Editing Tools

==Data entry tools==

[http://semanticpublishing.wordpress.com/2012/12/20/jats-metadata-entry-form/ JATS Metadata Input Form]

==Conversion Tools==

===To JATS===

====From Word DOCX and other Word-processor formats====

=====Biomedical Plain Text to JATS=====
[https://sci.ai/ sci.AI] semanticizes concepts, relationships and authors in a plain text paper. Then it generates enhanced JATS with biomedical metadata.

=====eXtyles=====

[http://www.inera.com/extyles-products/extyles eXtyles] automates time-consuming aspects of document editing in Microsoft Word and exports to JATS XML (as well as many other DTDs).

=====Article Authoring Add-in for Word (NLM JATS)=====

As described at http://authoring.codeplex.com/ , "[t]his add-in for Microsoft Word enables authors/editors to use Microsoft Office Word to create, edit, and save files in the National Library of Medicine's NLM DTD (article or book) format." Though released in 2012, it was developed many years ago.

=====meTypeset=====

[https://github.com/MartinPaulEve/meTypeset meTypeset] "is a fork of the OxGarage stack" "to convert from Microsoft Word .docx format to NLM/JATS-XML". It is implemented as part of the PKP XML parsing stack.

=====Open Typesetting Stack (PKP XML Parsing Service)=====

The Open Typesetting Stack (formerly the PKP XML Parsing Service: [https://github.com/pkp/xmlps sourcecode], [http://pkp-udev.lib.sfu.ca/ beta site]) converts Word documents to NLM DTD 3.0 XML, HTML, and PDF using meTypeset and other tools. As of April 2015, it's in beta, with metadata parsing disabled because of poor results. A plugin is being developed for Open Journal Systems (OJS) that will call this service. For more information, see [http://www.ncbi.nlm.nih.gov/books/NBK279666/ a paper presented at JATS-Con 2015].

=====Migrate (from Stilo)=====

A proprietary cloud-based service: http://www.stilo.com/migrate-jats/

=====OxGarage=====

[http://www.oucs.ox.ac.uk/oxgarage/ OxGarage] can convert documents from various formats into "National Library of Medicine (NLM) DTD 3.0" (as well as various other formats). See [http://wiki.tei-c.org/index.php/OxGarage documentation].

=====Markdown to JATS=====

[http://blog.martinfenner.org/2013/12/12/from-markdown-to-jats-xml-in-one-step/ pandoc-jats]

=====PDF to JATS=====

This is a very difficult problem to solve. Success depends on how well structured your PDFs are and, for batch conversion, how consistently structured your PDFs are.

* [http://www.shabash.net/merops/default.html Shabash Merops]
* [http://pkp.sfu.ca/ The Public Knowledge Project] is developing a pipeline for converting PDF to JATS. It will include use of [http://pdfx.cs.man.ac.uk/ pdfx].

=====bepress OAI-PMH XML to JATS=====

[https://github.com/gilmani/oaipmh_jats oaipmh_jats]: "This XSL stylesheet transforms OAI-PMH XML from the bepress Digital Commons platform to JATS DTD 1.1d2 XML. Input is issue-level data; output is as article-level files. Limited metadata fields are used, as this was originally created for the purpose of creating brief article records for deposit with Portico."

====Native editors====

[http://substance.io/texture/ Substance]

===from JATS===

====JATS to HTML====

[http://jatswiki.org/wiki/Tools#JATS_Preview_Stylesheets JATS Preview Stylesheets]

[http://lens.elifesciences.org/ eLife Lens] converts NLM XML to JSON for displaying using HTML and Javascript. See [https://github.com/elifesciences/lens/ the sourcecode on GitHub].

====JATS to PDF====

[http://jatswiki.org/wiki/Tools#JATS_Preview_Stylesheets JATS Preview Stylesheets]

====JATS to EPUB====

* http://www.biglist.com/lists/lists.mulberrytech.com/jats-list/archives/201204/msg00002.html
* http://www.ncbi.nlm.nih.gov/books/NBK159966/

==Editing Tools==

===JATS Framework for oXygen XML Editor===

Users of oXygen XML Editor and oXygen XML Author can now install support for current versions of NISO JATS (and as a bonus, NLM BITS). Based on a Formal Public Identifier given in a DOCTYPE declaration, oXygen will detect that you are editing a JATS document and provide stylesheets and utilities.

Find the framework at https://github.com/wendellpiez/oXygenJATSframework

Documentation is here: https://github.com/wendellpiez/oXygenJATSframework/wiki

Or skip the page and download a copy directly: https://github.com/wendellpiez/oXygenJATSframework/archive/master.zip. Unzip it and drop the JATS folder into the frameworks folder of your oXygen installation.

===Annotum===

[http://annotum.org/ Annotum]: a WordPress theme that contains WYSIWYG authoring in JATS (Kipling subset), peer-review and editorial management, and publishing. See [http://www.ncbi.nlm.nih.gov/books/NBK63828/ a JATS-Con 2011 presentation].

===ArticleExpress===

[http://www.sheridan.com/products-services/production-tools/content-preparation/article-express ArticleExpress] is a proprietary product from Dartmouth Journal Services that uses JATS underneath. See [http://www.ncbi.nlm.nih.gov/books/NBK159965/ a JATS-Con 2013(4) presentation] and [http://www.ncbi.nlm.nih.gov/books/NBK279927/ a JATS-Con 2015 presentation].


===PubRef===

[https://pubref.org/ PubRef] (whose homepage instead says "Pipeline") features a markdown-like editor that produces JATS XML. Documentation is limited, but more is expected well before March 2016.

