Journal Article Tag Suite

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The NISO Journal Article Tag Suite, or simply JATS, is formally the technical standard NISO Z39.96 2012-08-22 (NISO JATS 1.0). 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 formating 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]

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. With the introduction of JATS, it has been elevated to a true standard.

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.[2] There are three Tag Sets:

  • Journal Archiving and Interchange: the most permissive of the Tag Sets.
  • Journal Publishing: a moderately prescriptive Tag Set.
  • Article Authoring: the most prescriptive of the 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:
  • 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
XML schemas define each type of JATS (archiving, publishing and authoring) and use other standards as XHTML tables modularization and MathML.

Example[edit]

<?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>

Tools[edit]

There are a variety of tools for create, edit, convert and transform JATS. They range from simple forms [3] to complete conversion automation:

Conversion to JATS
Take as input a scientific document, and, with some human support, produce a JATS output.
  • OpenOffice and MS-Word documents to JATS:
    • OxGarage: OxGarage can convert documents from various formats into "National Library of Medicine (NLM) DTD 3.0". See documentation.
    • meTypeset: meTypeset "is a fork of the OxGarage stack" "to convert from Microsoft Word .docx format to NLM/JATS-XML".
    • eXtyles: eXtyles 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-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.
Conversion from JATS
Take JATS as input, produce another kind of document as output.
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 a identifier given in a DOCTYPE declaration, oXygen will detect that you are editing a JATS document and provide stylesheets and utilities.[4]
  • Annotum: a WordPress theme that contains WYSIWYG authoring in JATS (Kipling subset), peer-review and editorial management, and publishing. See a JATS-Con 2011 presentation.
Preview Tools
To render JATS as HTML (in general on fly).
  • JATS Preview Stylesheets (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.
  • PubReader - "The PubReader view is an alternative web presentation that offers another, more reader-friendly way (...) 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".[5]
Standard customization
jatsdoc, also included as part of the DtdAnalyzer, provides for the production of documentation pages like this for any particular JATS customization.

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. ^ http://jats.nlm.nih.gov/publishing/tag-library/1.0, General Introduction
  3. ^ A 2012's semanticpublishing.wordpress.com JATS Metadata Input Form
  4. ^ https://github.com/wendellpiez/oXygenJATSframework
  5. ^ NCBI/PubReader with source-code at github.com/ncbi/PubReader

External links[edit]