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pubmedmapper 0.1.1

pubmed-mapper: A Python Library that map PubMed XML to Python object
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1. Philosophy
view UML
Programmatically access PubMed article is a common task for me.
Luckily, with the help of eutils,
we can access full article data in XML format.
What I need is Python objects, not just XML strings, so pubmed-mapper was born.
2. Installation
pip install pubmed-mapper

3. Usage
3.1 use as library
3.1.1 parse a PubMed ID
from pubmed_mapper import Article

article = Article.parse_pmid('32329900')

# PubMed ID
print(article.pmid) # 32329900

# ids
print(article.ids) # [pubmed: 32329900, doi: 10.1111/jgs.16467]
print(article.ids[1].id_type) # doi
print(article.ids[1].id_value) # 10.1111/jgs.16467

# title
print(article.title) # Associations of Coffee...

# abstract
print(article.abstract) # <p><strong>Background: </strong>Coffee and tea...

# keywords
print(article.keywords) # ['aging', 'coffee; diet; longevity', 'tea']

# MeSH headings
print(article.mesh_headings) # ['Aged', 'Body Mass Index', '...']

# authors
print(article.authors) # [hadyab AH Aladdin H, Manson JE JoAnn E, ...]
print(article.authors[0].last_name) # Shadyab
print(article.authors[0].forename) # Aladdin H
print(article.authors[0].initials) # AH
print(article.authors[0].affiliation) # Department of Family...

# journal
print(article.journal) # Journal of the American Geriatrics Society
print(article.journal.issn) # 1532-5415
print(article.journal.issn_type) # Electronic
print(article.journal.title) # Journal of the American Geriatrics Society
print(article.journal.abbr) # J Am Geriatr Soc

# volume
print(article.volume) # 68

# issue
print(article.issue) # 9

# references
print(article.references) # [n. 2013;129:643-659....]
print(article.references[0].citation) # Lotfield E, Freedman ND...
print(article.references[0].ids) # []

# pubdate
print(article.pubdate) # 2020-09-01

3.1.2 parse a downloaded XML file
from lxml import etree
from pubmed_mapper import Article

infile = 'xxx.xml'
with open(infile) as fp:
root = etree.parse(fp)

articles = []
for pubmed_article_element in root.xpath('/PubmedArticleSet/PubmedArticle'):
article = Article.parse_element(pubmed_article_element)
articles.append(article)

3.2 use as command line software
3.2.1 parse PubMed ID
pubmed-mapper pmid -p 32329900

3.2.2 parse single PubMed XML file
pubmed-mapper file -i data/pubmed21n0001.xml -o output/pubmed21n0001.jl

3.2.3 parse a directory who contains multiple PubMed XML files
pubmed-mapper directory -i data/ -o output/pubmed-mapper.jl

4. FAQs
4.1 There many types of PubMed article publication date, how do you convert it to datetime.date object?
Parse publication date is a hard work, until now pubmed-mapper can't parse all types of them.
The types pubmed-mapper can be parsed and the parsed value are:

type
value

2021-03-13
2021-03-13

2021-03
2021-03-01

2021 Spring
2021-04-01

2021
2021-01-01

2021 Jan-Feb
2021-01-01

2021 Mar 13-15
2021-03-13

2021 Mar-2022 Jan
2021-03-01

2021-2022
2021-01-01

2021 Mar 13-Dec 15
2021-03-13

1976-1977 Winter
1976-01-01

1977-1978 Fall-Winter
1977-10-01

4.2 What is pubmed-mapper.log generated by pubmed-mapper?
pubmed-mapper.log is the default log file generate by pubmed-mapper,
you can change the file by using --log-file options:
pubmed-mapper --log-file my-custom.log file -i data/pubmed21n0001.xml -o output/pubmed21n0001.jl

You can go to this log file to find out more parsing details.
4.3 I want log detail message in my log file?
Using --log-level can log more detail message:
pubmed-mapper --log-file my-custom.log --log-level DEBUG file -i data/pubmed21n0001.xml -o output/pubmed21n0001.jl