PubMedArticle Properties Reference

The PubMedArticle class provides access to a comprehensive set of properties extracted from NCBI PubMed XML data. This document details all available properties, organized by category and type.

Overview

PubMedArticle objects automatically detect whether they represent a journal article or book chapter and populate properties accordingly. The pubmed_type attribute indicates the type (‘article’ or ‘book’).

Publication Date Access

New in this version: The pubdate property provides normalized access to publication dates.

pubdate

Normalized publication date as a datetime object. Returns the best available date from:

1. Article PubDate (Year/Month/Day or MedlineDate)

2. Book contribution date

3. History dates (pubmed, entrez, received, accepted)

Example:

article = fetch.article_by_pmid('12345')
if article.pubdate:
    print(f"Published: {article.pubdate.strftime('%Y-%m-%d')}")
    print(f"Year: {article.pubdate.year}")

Shared Properties (Articles & Books)

These properties are available for both journal articles and book chapters:

Core Identifiers

• pmid - PubMed ID (string)

• url - NCBI PubMed URL for the article

Author Information

• authors - List of author names in “LastName FirstInitials” format

• author_list - List of PubMedAuthor objects with detailed author data

• authors_str - Semicolon-separated string of all authors

• author1_last_fm - First author in “LastName FirstInitials” format

• author1_lastfm - First author in “LastNameFirstInitials” format (no space)

Content

• title - Article or chapter title

• abstract - Full text abstract (structured abstracts are concatenated)

• keywords - List of author-supplied keywords

• year - Publication year (string)

Journal/Publication

• journal - Journal name or book title

• history - Dictionary of publication history dates (pubmed, entrez, received, etc.)

Article-Only Properties

These properties are only available for journal articles (pubmed_type='article'):

Publication Details

• volume - Journal volume number

• issue - Journal issue number

• volume_issue - Combined volume(issue) format, e.g. “123(4)”

• pages - Page range, e.g. “45-67”

• first_page - First page number

• last_page - Last page number (computed from page range)

Identifiers

• doi - Digital Object Identifier

• pii - Publisher Item Identifier

• pmc - PubMed Central ID (without “PMC” prefix)

• issn - International Standard Serial Number

Indexing & Classification

• mesh - Dictionary of MeSH (Medical Subject Headings) terms with:

  • descriptor_name: Main MeSH term

  • descriptor_major_topic: Boolean indicating major topic

  • qualifiers: List of qualifier terms with names and major topic flags

• chemicals - Dictionary of chemical substances mentioned, keyed by substance ID:

  • substance_name: Chemical name

  • registry_number: CAS registry number or “0” if none

• publication_types - Dictionary of publication types (e.g., “Journal Article”, “Review”) keyed by type ID

• grants - List of grant information dictionaries with:

  • agency: Funding agency name

  • country: Country of funding agency

Book-Only Properties

These properties are only available for book chapters (pubmed_type='book'):

Book Metadata

• book_accession_id - NCBI Book ID (e.g. “NBK1403”)

• book_title - Full book title

• book_publisher - Publisher name

• book_language - Language code (e.g. “eng”)

• book_medium - Publication medium (e.g. “Internet”)

Book Content

• book_abstracts - Dictionary of abstract sections keyed by label

• book_sections - Dictionary of book sections

• book_copyright - Copyright information

• book_synonyms - List of disease/concept synonyms (for reference works)

Book Authors & Editors

• book_editors - List of book editors in “LastName FirstInitials” format

Book Dates

• book_contribution_date - Chapter contribution date as datetime object

• book_date_revised - Last revision date as datetime object

• book_history - Dictionary of book publication history dates

• book_publication_status - Publication status (e.g. “ppublish”)

Citation Properties

These properties provide formatted citations in different styles:

citation

Standard academic citation format:

McNally EM, et al. Genetic mutations and mechanisms in dilated cardiomyopathy.
Journal of Clinical Investigation. 2013; 123:19-26. doi: 10.1172/JCI62862.

citation_html

HTML-formatted citation with italics for journal names and bold for volume:

McNally EM, <i>et al</i>. Genetic mutations and mechanisms in dilated cardiomyopathy.
<i>Journal of Clinical Investigation</i>. 2013; <b>123</b>:19-26. doi: 10.1172/JCI62862.

citation_bibtex

BibTeX-formatted citation for reference managers:

@article{McNally2013,
author = {McNally, EM and et al},
title = {Genetic mutations and mechanisms in dilated cardiomyopathy},
journal = {Journal of Clinical Investigation},
year = {2013},
volume = {123},
pages = {19-26},
doi = {10.1172/JCI62862},
}

Property Availability by Type

Property	Article	Book
pmid	✓	✓
url	✓	✓
authors	✓	✓
title	✓	✓
abstract	✓	✓
year	✓	✓
journal	✓	✓
pubdate	✓	✓
volume	✓	✗
issue	✓	✗
pages	✓	✗
doi	✓	✗
mesh	✓	✗
chemicals	✓	✗
grants	✓	✗
book_title	✗	✓
book_editors	✗	✓
book_accession_id	✗	✓

Usage Examples

Basic Article Information:

from metapub import PubMedFetcher

fetch = PubMedFetcher()
article = fetch.article_by_pmid('23435529')

print(f"Title: {article.title}")
print(f"Journal: {article.journal} ({article.year})")
print(f"Authors: {article.authors_str}")
print(f"DOI: {article.doi}")

# New normalized date access
if article.pubdate:
    print(f"Published: {article.pubdate.strftime('%B %d, %Y')}")

Working with MeSH Terms:

if article.mesh:
    print("\\nMeSH Terms:")
    for ui, mesh_data in article.mesh.items():
        term = mesh_data['descriptor_name']
        major = mesh_data['descriptor_major_topic']
        marker = "*" if major else " "
        print(f"  {marker} {term}")

Book Chapter Information:

book_article = fetch.article_by_pmid('20301546')  # GeneReviews example

if book_article.pubmed_type == 'book':
    print(f"Chapter: {book_article.title}")
    print(f"Book: {book_article.book_title}")
    print(f"Editors: {'; '.join(book_article.book_editors)}")
    print(f"Book ID: {book_article.book_accession_id}")

Citation Generation:

# Different citation formats
print("Standard:", article.citation)
print("HTML:", article.citation_html)
print("BibTeX:", article.citation_bibtex)

Error Handling

Properties gracefully handle missing data:

• Missing optional fields return None

• Missing list fields return empty lists []

• Missing dictionary fields return empty dictionaries {}

• Invalid dates return None from date-related properties

Always check for None values before using date operations:

if article.pubdate:
    days_old = (datetime.now() - article.pubdate).days
    print(f"Article is {days_old} days old")

See Also

• Citation Formatting - Detailed citation formatting guide

• Data Model Classes - Complete API reference for PubMedArticle

• Examples - More usage examples and patterns