Guide

Complete JATS XML Guide for Scientific Journals

Comprehensive pillar resource on JATS XML: NISO standard, structure, metadata, validation, editorial production, and best practices for academic 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, updated to version 1.3 in 2021.

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, Crossref, DOAJ, and hundreds of commercial and university publishers produce or accept JATS XML.

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 profiles

JATS defines three schema profiles, each optimized for a use case:

JATS Archiving (JATS-archive)

The most widely used profile for exchange between repositories. Required by SciELO SPS and PubMed Central. Prioritizes metadata completeness and long-term preservation over presentation flexibility.

When to use: Repository delivery, digital archiving, international indexing.

JATS Publishing (JATS-publish)

Designed for the editorial production chain. Allows greater flexibility in presentation elements and production metadata (editing, revision, composition).

When to use: Commercial publisher workflows with proprietary composition systems.

JATS Authoring (JATS-author)

Simplified for content creation by authors. Fewer mandatory elements, more permissive structure.

When to use: Author writing tools, initial conversion from Word.

For Latin American journals targeting SciELO or PMC, JATS Archiving is the mandatory profile.

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="1.3"
         xml:lang="en">

Critical attributes:

Attribute	Values	Required
`article-type`	research-article, review-article, case-report, editorial, letter, etc.	Yes
`dtd-version`	1.3 (current version)	Yes
`xml:lang`	ISO language code	Recommended
`specific-use`	sps-1.9 (for SciELO)	Per destination

`<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)

Selecting the correct article-type is mandatory and affects validation in repositories:

Type	Use
`research-article`	Original research
`review-article`	Narrative or systematic review
`case-report`	Clinical case report
`brief-report`	Short communication
`editorial`	Issue editorial
`letter`	Letter to the editor

5. JATS validation

Validation levels

Well-formed: XML parses without syntax errors.
Valid: Complies with JATS Archiving schema.
Business rules: Meets SciELO SPS, PMC, or other destination requirements.

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 automatically generate HTML, PDF, ePub, Crossref metadata, and PMC/SciELO XML with minimal adjustments. The "XML as canonical source" principle means all other formats are regenerable —never the reverse.

7. JATS and repositories

SciELO (SPS)

Extends JATS Archiving 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)

NIH requirements: open access, declared funding, MathML for equations. See PMC requirements for open access journals.

Crossref

Not an article repository, but registers DOIs and metadata. JATS XML feeds metadata registration.

8. Best practices

For journal directors

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

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

For production teams

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

9. Tools and services

Tool	Function
JATS validator	Online validation
JATS XML production	Conversion service
SciELO preparation	Complete SPS service
NISO JATS 1.3	Official standard documentation

10. Glossary

Term	Definition
JATS	Journal Article Tag Suite — NISO Z39.96 XML standard
SPS	SciELO Publishing Schema — JATS extension for SciELO
PMC	PubMed Central — NIH open access repository
ORCID	Persistent researcher identifier
DOI	Digital Object Identifier — persistent publication identifier
front/body/back	Three main blocks of a JATS article

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.