elife-pubmed-xml-generation

Generate PubMed deposit of journal articles.

Using JATS XML file as input, this library can generate a PubMed deposit XML file. The XML is parsed using the module from a different library, elifearticle, to extract the data from the XML file and to populate the objects defined in elifearticle.

It would be possible, with some additional code, to populate the elifearticle with data from a different data source and still generate a PubMed deposit, if all or a portion of the data is not stored in JATS XML format.

The PubMed deposit file will include the following output if the data is available in the elifearticle objects:

• Journal (journal title, publisher name, issn, volume, issue, pub date)
• Article metadata (title, doi, pii, language, pub date, abstract, copyright, keywords)
• Authors, group authors, author affiliations
• Funding data
• aheadofprint publishing status

It is possible to generate a PubMed deposit XML which includes one article or mulitple articles, depending on how many articles are in the list when generating the output.

Some sample input and output files can be found in the tests/test_data/ folder, which are the basis for the automated tests.

Requirements and install

a) Install from pypi package index

pip install elifepubmed

b) Install locally

Clone the git repo

git clone https://github.com/elifesciences/elife-pubmed-xml-generation.git

Create a python virtual environment and activate it

python3 -m venv venv
source venv/bin/activate

Install it locally

pip install -r requirements.txt
python setup.py install

Configuration

The pubmed.cfg configuration file provided in this repository can be changed in order to read slightly different JATS XML attributes, depending on the journal.

The publication_types.yaml file, referenced in the pubmed.cfg file, is where a JATS XML article type value can be mapped to a PubMed publication_type value.

Example usage

This library is meant to be integrated into another operational system, however the following are examples using interactive Python:

Example 1 - Convert a test fixture XML to elifearticle Article() object, then generate PubMed XML

>>> from letterparser import generate
>>> articles = generate.build_articles_for_pubmed(["tests/test_data/elife-00666.xml"])
>>> p_xml = generate.pubmed_xml(articles)
>>> print(p_xml)

Example 2 - Convert a test fixture XML to elifearticle Article() object, set the article is_poa property, then generate PubMed XML, the output XML will contain <PubDate PubStatus="aheadofprint">

>>> from letterparser import generate
>>> articles = generate.build_articles_for_pubmed(["tests/test_data/elife-00666.xml"])
>>> articles[0].is_poa = True
>>> p_xml = generate.pubmed_xml(articles)
>>> print(p_xml)

Example 3 - Convert two test fixture XML files to elifearticle Article() objects, then generate PubMed XML to disk, the output will be written in the local tmp/ folder

>>> from letterparser import generate
>>> articles = generate.build_articles_for_pubmed(["tests/test_data/elife-00666.xml", "tests/test_data/elife-02935-v2.xml"])
>>> generate.pubmed_xml_to_disk(articles)

Run code tests

Use pytest for testing, install it if missing:

pip install pytest

Run tests

pytest

Run tests with coverage (install it if missing)

coverage run -m pytest

then report on code coverage

coverage report -m

License

Licensed under MIT.