Journal Article Tag Suite

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Journal Article Tag Suite
Jats-logo.jpg
Status Published
First published 31 March 2003 (2003-03-31)
Latest version NISO JATS 1.1
6 January 2016 (2016-01-06)
Organization
Authors
Base standards XML
Related standards
  • ISO Standards Tag Set (ISOSTS)
  • NISO Book Interchange Tag Suite (BITS)
  • SciELO Publishing Schema (SPS)
Domain
Abbreviation JATS
Website jats.niso.org

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[edit]

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]

Timeline[edit]

NLM JATS
NLM JATS, version 1
  • March 31, 2003 (2003-03-31): NLM DTD v1.0 introduced.[6]
  • November 5, 2003 (2003-11-05): Version 1.1 update released.[6]
NLM JATS, version 2
  • December 30, 2004 (2004-12-30): Version 2.0 major update released. It is designed to support customization best-practices.[6]
  • November 14, 2005 (2005-11-14): Version 2.1 update released with the addition the Article Authoring DTD.[6][7]
  • June 8, 2006 (2006-06-08): Version 2.2 update released.[6]
  • March 28, 2007 (2007-03-28): Version 2.3 update released.[6]
NLM JATS, version 3
  • November 21, 2008 (2008-11-21): Version 3.0 major update released.[6][7]
NISO JATS
NISO JATS, version 1.0
  • March 30, 2011 (2011-03-30)–September 30, 2011 (2011-09-30): First draft, NISO Z39.96.201x version 0.4 released; six-month comment period.[8]
  • July 15, 2012 (2012-07-15): NISO JATS, v1.0 received NISO approval.[9]
  • August 9, 2012 (2012-08-09): NISO JATS, v1.0 received ANSI approval.[9]
  • August 22, 2012 (2012-08-22): ANSI/NISO Z39.96-2012, JATS: Journal Article Tag Suite (version 1.0) published. It supports full backward-compatibility with NLM JATS v3.0.[6][9]
NISO JATS, version 1.1
  • December 9, 2013 (2013-12-09): First draft, NISO JATS, v1.1d1 released.[10]
  • December 29, 2014 (2014-12-29): Second draft, NISO JATS, v1.1d2 released.[11]
  • April 14, 2015 (2015-04-14): Third draft, NISO JATS, v1.1d released.[12]
  • October 22, 2015 (2015-10-22): NISO JATS, v1.1 received NISO approval.[13]
  • November 19, 2015 (2015-11-19): NISO JATS, v1.1 received ANSI approval[13]
  • January 6, 2016 (2016-01-06): ANSI/NISO Z39.96-2015, JATS: Journal Article Tag Suite, version 1.1 published.[13]

Technical scope[edit]

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.[14]

Tag sets[edit]

There are three tag sets, which due to their color-coded documentation, are colloquially referred to by color:

Journal Archiving and Interchange (Green)
"The most permissive of the Tag Sets,"[15] primarily intended for the capture and archiving of extant journal data.
Journal Publishing (Blue)
"A moderately prescriptive Tag Set,"[15] intended for general use in journal production and publication.
Formally this model is a subset of the Archiving model.
Article Authoring (Orange)
"The most prescriptive [tightest and smallest] of the Tag Sets,"[15] intended for the relatively lightweight creation of journal articles valid to JATS.
Formally this model a subset of the Publishing model.

Document type definitions (also released in the form of RELAX NG and XML schema) define each set and incorporate other standards such as MathML and XHTML Tables (although not in the XHTML namespace).

Document structure[edit]

JATS Publishing set 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 front matter (required) and up to three optional parts.[14] These must appear in the following order:

Front matter
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)
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
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
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.[14]

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.[14]

Example[edit]

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[edit]

There are a variety of tools for create, edit, convert and transform JATS. They range from simple forms[16] to complete conversion automation:

Conversion[edit]

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:[17] can convert documents from various formats into "National Library of Medicine (NLM) DTD 3.0".
    • meTypeset: meTypeset[18] "is a fork of the OxGarage stack" "to convert from Microsoft Word .docx format to NLM/JATS-XML".
    • eXtyles:[19] 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.[20]
  • 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[21]
    • The Public Knowledge Project[22] is developing a pipeline for converting PDF to JATS. It will include use of pdfx.[23]
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[24] 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.[25]
  • Generic (from JATS DTD): DtdAnalyzer[26] — compare JATS with other DTDs and helps into create a XML representation, XSLT and Schematron generation, and other tools.

Editors[edit]

  • 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.[27]
  • FontoXML for JATS: WYSIWYS editor for editing and reviewing JATS content: [28]
  • Annotum:[29] a WordPress theme that contains WYSIWYG authoring in JATS (Kipling subset), peer-review and editorial management, and publishing.[30]
  • JATS edition for web-based XML editor Xeditor.
  • Texture Editor[31] of the Substance Consortium.[32]

Preview[edit]

Tools that render JATS as HTML, usually on fly.

