PubMed Client - Python Bindings

Python bindings for the PubMed and PMC (PubMed Central) API client library.

Overview

This package provides Python bindings to the Rust-based PubMed client library, enabling high-performance access to PubMed and PMC APIs from Python.

Features

PubMed API: Search and retrieve article metadata
PMC API: Access full-text articles from PubMed Central
ELink API: Get related articles, citations, and PMC links
Europe PMC API: Cross-source search (preprints, patents, Agricola, CBA), JATS full text, reference and citation graphs, external database links — no API key needed
SearchQuery Builder: Build complex queries programmatically with filters
High Performance: Built with Rust for speed and reliability
Type-Safe: Full type hints for better IDE support

Installation

From PyPI

pip install pubmed-client-py

With uv

uv add pubmed-client-py

From Source

# Clone the repository
git clone https://github.com/illumination-k/pubmed-client.git
cd pubmed-client/pubmed-client-py

# Create virtual environment and install
uv venv
uv run --with maturin maturin develop

Quick Start

Basic Usage

import pubmed_client

# Create a unified client
client = pubmed_client.Client()

# Search PubMed
articles = client.pubmed.search_and_fetch("covid-19 vaccine", max_results=10)

for article in articles:
    print(f"Title: {article.title}")
    print(f"PMID: {article.pmid}")
    print(f"Journal: {article.journal}")
    print()

Fetch Single Article

import pubmed_client

client = pubmed_client.Client()

# Fetch article by PMID
article = client.pubmed.fetch_article("31978945")

print(f"Title: {article.title}")
print(f"Authors: {article.author_count}")
print(f"Abstract: {article.abstract_text[:200]}...")

# Access authors and affiliations
for author in article.authors():
    print(f"  {author.full_name}")
    if author.orcid:
        print(f"    ORCID: {author.orcid}")

Fetch PMC Full-Text

import pubmed_client

client = pubmed_client.Client()

# Fetch full text from PMC
full_text = client.pmc.fetch_full_text("PMC7906746")

print(f"Title: {full_text.title}")
print(f"Sections: {len(full_text.sections())}")
print(f"References: {len(full_text.references())}")

# Access article sections
for section in full_text.sections():
    print(f"Section: {section.title}")
    print(f"Content: {section.content[:200]}...")

# Access figures and tables
for figure in full_text.figures():
    print(f"Figure: {figure.label}")
    print(f"Caption: {figure.caption}")

# Convert to Markdown
markdown = full_text.to_markdown()
print(markdown)

Citation Analysis

import pubmed_client

client = pubmed_client.Client()

# Get citations for an article
citations = client.get_citations([31978945])
print(f"Citation count: {len(citations)}")

# Get citing article PMIDs
for citing_pmid in citations.citing_pmids[:10]:
    print(f"Cited by: {citing_pmid}")

Using SearchQuery Builder

import pubmed_client

client = pubmed_client.Client()

# Build a complex query
query = (
    pubmed_client.SearchQuery()
    .query("cancer")
    .published_between(2020, 2024)
    .article_type("Clinical Trial")
    .free_full_text_only()
    .limit(50)
)

# Execute the search
articles = client.pubmed.search_and_fetch(query, 0)  # limit ignored when using SearchQuery

for article in articles:
    print(f"[{article.pmid}] {article.title}")

Field, MeSH, and Validation Filters

import pubmed_client

query = (
    pubmed_client.SearchQuery()
    .title_or_abstract("gene therapy")
    .author("Doudna JA")
    .journal("Nature")
    .mesh_term("Neoplasms")
    .mesh_major_topic("Genetic Therapy")
    .affiliation("Harvard")
    .language("english")
    .human_studies_only()
    .has_abstract()
)

# Raises InvalidQueryException if the query is malformed
query.validate()

# Drop duplicate terms/filters, then inspect the query
query.optimize()
terms, filters, complexity = query.get_stats()

print(query.build())

Also available: first_author(), last_author(), journal_abbreviation(), title_contains(), abstract_contains(), grant_number(), isbn(), issn(), mesh_terms(), mesh_subheading(), orcid(), organism_mesh(), animal_studies_only(), age_group(), and custom_filter() for raw PubMed syntax.

Boolean Query Combinations

import pubmed_client

# Build complex queries with boolean logic
q1 = pubmed_client.SearchQuery().query("covid-19")
q2 = pubmed_client.SearchQuery().query("vaccine")
q3 = pubmed_client.SearchQuery().query("efficacy")

# Combine with AND
combined = q1.and_(q2).and_(q3)
print(combined.build())  # ((covid-19) AND (vaccine)) AND (efficacy)

# Combine with OR
either = q1.or_(q2)
print(either.build())  # (covid-19) OR (vaccine)

# Exclude specific terms
base = pubmed_client.SearchQuery().query("treatment")
excluded = pubmed_client.SearchQuery().query("animal studies")
human_only = base.exclude(excluded)
print(human_only.build())  # (treatment) NOT (animal studies)

Extract Figures from PMC Articles

import pubmed_client

client = pubmed_client.Client()

# Download and extract figures with captions
figures = client.pmc.extract_figures_with_captions("PMC7906746", "./output")

for fig in figures:
    print(f"Figure: {fig.figure.label}")
    print(f"Caption: {fig.figure.caption}")
    print(f"File: {fig.extracted_file_path}")
    print(f"Size: {fig.file_size} bytes")
    if fig.dimensions:
        print(f"Dimensions: {fig.dimensions[0]}x{fig.dimensions[1]}")

Europe PMC

Europe PMC complements the NCBI E-utilities: it indexes preprints (PPR), patents (PAT), Agricola (AGR) and Chinese Biological Abstracts (CBA) alongside PubMed (MED) and PMC, and needs no API key.

