Journal Article Tag Suite

The Journal Article Tag Suite (JATS) is an XML format used to describe scientific literature published online. It is a technical standard developed by the National Information Standards Organization (NISO) and approved by the American National Standards Institute with the code Z39.96-2012.

The NISO project was a continuation of the work done by NLM/NCBI, and popularized by the NLM's PubMed Central as an de facto standard for archiving and interchange of scientific open-access journals and its contents with XML.

With the NISO standardization the NLM initiative has gained a wider reach, and several other repositories, such as SciELO, adopted the XML formatting for scientific articles.

The JATS provides a set of XML elements and attributes for describing the textual and graphical content of journal articles as well as some non-article material such as letters, editorials, and book and product reviews.[1] JATS allows for descriptions of the full article content or just the article header metadata; and allows other kinds of contents, including research and non-research articles, letters, editorials, and book and product reviews.

History

Summarized timeline:

Since its introduction, NCBI's NLM Archiving and Interchange DTD suite has become the de facto standard for journal article markup in scholarly publishing.[2] With the introduction of NISO JATS, it has been elevated to a true standard.[3] Even without public data interchange, the advantages of NISO JATS adoption affords publishers in terms of streamlining production workflows and optimizing system interoperability.[4][5]

Technical scope

By design, this is a model for journal articles, such as the typical research article found in an STM journal, and not a model for complete journals.[6] There are three Tag Sets:

Structural Overview
JATS defines a document that is a top-level component of a journal such as an article, a book or product review, or a letter to the editor. Each such document is composed of one or more parts; if there is more than one part, they must appear in the following order:
Tag Sets Developed from the Suite
Document type definitions (also released in the form of RELAX NG and XML schema) define each type of JATS (archiving, publishing and authoring) and incorporate other standards such as MathML and XHTML Tables (although not in the XHTML namespace).

Example

This is the minimal article's structure,

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE article
  PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.0 20120330//EN"
         "JATS-journalpublishing1.dtd"
>
<article dtd-version="1.0" article-type="article" specific-use="migrated"
 xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" 
>
  <front>...</front>
  <body>...</body>
  <back>...</back>
</article>

The DOCTYPE header is optional, a legacy from SGML and DTD-oriented validators. The dtd-version attribut can be used even without a DTD header.

The root element article is commom for any version of JATS or "JATS family", as NLM DTDs. The rules for front, body and back tags validation, depends on the JATS version, but all versions have similar structure, with good compatibility in a range of years. The evolution of the schema preserves an overall stability.

Less commom, "only front", "only front and back" variations are also used for other finalities tham full-content representation. The general article composition (as an DTD-content expression) is

   (front, body?, back?, floats-group?, (sub-article* | response*))

Tools

There are a variety of tools for create, edit, convert and transform JATS. They range from simple forms [7] to complete conversion automation:

Conversion to JATS
Take as input a scientific document, and, with some human support, produce a JATS output.
Conversion from JATS
Take JATS as input, produce another kind of document as output.
Editing Tools
Edit JATS code.
Preview Tools
To render JATS as HTML (in general on fly).
Standard customization
"jatsdoc",[24] also included as part of the DtdAnalyzer,[25] provides for the production of documentation pages like this for any particular JATS customization.

JATS central repositories

As NISO JATS began the de facto and de juri standard for open access journals, the scientific community has adopted the JATS repositories as a kind of legal deposit, more valuable than the traditional digital libraries where only a PDF version is stored. Open knowledge need richer and structured formats as JATS: PDF and JATS must be certified as "same content", and the set "PDF+JATS" forming the unit of legal deposit. List of JATS repositories and its contained:

NOTE: there are some overlapping in the repositories, the same article can be accessed in more than one repositories.

See also

Related to

        

Used by

        

Similar to

References

  1. ↑ ANSI/NISO Z39.96-2012 ISSN 1041-5653. See z39.96-2012.pdf at www.niso.org/standards/z39-96-2012
  2. ↑ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227009/
  3. ↑ http://river-valley.zeeba.tv/the-new-niso-journal-article-tag-suite-standard/
  4. ↑ "The Long Road to JATS", 2015, http://www.ncbi.nlm.nih.gov/books/NBK279831/
  5. ↑ "Superimposing Business Rules on JATS", 2015, http://www.ncbi.nlm.nih.gov/books/NBK279902/
  6. ↑ http://jats.nlm.nih.gov/publishing/tag-library/1.0, General Introduction
  7. ↑ A 2012's semanticpublishing.wordpress.com JATS Metadata Input Form
  8. ↑ http://www.oucs.ox.ac.uk/oxgarage/ (documentation)
  9. ↑ "MartinPaulEve/meTypeset". GitHub.
  10. ↑ "eXtyles".
  11. ↑ https://github.com/mfenner/pandoc-jats (how-to and explain)
  12. ↑ http://shabash.net/merops/automatic_text_editing.php
  13. ↑ "Public Knowledge Project".
  14. ↑ Constantin, S.Pettifer (2013). "PDFX: fully-automated PDF-to-XML conversion of scientific literature". Proceedings of the 2013 ACM symposium on Document engineering - DocEng 13. doi:10.1145/2494266.2494271.
  15. ↑ "eLife Lens".
  16. ↑ biglist.com/mulberrytech msg and ncbi.nlm.nih.gov/books article description
  17. ↑ "ncbi/DtdAnalyzer". GitHub.
  18. ↑ "wendellpiez/oXygenJATSframework". GitHub.
  19. ↑ "Annotum". Annotum.
  20. ↑ Carl Leubsdorf, Jr. "Annotum: An open-source authoring and publishing platform based on WordPress". Journal Article Tag Suite Conference (JATS-Con) Proceedings 2011 - NCBI Bookshelf.
  21. ↑ "ncbi/JATSPreviewStylesheets". GitHub.
  22. ↑ Wendell Piez. "Fitting the Journal Publishing 3.0 Preview Stylesheets to Your Needs: Capabilities and Customizations". Journal Article Tag Suite Conference (JATS-Con) Proceedings 2010 - NCBI Bookshelf.
  23. ↑ NCBI/PubReader with source-code at github.com/ncbi/PubReader
  24. ↑ "Klortho/jatsdoc". GitHub.
  25. ↑ "DtdAnalyzer".
  26. ↑ PMC home, http://www.ncbi.nlm.nih.gov/pmc/
  27. ↑ PMC Europe, "about" page, http://europepmc.org/About
  28. ↑ PMC-Canadá FAQ, http://pubmedcentralcanada.ca/pmcc/static/aboutUs/#q6
  29. ↑ SciELO home, http://www.scielo.org/php/index.php?lang=en

External links

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