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jats-fundamentals

What Is JATS XML and Why It Matters for Scholarly Journals

EditorialXML5 min read
  • jats
  • xml
  • scholarly-journals

Journal Article Tag Suite (JATS) is the world's most widely used XML standard for representing scholarly journal articles in structured format. Originally developed by the National Center for Biotechnology Information (NCBI) and maintained by the National Information Standards Organization (NISO), JATS defines a vocabulary of tags that precisely describes the semantic structure of an article—from bibliographic metadata to references, tables, figures, and body sections.

For editors, journal managers, and editorial production teams in Latin America and beyond, understanding JATS is not a technical luxury: it is a prerequisite for participating in international indexing ecosystems, meeting repository requirements such as SciELO and PubMed Central (PMC), and automating workflows that still depend on PDFs and manual processes.

Why XML and Not Just PDF?

For decades, PDF was the dominant format for publishing scientific articles. It is readable, portable, and familiar. However, a PDF is fundamentally a presentation document: machines cannot reliably extract section hierarchy, author names, ORCID identifiers, or bibliographic references without human intervention or costly processing.

JATS XML solves this problem by separating content from presentation. Every element of the article—title, abstract, paragraph, equation, table, footnote—is tagged with semantic meaning. This enables:

  • Automatic indexing in databases such as PubMed, Crossref, and SciELO.
  • Content reuse across multiple formats: HTML, ePub, PDF, RSS feeds.
  • Programmatic validation before publication, detecting structural errors early.
  • Improved accessibility for readers using assistive technologies and search engines.

Basic Structure of a JATS Document

A JATS article is organized into three main blocks within the root <article> element:

<?xml version="1.0" encoding="UTF-8"?>
<article xmlns:xlink="http://www.w3.org/1999/xlink"
         article-type="research-article"
         dtd-version="1.3">
  <front>
    <journal-meta>
      <journal-title-group>
        <journal-title>Journal of Scientific Research</journal-title>
      </journal-title-group>
      <issn pub-type="epub">1234-5678</issn>
    </journal-meta>
    <article-meta>
      <article-id pub-id-type="doi">10.1234/jsr.2026.001</article-id>
      <title-group>
        <article-title>Title of the research article</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <name>
            <surname>García</surname>
            <given-names>María</given-names>
          </name>
          <contrib-id contrib-id-type="orcid">https://orcid.org/0000-0001-2345-6789</contrib-id>
        </contrib>
      </contrib-group>
      <abstract>
        <p>Structured abstract of the article...</p>
      </abstract>
      <kwd-group>
        <kwd>keyword one</kwd>
        <kwd>keyword two</kwd>
      </kwd-group>
    </article-meta>
  </front>
  <body>
    <sec sec-type="intro">
      <title>Introduction</title>
      <p>First paragraph of the article body...</p>
    </sec>
  </body>
  <back>
    <ref-list>
      <ref id="ref1">
        <element-citation publication-type="journal">
          <person-group person-group-type="author">
            <name><surname>López</surname><given-names>Juan</given-names></name>
          </person-group>
          <article-title>Title of the reference</article-title>
          <source>Journal Name</source>
          <year>2024</year>
        </element-citation>
      </ref>
    </ref-list>
  </back>
</article>

The <front> Block

Contains two sections: <journal-meta> (journal data: ISSN, title, publisher) and <article-meta> (article metadata: DOI, authors, affiliations, abstract, keywords, submission and acceptance dates). The quality of this metadata largely determines the article's visibility in directories and academic search engines.

The <body> Block

Houses the narrative content of the article, organized into sections (<sec>) with titles, paragraphs, lists, tables (<table-wrap>), figures (<fig>), and mathematical formulas. Each element can carry identifiers (id) that enable internal links and cross-references.

The <back> Block

Includes bibliographic references (<ref-list>), acknowledgments, funding notes, conflict of interest statements, and supplementary material. References can be expressed in structured format (<element-citation>) or as free text (<mixed-citation>), though structured format facilitates validation and interoperability.

JATS Variants: Archiving, Publishing, and Authoring

JATS defines three DTD/Schema profiles:

ProfilePrimary use
JATS ArchivingExchange between repositories and archives (PMC, SciELO)
JATS PublishingEditorial production and online publication
JATS AuthoringCreation and editing by authors

Most Latin American journals aspiring to indexing in SciELO or PMC work with the Archiving profile, which is the strictest regarding structure and mandatory metadata.

JATS in the Latin American Ecosystem

In Latin America, JATS XML adoption has grown alongside initiatives such as SciELO, Redalyc, and various open access programs funded by national research agencies. Journals migrating from Word- or LaTeX-based workflows to XML production report:

  • Fewer metadata errors before indexing.
  • More predictable publication timelines.
  • Greater compatibility with international standards (DOI, ORCID, funders).
  • Ability to automatically generate responsive HTML versions from the same source file.

However, the learning curve is real. Small editorial teams—common in university journals—need accessible tools and automated validation to avoid depending exclusively on external consultants.

Validation: The Step You Cannot Skip

A well-formed XML file is not necessarily valid JATS. Validation against the JATS schema and repository-specific rules (SciELO SPS, PMC) is essential before submitting articles for indexing.

You can validate your JATS files for free with the EditorialXML JATS validator, which detects structural errors, missing attributes, and reference problems before they block your publication process.

JATS Production: From Manuscript to XML

The path from a Word or PDF manuscript to compliant JATS XML passes through several stages:

  1. Ingestion and cleanup of the source document.
  2. Semantic tagging of sections, figures, and tables.
  3. Metadata normalization (authors, affiliations, ORCID, DOI).
  4. Reference conversion to structured format.
  5. Validation against JATS and destination repository rules.
  6. Derivative generation (HTML, PDF, ePub).

If your journal lacks internal capacity for these stages, EditorialXML's JATS XML production service offers a complete workflow with validation included and delivery in the formats your indexer requires.

Frequently Asked Questions

Does JATS replace LaTeX? Not necessarily. Many mathematics and physics journals still accept LaTeX for typographic composition, but convert the final output to JATS XML for archiving and indexing.

How much does implementing JATS cost? The standard itself is open and free. The real cost lies in team training, conversion tools, and ongoing validation. Investing in automation reduces costs in the medium term.

Can I generate JATS from an editorial management system (OJS)? Yes. Open Journal Systems and other platforms offer JATS export plugins, though the quality of generated XML varies and usually requires manual review.

Conclusion

JATS XML is the structured language that connects editorial production with open science, international indexing, and knowledge reuse. For Spanish- and Portuguese-language scientific journals seeking global visibility, adopting JATS—with rigorous validation and normalized metadata—is no longer optional: it is the foundation on which sustainable, discoverable publishing is built.

Start by validating a test article in the JATS validator or request an evaluation of your production workflow through JATS XML production.

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