Journal Article Tag Suite

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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:

  • 2003: NLM introduced the NLM DTD v1.0
  • 2004: update to NLM DTD v2.0
  • 2008: update to NLM DTD v3.0
  • 2012: NISO introduced the JATS v1.0 as adaptation of NLM DTD v3.1

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:

  • Journal Archiving and Interchange: the most permissive of the Tag Sets, primarily intended for the capture and archiving of extant journal data. Its documentation is color-coded green and the model is colloquially referred to as the Green Tag Set.
  • Journal Publishing: a moderately prescriptive Tag Set, intended for general use in journal production and publication. Formally this model is a subset of the Archiving model. Due to the color scheme of its documentation it is referred to as the Blue Tag Set.
  • Article Authoring: the most prescriptive ("tightest" and smallest) of the Tag Sets, intended for the relatively lightweight creation of journal articles valid to JATS. Formally a subset of Blue, it is referred to as the Orange Tag Set.
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:
  • Front matter (required). The article front matter contains the metadata for the article (also called article header information), for example, the article title, the journal in which it appears, the date and issue of publication for that issue of that journal, a copyright statement, etc. Both article-level and issue-level metadata (in the element <article-meta>) and journal-level metadata (in the element <journal-meta>) may be captured.
  • Body of the article (optional). The body of the article is the main textual and graphic content of the article. This usually consists of paragraphs and sections, which may themselves contain figures, tables, sidebars (boxed text), etc. The body of the article is optional to accommodate those repositories that just keep article header information and do not tag the textual content.
  • Back matter for the article (optional). If present, the article back matter contains information that is ancillary to the main text, such as a glossary, appendix, or list of cited references.
  • Floating Material (optional). A publisher may choose to place all the floating objects in an article and its back matter (such as tables, figures, boxed text sidebars, etc.) into a separate container element outside the narrative flow for convenience of processing.
  • Following the front, body, back, and floating material, there may be either one or more responses to the article or one or more subordinate articles.
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.
  • OpenOffice (LibreOffice) and MS Word documents to JATS:
    • OxGarage:[8] can convert documents from various formats into "National Library of Medicine (NLM) DTD 3.0".
    • meTypeset: meTypeset[9] "is a fork of the OxGarage stack" "to convert from Microsoft Word .docx format to NLM/JATS-XML".
    • eXtyles:[10] automates time-consuming aspects of document editing in Microsoft Word and exports to JATS XML (as well as many other DTDs).
  • Markdown to JATS: pandoc's "pandoc-jats" plugin.[11]
  • 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.
    • Shabash Merops[12]
    • The Public Knowledge Project[13] is developing a pipeline for converting PDF to JATS. It will include use of pdfx.[14]
Conversion from JATS
Take JATS as input, produce another kind of document as output.
  • from JATS to HTML
    • JATS Preview Stylesheets (canonical XSLT conversion)
    • eLife Lens[15] converts NLM XML to JSON for displaying using HTML and Javascript.
  • from JATS to PDF: some JATS Preview Stylesheets, XSLT + XSL-FO conversion.
  • from JATS to EPUB.[16]
  • Generic (from JATS DTD): DtdAnalyzer[17] — compare JATS with other DTDs and helps into create a XML representation, XSLT and Schematron generation, and other tools.
Editing Tools
Edit JATS code.
  • 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 an identifier given in a DOCTYPE declaration, oXygen will detect that you are editing a JATS document and provide stylesheets and utilities.[18]
  • Annotum:[19] a WordPress theme that contains WYSIWYG authoring in JATS (Kipling subset), peer-review and editorial management, and publishing.[20]
Preview Tools
To render JATS as HTML (in general on fly).
  • JATS Preview Stylesheets:[21] 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. It is primarily intended for internal use by publishers and a basis for customization.[22]
  • PubReader – "The PubReader view is an alternative web presentation ... Designed particularly for enhancing readability on tablet and other small screen devices, PubReader can also be used on desktops and laptops and from multiple web browsers".[23]
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. Lua error in package.lua at line 80: module 'strict' not found.
  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. Lua error in package.lua at line 80: module 'strict' not found.
  10. Lua error in package.lua at line 80: module 'strict' not found.
  11. https://github.com/mfenner/pandoc-jats (how-to and explain)
  12. http://shabash.net/merops/automatic_text_editing.php
  13. Lua error in package.lua at line 80: module 'strict' not found.
  14. Lua error in package.lua at line 80: module 'strict' not found.
  15. Lua error in package.lua at line 80: module 'strict' not found.
  16. biglist.com/mulberrytech msg and ncbi.nlm.nih.gov/books article description
  17. Lua error in package.lua at line 80: module 'strict' not found.
  18. Lua error in package.lua at line 80: module 'strict' not found.
  19. Lua error in package.lua at line 80: module 'strict' not found.
  20. Lua error in package.lua at line 80: module 'strict' not found.
  21. Lua error in package.lua at line 80: module 'strict' not found.
  22. Lua error in package.lua at line 80: module 'strict' not found.
  23. NCBI/PubReader with source-code at github.com/ncbi/PubReader
  24. Lua error in package.lua at line 80: module 'strict' not found.
  25. Lua error in package.lua at line 80: module 'strict' not found.
  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