", "No authors listed")

Getting Help

Where can I find more examples?

How do I report bugs or request features?

How can I contribute to the project?

See our Contributing Guide for:

Where is the official Europe PMC documentation?

Best Practices

Query Construction

# Good: Specific, well-structured queries
query = 'TITLE:"machine learning" AND PUB_YEAR:[2020 TO 2023]'

# Avoid: Too broad or ambiguous
query = "data"  # Too broad, millions of results

Resource Management

# Good: Use context managers
with SearchClient() as client:
    results = client.search("query")

# Good: Implement proper error handling
try:
    results = client.search("query")
except EuropePMCError as e:
    logger.error(f"Search failed: {e}")

Data Processing

# Good: Process results efficiently
def extract_key_info(results):
    return [
        {
            "title": paper.get("title"),
            "year": paper.get("pubYear"),
            "citations": paper.get("citedByCount", 0)
        }
        for paper in results["resultList"]["result"]
    ]
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