pyEuropePMC

API Reference

Complete API documentation - All classes, methods, and parameters

API Overview

This section provides detailed documentation for all PyEuropePMC classes and methods. The API is organized around several core clients:

Client Purpose Key Methods
SearchClient Query Europe PMC database search(), get_by_id()
FullTextClient Download full-text content download_pdf(), get_xml()
ArticleClient Article-specific operations get_citations(), get_references()
FullTextXMLParser Parse XML documents extract_metadata(), extract_tables()
FTPDownloader Bulk downloads via FTP download_bulk()

Core Classes

QueryBuilder

from pyeuropepmc import QueryBuilder

qb = QueryBuilder(validate=True)

The advanced fluent API for building complex search queries with type safety and validation.

Key Features

Complete QueryBuilder API →

EuropePMC Client

from pyeuropepmc import EuropePMC

client = EuropePMC()

The main client class for interacting with the Europe PMC API.

Constructor

EuropePMC(
    base_url: str = "https://www.ebi.ac.uk/europepmc/webservices/rest",
    timeout: int = 30,
    retries: int = 3,
    rate_limit: float = 1.0
)

Parameters:

Methods

Search for articles in the Europe PMC database.

search(
    query: str,
    source: str = "MED",
    limit: int = 25,
    offset: int = 0,
    sort: str = "relevance",
    format: str = "json",
    **kwargs
) -> List[Article]

Parameters:

Returns: List of Article objects

Example:

results = client.search("cancer therapy", limit=10, sort="date", format="json")
fetch_by_id()

Fetch a specific article by its ID.

fetch_by_id(
    pmid: str = None,
    pmcid: str = None,
    doi: str = None,
    format: str = "json"
) -> Article
fetch_citations()

Get citations for a specific article.

fetch_citations(
    pmid: str = None,
    pmcid: str = None,
    limit: int = 25,
    offset: int = 0
) -> List[Citation]
fetch_references()

Get references cited by a specific article.

fetch_references(
    pmid: str = None,
    pmcid: str = None,
    limit: int = 25,
    offset: int = 0
) -> List[Reference]

Data Models

Article

Represents a scientific article from Europe PMC.

Attributes:

Citation

Represents a citation to an article.

Attributes:

Reference

Represents a reference cited by an article.

Attributes:

Error Handling

Exception Classes

Example Error Handling

from pyeuropepmc import EuropePMC, APIError, RateLimitError

try:
    client = EuropePMC()
    results = client.search("invalid query")
except APIError as e:
    print(f"API Error: {e}")
except RateLimitError as e:
    print(f"Rate limit exceeded: {e}")
except Exception as e:
    print(f"Unexpected error: {e}")

Type Safety & Validation

All public methods use type annotations and validate input parameters. Invalid arguments will raise exceptions with clear error messages.

Configuration

Environment Variables

Configuration File

Create a .pyeuropepmc.conf file in your home directory:

[api]
base_url = https://www.ebi.ac.uk/europepmc/webservices/rest
timeout = 30
retries = 3
rate_limit = 1.0

[logging]
level = INFO
format = %(asctime)s - %(name)s - %(levelname)s - %(message)s
Section Why Visit?
Getting Started Installation and basics
Features What PyEuropePMC can do
Examples Working code samples
Advanced Power user features
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