pyEuropePMC

PyEuropePMC

A comprehensive Python toolkit for searching, retrieving, and analyzing biomedical literature from Europe PMC.

Overview

PyEuropePMC provides a powerful, type-safe interface to the Europe PMC database, offering advanced search capabilities, full-text content retrieval, XML parsing, and analytics tools for biomedical research.

Key Capabilities

Search & Query – Advanced search with boolean operators, field-specific queries, and a fluent Query Builder API supporting 150+ searchable fields
Full-Text Retrieval – Download PDFs, XML, and HTML content from open-access articles with automatic endpoint fallback
XML Parsing – Extract structured data from JATS XML articles including metadata, sections, tables, figures, and references
Analytics & Visualization – Citation analysis, publication trends, quality metrics, and interactive dashboards
Systematic Reviews – PRISMA-compliant search logging, deduplication, and audit trails
Caching – Multi-layer caching with memory, disk, and HTTP backends for optimal performance
Knowledge Graph – RDF/Turtle export with RML mapping support for knowledge graph construction

Quick Start

Installation

pip install pyeuropepmc

Basic Usage

from pyeuropepmc.clients.search import SearchClient

with SearchClient() as client:
    results = client.search("CRISPR gene editing", limit=10)
    for paper in results:
        print(f"{paper['title']} ({paper['pubYear']})")

Query Builder

from pyeuropepmc.query import QueryBuilder

query = (
    QueryBuilder()
    .keyword("CRISPR")
    .and_()
    .date_range("2020-01-01", "2024-12-31")
    .and_()
    .has_full_text()
    .and_()
    .open_access()
)

with SearchClient() as client:
    results = client.search(str(query), limit=50)

Full-Text Download

from pyeuropepmc.clients.fulltext import FullTextClient

with FullTextClient() as client:
    content = client.get_fulltext("PMC7512345")
    if content.xml:
        print(content.xml[:500])

Documentation Structure

Section	Description
Getting Started	Installation, quick start, and FAQ
Features	Search, full-text, parsing, and caching
API Reference	Complete method documentation
Guides	Enrichment and integration guides
Advanced	Caching, performance, and power features
Reference	Data models and RDF mapping
Development	Contributing and development setup
Examples	Working code samples

Requirements

Python 3.10+
Dependencies: requests, pandas, lxml, tqdm

License

MIT License