Records are addressed by a source database plus an id. Every method accepts the id bare ("PMC3258128", "33515491"), with an explicit source, or fully qualified ("PPR/PPR123456"). Given no source, a PMC-prefixed id is read as a PMC record and anything else as a PubMed record.

import pubmed_client

client = pubmed_client.Client()

# Cross-source search, including preprints
for result in client.europe_pmc.search("TITLE:CRISPR AND SRC:PPR", 5):
    print(result.europe_pmc_id, result.title)

# Full text as a parsed article, or as raw JATS XML for non-PMC sources
article = client.europe_pmc.fetch_full_text("PMC3258128")
xml = client.europe_pmc.fetch_full_text_xml("PMC3258128")

# Citation graph in both directions
references = client.europe_pmc.get_references("PMC3258128")
citations = client.europe_pmc.get_citations("33515491", source="MED")

# Cross-references to external databases (UniProt, EMBL, PDB, ...)
for link in client.europe_pmc.get_database_links("PMC3258128"):
    print(link.db_name, link.db_count)

# `resultType="core"` returns far more than is modelled; the remainder is
# available as a plain dict rather than pinned to a schema Europe PMC may change
for result in client.europe_pmc.search_all("malaria vaccine", 10, result_type="core"):
    print(result.extra().get("citedByCount"))

Paging is explicit where Europe PMC exposes it — search_page returns a next_cursor_mark, and get_references_page / get_citations_page return (hit_count, entries).

Configuration

With API Key

Using an NCBI API key increases rate limits from 3 to 10 requests per second:

import pubmed_client

config = (
    pubmed_client.ClientConfig()
    .with_api_key("your_ncbi_api_key")
    .with_email("your@email.com")
    .with_tool("YourAppName")
)

client = pubmed_client.Client.with_config(config)

Rate Limiting

import pubmed_client

config = (
    pubmed_client.ClientConfig()
    .with_rate_limit(2.0)  # 2 requests per second
    .with_timeout_seconds(60)  # 60 second timeout
)

client = pubmed_client.Client.with_config(config)

Type Hints and IDE Support

The package includes complete type stubs (.pyi files) for full IDE autocomplete and type checking:

import pubmed_client

# Type hints work automatically
config: pubmed_client.ClientConfig = pubmed_client.ClientConfig()
client: pubmed_client.Client = pubmed_client.Client.with_config(config)
articles: list[pubmed_client.PubMedArticle] = client.pubmed.search_and_fetch("query", 10)

Run type checking with mypy:

mypy your_script.py

Maintaining the type stub

pubmed_client.pyi is generated, not hand-edited. It is produced from the #[gen_stub_pyclass] / #[gen_stub_pymethods] annotations in the Rust source by the stub_gen binary, which then splices in the members pyo3-stub-gen cannot introspect (__version__ and the create_exception! hierarchy).

When you add or change a PyO3 class, method, or attribute:

Annotate the new #[pyclass] with #[gen_stub_pyclass] and every #[pymethods] block with #[gen_stub_pymethods] (module-level items added via m.add(...), such as new exceptions, also need to be listed in stub_gen.rs).

Regenerate the stub:

MISE_ENV=python mise run stubgen:py     # or: cargo run --bin stub_gen

Verify it matches the compiled module:

MISE_ENV=python mise run stubtest:py    # maturin develop + python -m mypy.stubtest

Commit the regenerated pubmed_client.pyi.

CI enforces both halves: the Python Type Stub Check job regenerates the stub and fails on git diff if the checked-in copy is stale, then runs stubtest so the stub can never silently drift from the compiled module. stubtest-allowlist.txt records the intentionally-unstubbed internal extension submodule.

Development

Prerequisites

Python >= 3.12
Rust toolchain (installed via rustup)
uv (for Python package management)
maturin (for building Python bindings)

Setup Development Environment

# Install uv if not already installed
curl -LsSf https://astral.sh/uv/install.sh | sh

# Create virtual environment
cd pubmed-client-py
uv venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate

# Build and install in development mode
uv run --with maturin maturin develop

Running Tests

# Install dev dependencies
uv sync --group dev

# Run tests
uv run pytest

# Run tests with coverage
uv run pytest --cov=pubmed_client

Code Quality

# Format code
uv run ruff format

# Lint code
uv run ruff check

# Type checking
uv run mypy tests/

Building

# Build wheel
uv run --with maturin maturin build --release

# Build for distribution
uv run --with maturin maturin build --release --sdist

Publishing

# Publish to PyPI (requires credentials)
uv run --with maturin maturin publish

License

MIT

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This release

0.4.0 This release

Aug 30, 2026 11 files

0.3.1

Aug 3, 2026 11 files

0.3.0

Jul 13, 2026 11 files

0.2.0

Jun 24, 2026 11 files

0.0.2

Nov 16, 2025 11 files

0.0.1

Nov 1, 2025 9 files

pubmed-client-py 0.4.0

PubMed Client - Python Bindings

Overview

Features

Installation

From PyPI

With uv

From Source

Quick Start

Basic Usage

Fetch Single Article

Fetch PMC Full-Text

Citation Analysis

Related Articles and PMC Links

Using SearchQuery Builder

Field, MeSH, and Validation Filters

Boolean Query Combinations

Extract Figures from PMC Articles

Europe PMC

Configuration

With API Key

Rate Limiting

Type Hints and IDE Support

Maintaining the type stub

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Prerequisites

Setup Development Environment

Running Tests

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Building

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1 maintainer

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