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wendellpiez edited this page Nov 12, 2012 · 24 revisions

Welcome to the oXygenJATSframework wiki --

  • What's the JATS framework for oXygen
  • What's in it
  • How to extend it
  • Feature requests / developers' discussion

For all matters related to JATS:

For oXygen XML editor:

What's the JATS framework for oXygen

Licensed users of oXygen XML Editor or Author (http://oxygenxml.com) who wish to work in the JATS format or with JATS-formatted data can take advantage of CSS stylesheets (for authoring) and XSLT transformations (for production of HTML and other outputs) bundled in a framework that recognizes these document types by their Formal Public Identifiers (FPIs).

The framework was developed and tested with oXygen 14.1.

Support for BITS 0.2, the book-description format (draft of Oct 2012), designed to be compatible with JATS, is included as a bonus.

How it works

Once the framework is available in oXygen (simply copy the JATS directory in the distribution into the frameworks folder of your oXygen installation), oXygen will recognize as JATS any document whose DOCTYPE declaration includes an FPI (Formal Public Identifier) starting with the string "-//NLM//DTD". Given this binding, oXygen will

  • Provide CSS stylesheet(s) for two views, "Clean" and "Labelled", in the Author view.
  • Provide a transformation scenario for HTML conversion.
  • For the current versions of JATS (NISO JATS 1.0 and BITS 0.2), an optimized DTD is provided which supplies content for oXygen tooltips (content completion) when inserting elements. (This feature is not available for older versions of the NLM DTDs. Instead, your own DTD will be used in the normal way.)

The framework can be extended to provide more transformation or validation scenarios or to recognize other DTDs. (The details of how this is best done will depend on the particulars of your organization and uses. Feel free to ask on JATS-List or the oXygen Users List.)

What's in it

CSS stylesheets for editing JATS data in oXygen Author, the WYSIWYG-like, formatted "pretty" view of the editor.

Derivative copies of the DTDs, JATS versions 1.0 in several variants

  • Authoring ("Orange")
  • Publishing ("Blue"), with and without OASIS tables
  • Archiving ("Green"), with and without OASIS tables
  • (Plus) BITS 0.2 (draft book description format), also with and without OASIS tables

Document templates

Starting new instances of each of these is available from File/New:

  • Article (valid to Orange)
  • Article (valid to Blue with JATS tables)
  • Article (valid to Green, with JATS tables)
  • Book (valid to BITS 0.2 with JATS tables)

(Please note that JATS tables closely resemble HTML tables.)

Preview stylesheets for HTML and PDF production

Prewired with a scenario for HTML preview production using the NLM/NCBI JATS Preview stylesheets (https://github.com/NCBITools/JATSPreviewStylesheets).

The entire set of Preview stylesheets is also in the distribution, for those who wish to set up and use others. In particular, if you have a capable XSL-FO formatter, you can set up oXygen to call it and generate PDF outputs from inside oXygen.

How to extend it

oXygen has a nice video on how to set up a framework. (They even use an earlier version of JATS as their example: not bad!) Costin Sandoi does an excellent job explaining everything at http://www.oxygenxml.com/demo/FrameworkConfiguration.html. Of course, you modify an existing framework in much the same way as you create a new one.

You can add to or replace CSS or XSLT. Or you can perform routine modifications to support your own use of JATS. For example, if you have your own stylesheets (or your own profiles for the Preview stylesheets included) you can add transformation scenarios to use them.

Feature requests / developers' discussion

See Plans for plans.

Or write to me or to the JATS-List at www.mulberrytech.com if you have ideas or requests, or to volunteer to implement.

-- Wendell Piez (wapiez -at- wendellpiez -dot- com)

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