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Update JATS dtd #6020

Merged
merged 3 commits into from Dec 31, 2019
Merged

Update JATS dtd #6020

merged 3 commits into from Dec 31, 2019

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arfon
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@arfon arfon commented Dec 29, 2019

The current DTD for the JATS writer template is for Journal Publishing (JATS-journalpublishing1.dtd), which does not permit ext-link as a valid child (https://jats.nlm.nih.gov/publishing/tag-library/1.1/element/publisher-name.html).

This update modifies the default output template to be the less restrictive JATS archiving and interchange DTD which systems like PubMed use internally to represent their articles. The new dtd is as follows:

<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.2d1 20190208//EN" "JATS-archivearticle1.dtd">

As suggested by @jgm - I proposed this change to the Pandoc mailing list a few weeks ago and haven't received any feedback on this suggestion.

Running the following command in jats-example-files.zip

pandoc -s --metadata-file metadata.json --bibliography references.bib --filter pandoc-citeproc --to jats example.md -o output.xml

Produces the file output.xml which is currently invalid. Updating the default.jats template as modified in this pull request produces updated-output.xml which is valid JATS according to the Pubmed central validator

Fixes #5634

@tarleb
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tarleb commented Dec 30, 2019

I'm in very much in favor of this, as it would also remove the requirement to specify journal-metadata (which is required for the "publishing" tag set.)

Maybe we can even make this configurable? See also: #6014.

@@ -2,12 +2,12 @@
$if(xml-stylesheet)$
<?xml-stylesheet type="text/xsl" href="$xml-stylesheet$"?>
$endif$
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.1 20151215//EN"
"JATS-journalpublishing1.dtd">
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.2d1 20190208//EN"
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@tarleb tarleb Dec 30, 2019

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The draft versions are not recognized by some validators. I'd recommend to use v1.2 instead.

@jgm jgm merged commit 5847624 into jgm:master Dec 31, 2019
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@misc bibtex items cause invalid JATS output
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