Complete JATS XML Guide for Scientific Journals

This complete guide brings together everything a journal director, editor, or production manager needs to know about JATS XML —the standard that defines how to represent scientific articles in structured format for archiving, indexing, and digital publication. From NISO standard fundamentals to advanced production workflows, this pillar resource is designed as a permanent reference for editorial teams publishing in English, Spanish, and Portuguese.

1. Origin and context of the JATS standard

From NLM DTD to NISO Z39.96

JATS has its roots in the NLM Journal Archiving and Interchange DTD, developed by the National Library of Medicine (NLM) and the National Center for Biotechnology Information (NCBI) to support PubMed Central. In 2012, NISO formalized the standard as Z39.96-2012. That base schema went through successive revisions —including version 1.3 in 2021, which was the industry's common reference for several years— up to the current version, JATS 1.4, published as ANSI/NISO Z39.96-2024.

The standard is open, free, and maintained by a community that includes publishers, repositories, tool developers, and libraries. Its adoption extends far beyond PubMed: SciELO, Redalyc, DOAJ, and hundreds of commercial and university publishers produce or accept JATS XML; Crossref, for its part, registers DOIs and metadata through workflows that often start from JATS or other formats.

Why an XML standard for articles?

Academic science depends on interoperability: an article published in a Chilean journal must be discoverable by a researcher in Germany, citable with persistent identifiers, and reusable in systematic reviews. PDF does not provide the semantic structure machines need to:

• Index authors, affiliations, and keywords.
• Resolve DOIs and link citations.
• Extract tables and figures for databases.
• Generate multiple output formats from a single source.

JATS XML is the industry's consensus answer to this problem.

2. The three JATS Tag Sets

JATS defines three Tag Sets (schema profiles), each with a different level of restriction:

JATS Archiving and Interchange Tag Set

The most permissive of the three: its content model allows the widest range of structures, precisely because it needs to represent the heterogeneous universe of articles arriving at a repository or archive from publishers with different conventions. Prioritizes metadata completeness and long-term preservation.

When to use: Repository exchange, long-term digital archiving, retrospective conversion of heterogeneous editorial backfiles.

JATS Journal Publishing Tag Set

Moderately prescriptive: more restrictive than Archiving, but flexible enough for different editorial production workflows (editing, revision, composition). It is the basis SciELO builds its SPS schema on.

When to use: Publisher workflows producing and publishing new content on an ongoing basis.

JATS Article Authoring Tag Set

The most restrictive and prescriptive of the three: it deliberately narrows structural options to simplify and standardize the creation of new articles by authors or authoring tools.

When to use: Author writing tools, initial submission templates.

No standards body mandates the Archiving Tag Set as a universal requirement: SciELO SPS is built on the Journal Publishing Tag Set (DTD 1.1), not Archiving, and PMC recommends the Journal Publishing Tag Set together with its own PMC Tagging Guidelines. Conforming to a JATS schema — any of the three Tag Sets — is necessary but not sufficient: XML that is schema-valid JATS is not automatically valid for SciELO's or PMC's additional business rules.

3. Anatomy of a JATS document

Root element: <article>

<article xmlns:xlink="http://www.w3.org/1999/xlink"
         xmlns:mml="http://www.w3.org/1998/Math/MathML"
         article-type="research-article"
         dtd-version="1.4"
         xml:lang="en">

Critical attributes:

<front> block: metadata

The front matter divides into:

<journal-meta>

Identifies the journal:

<journal-meta>
  <journal-id journal-id-type="publisher-id">JSR</journal-id>
  <journal-title-group>
    <journal-title>Journal of Scientific Research</journal-title>
    <abbrev-journal-title abbrev-type="publisher">J. Sci. Res.</abbrev-journal-title>
  </journal-title-group>
  <issn pub-type="epub">1234-5678</issn>
  <publisher>
    <publisher-name>National University</publisher-name>
  </publisher>
</journal-meta>

<article-meta>

Individual article metadata including DOI, authors, affiliations, abstract, keywords, submission dates, funding, and license. Complete <article-meta> is the foundation of discoverability in directories and academic search engines.