  • JATS Preview Stylesheets:[33] 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.[34]
  • 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".[35]

Customization[edit]

Jatsdoc
Produces documentation for any particular JATS customization. Jatsdoc is integrated with NCBI's DtdAnalyzer.[36][37]

JATS central repositories[edit]

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[edit]

References[edit]

  1. ^ ANSI/NISO Z39.96-2012 ISSN 1041-5653. See z39.96-2012.pdf at www.niso.org/standards/z39-96-2012
  2. ^ Beck, J (2011). "NISO Z39.96The Journal Article Tag Suite (JATS): What Happened to the NLM DTDs?". J Electron Publ. 14. doi:10.3998/3336451.0014.106. PMC 3227009Freely accessible. PMID 22140303. 
  3. ^ Zimmerman, Sara (2012). "The new NISO journal Article Tag Suite standard". Zeeba.tv. 
  4. ^ Donohoe, Paul; Sherman, Jenny; Mistry, Ashwin (2015). "The Long Road to JATS". Journal Article Tag Suite Conference (JATS-Con) Proceedings 2015. JATS-Con 2015. Bethesda, MD: National Center for Biotechnology Information. 
  5. ^ Usdin, Tommie; Lapeyre, Deborah Aleyne; Glass, Carter M. (2015). "Superimposing Business Rules on JATS". Journal Article Tag Suite Conference (JATS-Con) Proceedings 2015. JATS-Con 2015. Bethesda, MD: National Center for Biotechnology Information. 
  6. ^ a b c d e f g h "NLM Journal Archiving and Interchange Tag Suite". National Center for Biotechnology Information. 13 September 2012. Archived from the original on 27 August 2016. 
  7. ^ a b "JATS and the NLM DTDs". Journal Article Tag Suite. National Center for Biotechnology Information. 8 January 2016. Archived from the original on 7 March 2016. 
  8. ^ "NISO JATS v0.4: Draft Standard for Trial Use". Journal Article Tag Suite. National Center for Biotechnology Information. 
  9. ^ a b c "ANSI/NISO Z39.96-2012 JATS: Journal Article Tag Suite". National Information Standards Organization. 26 July 2013. 
  10. ^ "JATS v1.1d1 (DRAFT)". Journal Article Tag Suite. National Center for Biotechnology Information. 14 April 2015. 
  11. ^ "JATS v1.1d2 (DRAFT)". Journal Article Tag Suite. National Center for Biotechnology Information. 14 April 2015. 
  12. ^ "JATS v1.1d3 (DRAFT)". Journal Article Tag Suite. National Center for Biotechnology Information. 14 April 2015. 
  13. ^ a b c "ANSI/NISO Z39.96-2015 JATS: Journal Article Tag Suite". National Information Standards Organization. 8 January 2016. 
  14. ^ a b c d "General Introduction". Journal Publishing Tag Library NISO JATS Version 1.0. National Center for Biotechnology Information. August 2012. 
  15. ^ a b c "JATS: Journal Article Tag Suite". National Center for Biotechnology Information. 
  16. ^ A 2012's semanticpublishing.wordpress.com JATS Metadata Input Form.
  17. ^ http://www.oucs.ox.ac.uk/oxgarage/ (documentation)
  18. ^ "MartinPaulEve/meTypeset". GitHub. 
  19. ^ "eXtyles". 
  20. ^ https://github.com/mfenner/pandoc-jats (how-to and explain)
  21. ^ http://shabash.net/merops/automatic_text_editing.php
  22. ^ "Public Knowledge Project". 
  23. ^ 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. 
  24. ^ "eLife Lens". 
  25. ^ biglist.com/mulberrytech msg and ncbi.nlm.nih.gov/books article description
  26. ^ "ncbi/DtdAnalyzer". GitHub. 
  27. ^ "wendellpiez/oXygenJATSframework". GitHub. 
  28. ^ https://fontoxml.com/jats/
  29. ^ "Annotum". Annotum. 
  30. ^ 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. 
  31. ^ https://github.com/substance/texture
  32. ^ http://substance.io/consortium/
  33. ^ "ncbi/JATSPreviewStylesheets". GitHub. 
  34. ^ 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. 
  35. ^ NCBI/PubReader with source-code at github.com/ncbi/PubReader
  36. ^ Maloney, Chris. "Jatsdoc Documentation Browser". GitHub. 
  37. ^ "DtdAnalyzer: A tool for analyzing and manipulating DTDs". Journal Archiving and Interchange Tag Suite. National Center for Biotechnology Information. 
  38. ^ PMC home, http://www.ncbi.nlm.nih.gov/pmc/
  39. ^ PMC Europe, "about" page, http://europepmc.org/About
  40. ^ PMC-Canadá FAQ, http://pubmedcentralcanada.ca/pmcc/static/aboutUs/#q6
  41. ^ SciELO home, http://www.scielo.org/php/index.php?lang=en

Further reading[edit]

External links[edit]