===ARPHA Writing Tool===

The [http://arpha.pensoft.net/ ARPHA Writing Tool] is an online collaborative authoring tool, providing editing, peer-review and submission functionalities, as an integral component of the [http://arphahub.com/ ARPHA JATS XML-based publishing platform].

===FontoXML===

https://fontoxml.com/jats/

==Validation Tools==

===PMC XML Validator===

The [http://www.ncbi.nlm.nih.gov/pmc/tools/xmlchecker/ PMC XML Validator] can be used to confirm that a document is valid according to one of the JATS DTDS.

===PMC Style Checker===

The [http://www.ncbi.nlm.nih.gov/pmc/tools/stylechecker/ PMC Style Checker] is an online web service that confirm whether an XML document conforms to PMC Style as defined in the [http://www.pubmedcentral.nih.gov/pmcdoc/tagging-guidelines/article/style.html PMC XML Tagging Guidelines]. Note that the PMC Tagging Guidelines are a profile of JATS -- not every valid JATS document need conform to the PMC Tagging Guidelines.

===JATS4R Validator===

The [https://github.com/JATS4R/validation JATS4R Validator] is a work-in-progress. It is a set of schematron files that can be used to confirm that a document conforms to the recommended tagging practices of the [https://github.com/JATS4R JATS for reuse] group.

==Preview Tools==

===JATS Preview Stylesheets===

[https://github.com/NCBITools/JATSPreviewStylesheets code on GitHub]

The JATS Preview Stylesheets are a series of .xsl, .xpl, .css, and .sch files that will create .html or .pdf versions of valid NISO Z39.96-2012 JATS 1.0 files. The primary purpose of the stylesheets is to support version 1.0 of the Publishing ("blue") tag set of JATS, but they will also work on data valid to JATS 1.0 Authoring ("orange"). Additionally, the stylesheets will work with versions 3.0 and 2.3 of NLM Journal Publishing ("blue") or Authoring ("orange").

These stylesheets are not intended to create production ready files. They can be customized as needed to produce output for any aspect of a publishing system.

===oXygen Preview===

See the [http://jatswiki.org/wiki/Tools#JATS_Framework_for_oXygen_XML_Editor JATS Framework for oXygen] in the XML Editor Tools section below.

==End-to-end publishing==

===ARPHA Publishing Platform===

The [http://arphahub.com/ ARPHA Publishing Platform] is a JATS XML-based, end-to-end, online, collaborative, journal publishing workflow that supports the full life cycle of a manuscript, from authoring, to peer-review, publication, dissemination and archiving.

===RVPublisher===

[http://rivervalleytechnologies.com/rvpublisher2015/ RVPublisher] is River Valley Technology’s end to end publishing platform. Technical details are described in [http://www.ncbi.nlm.nih.gov/books/NBK279828/ this JATS-Con paper].

==Documentation Tools==

Tools to improve upon the existing documentation for the JATS tag library

===Alternative Tag Library viewer===

The NISO JATS 1.0 and 1.1d1 Tag Libraries have been ported into an alternative, user-friendly HTML viewer here:

Archiving and Interchange

* [https://www.ncbi.nlm.nih.gov/staff/maloneyc/jatspan/niso/archiving-1.1d3/ NISO JATS Draft Version 1.1d3]
* [https://www.ncbi.nlm.nih.gov/staff/maloneyc/jatspan/niso/archiving-1.1d1/ NISO JATS Draft Version 1.1d1]
* [https://www.ncbi.nlm.nih.gov/staff/maloneyc/jatspan/niso/archiving-1.0/ NISO JATS Version 1.0]

Publishing

* [https://www.ncbi.nlm.nih.gov/staff/maloneyc/jatspan/niso/publishing-1.1d3/ NISO JATS Draft Version 1.1d3]
* [https://www.ncbi.nlm.nih.gov/staff/maloneyc/jatspan/niso/publishing-1.1d1/ NISO JATS Draft Version 1.1d1]
* [https://www.ncbi.nlm.nih.gov/staff/maloneyc/jatspan/niso/publishing-1.0/ NISO JATS Version 1.0]

Article Authoring

* [https://www.ncbi.nlm.nih.gov/staff/maloneyc/jatspan/niso/authoring-1.1d3/ NISO JATS Draft Version 1.1d3]
* [https://www.ncbi.nlm.nih.gov/staff/maloneyc/jatspan/niso/authoring-1.1d1/ NISO JATS Draft Version 1.1d1]
* [https://www.ncbi.nlm.nih.gov/staff/maloneyc/jatspan/niso/authoring-1.0/ NISO JATS Version 1.0]

Book Interchange Tag Suite (BITS)

* [https://www.ncbi.nlm.nih.gov/staff/maloneyc/jatspan/nlm/bits-1.0/ Version 1.0]

See [https://www.ncbi.nlm.nih.gov/staff/maloneyc/jatspan/jatsdoc-tag-sets.html this page] for the definitive, up-to-date list.

These pages use [https://github.com/Klortho/jatsdoc jatsdoc], which is also included as part of the [http://dtd.nlm.nih.gov/ncbi/dtdanalyzer/ DtdAnalyzer], meaning that you can easily produce documentation pages like this for your own JATS customizations.

===Browser userscript TagLibPermalink===

[https://github.com/Klortho/TagLibPermalink TagLibPermalink on GitHub]

A small browser extension that will add a "permalink" to each of the JATS tag library documentation pages, making it much easier to bookmark specific pages in the documentation and to share links to them, getting around the problem caused by the pages being within frames. Tested for Firefox and Chrome. Instructions and a video are found at the link above.