Applications can be extensions made to one of the tag sets or uses or users of the one or more of the tag sets.
Publicly Available Extensions
TaxPub is an extension of the NLM/NCBI Journal Archiving DTD for markup of taxonomic treatments. It is available from GitHub: https://github.com/tcatapano/TaxPub .
BITS is the Book Interchange Tag Suite created by NLM. It is an extension to NISO JATS v1.0 to handle book content. The home page for BITS is http://jats.nlm.nih.gov/extensions/bits/.
Hogrefe Book Tag Set (HoBoTS)
See the announcement.
ISO Standards Tag Set (ISOSTS)
SciELO Publishing Schema (SPS)
Adaptations to other XML vocabularies
Implementing MathML 3
If you are adding MathML 3.0 to the XSD Schema version of JATS, just replace the modules and all is golden.
If you are using a DTD version of JATS, things are SLIGHTLY more complicated.
1. Replace all the MathML 2.0 modules with MathML 3.0 modules. 2. Replace all calls to MathML modules with the new names in the catalog and modules files. 3. There is one additional modification required because of a name clash between a new MathML 3 parameter entity and one in JATS: %product.class;. This is defined in JATS-default-classes.ent.
The easiest way around this (and the one approved by two members of the MathML Working Group) is to hack the MathML directly. After all, parameter entity names have no impact on the tag set.
For example, you can change the %product.class; name in the MathML 3.0 DTD to %mml-product.class;.
There is a request in that JATS consider modifying its PE names to remove this problem. It is a silent failure problem with no parsing warning, since this is how parameter entities are intended to function.