<body> block: narrative content

The article body organizes into nested sections:

<body>
  <sec sec-type="intro" id="sec1">
    <title>Introduction</title>
    <p>First paragraph with citation <xref ref-type="bibr" rid="ref1">1</xref>
       and figure reference <xref ref-type="fig" rid="fig1">1</xref>.</p>
  </sec>
  <sec sec-type="methods" id="sec2">
    <title>Materials and methods</title>
    <p>Methods description...</p>
  </sec>
  <fig id="fig1">
    <label>Figure 1</label>
    <caption><title>Frequency distribution</title></caption>
    <graphic xlink:href="fig1.png" mime-subtype="png"/>
  </fig>
</body>

<back> block: closing material

Includes bibliographic references (<ref-list>), acknowledgments, funding notes, conflict of interest statements, and supplementary material. Structured references (<element-citation>) facilitate validation and interoperability.

4. Article types (article-type)

In the generic JATS 1.4 schema, article-type is an optional attribute; however, destinations such as SciELO's SPS require it, and its correct value affects business-rule validation at that and other repositories:

5. JATS validation

Validation levels

1. Well-formed: XML parses without syntax errors.
2. Valid: Complies with the applicable JATS schema (Archiving, Journal Publishing, or Article Authoring, depending on destination).
3. Business rules: Meets additional SciELO SPS, PMC, or other destination requirements — a separate step from JATS schema validation.

Tools

• EditorialXML JATS validator — free online validation
• xmllint with JATS schema — command line
• Oxygen XML Editor — professional IDE with integrated validation

Most frequent errors

See our error guides library for detailed diagnosis. The most common:

• Element in disallowed position
• Missing required attribute
• Duplicate IDs
• Malformed references
• Invalid document structure

6. Editorial production with JATS

Recommended workflow

Accepted manuscript
    ↓
Structured metadata collection
    ↓
Conversion / XML tagging
    ↓
Author, ORCID, DOI normalization
    ↓
Reference conversion to element-citation
    ↓
JATS validation
    ↓
Error correction
    ↓
Revalidation
    ↓
Derivative generation (HTML, PDF)
    ↓
Repository delivery

Derivatives from JATS

Validated JATS XML can support generation of HTML, PDF, ePub, and Crossref deposit metadata, and can be adapted for PMC or SciELO once the Tag Set, version, and platform rules match the destination. The "XML as canonical source" principle means other formats are regenerable —never the reverse.

7. JATS and repositories

SciELO (SPS)

The SciELO Publishing Schema (SPS) extends the JATS Journal Publishing 1.1 DTD with Latin American rules. Requires CC license, electronic ISSN, translated abstract, and complete affiliations. See the step-by-step SciELO preparation guide.

PubMed Central (PMC)

PMC recommends the Journal Publishing Tag Set together with its PMC Tagging Guidelines and minimum data criteria. NIH requirements: open access or a declared embargo, identified funding, MathML for equations. See PMC requirements for open access journals.

Crossref

Crossref is not an index or article repository comparable to SciELO or PMC: it is DOI registration and citation-metadata infrastructure. Producing JATS XML does not automatically register or index an article with Crossref — metadata deposit with Crossref is a separate step, even though it can be generated from the same source JATS.

8. Best practices

For journal directors

1. Adopt JATS as source format, not as a PDF derivative.
2. Invest in continuous validation, not just pre-delivery.
3. Document internal XML conventions.
4. Train at least one team member in basic JATS.
5. Evaluate outsourcing when volume exceeds 20 articles/year.

See the editorial XML production guide for editors for strategic planning.

For production teams

1. Use XML templates with predefined mandatory fields.
2. Validate each article as it enters the workflow.
3. Normalize metadata systematically (ORCID, DOI, affiliations).
4. Maintain a log of recurring errors and solutions.
5. Version XML files with change control.

9. Tools and services

10. Glossary

Conclusion

JATS XML is not a technical fad or bureaucratic requirement: it is the infrastructure that allows scientific journals to participate in global open science with standards equivalent to the world's largest publishers. This complete guide is your starting point; continuous practice, systematic validation, and iterative process improvement transform theoretical knowledge into frictionless publication.

Take the next step by validating an article in the JATS validator or explore JATS XML production and SciELO preparation services.