jats-to-mediawiki.xsl transforms XML files written in the NLM/NISO Journal Archiving Tag Suite XML into MediaWiki XML. It is a part of the Encyclopedia of Original Research (EOR), and we expect it to be tightly integrated with the open-access-media-importer.
For more documentation, see the wiki.
Converting with the Python script
The following examples assume you are working in a
The jats-to-mediawiki.py python script provides a robust and human-friendly interface, including streaming
using stdin, stdout, and stderr. Article IDs can be passed to the script as stdin,
listed by line in an input file
-i, or are as arguments to the
After cloning the repository to a new local copy, set up the Python run environment with the following commands:
virtualenv env/ source env/bin/activate pip install -r requirements.txt
Subsequently, when starting to work on the project in a new shell, you will need to source the environment's activate script:
For command line usage, use python or otherwise execute the script with a
python jats-to-mediawiki.py --help
The instructions below assume you'll use
xsltproc to run the XSLT transformation.
To see if it exists on your system:
command -v xsltproc
Set up environment
# Set up XML catalog file export XML_CATALOG_FILES=`pwd`/dtd/catalog-test-jats-v1.xml
Convert an Article
The following are manual instructions for converting a single article, given its DOI.
First, find the PMCID for the article. If you have the DOI (for example,
10.1371/journal.pone.0010676) the easiest way to do this is with the PMC ID converter
API. Point your browser at
and make a note of the
pmcid value (in this example,
Next, find the location of the gzip archive file for this article, using the PMC OA web
service. Point your browser at
and look for the link with format
Download that gzip archive with, for example (note the single quotes around the URL):
Unzip that, and change into that directory. For example,
tar xvfz 'PLoS_One_2010_May_21_5(5)_e10676.tar.gz' cd 'PLoS_One_2010_May_21_5(5)_e10676'
Find the NXML file with
ls *.nxml. Now convert it with, for example
xsltproc ../jats-to-mediawiki.xsl pone.0010676.nxml > PMC2873961.mw.xml
Checking the result
In a browser, go to the
Special:Import page of your target mediawiki installation,
and import it.
You could use the scripts/fetch_samples.sh script to grab several examples articles, which were used in testing.
Is on our Github wiki.
Bugs / issues
We're using the Github issue tracker for bug reports and to-do items.
Contact / Collaborate
Join our Google Group jats-to-mediawiki
- Jeremy Morse
- Chris Maloney
- Konrad Foerstner firstname.lastname@example.org
This work is in the public domain and may be used and reproduced without special permission.