JATS XML Workflows for Open Access Journals: A Guide for STM Publishers

 

A JATS XML workflow converts journal manuscripts into Journal Article Tag Suite (JATS) format the NLM/NISO standard used by PubMed Central, DOAJ, Crossref, and most major repositories. For open access (OA) publishers, a structured JATS workflow is what makes articles discoverable, indexable, and compliant with funder mandates like Plan S, all while reducing production turnaround time by 30–50% compared to manual tagging.

Key Takeaways

• JATS XML is the de facto global standard for structuring journal article content for archiving, indexing, and distribution.
• Open access mandates (Plan S, Horizon Europe, NIH Public Access Policy) increasingly require XML-first or XML-parallel output, not just PDF.
• A well-built JATS workflow reduces time-to-publication, minimizes manual rework, and improves metadata accuracy for discovery platforms.
• Publishers across the EU including those based in the Netherlands, home to Elsevier’s global headquarters are under growing pressure to standardize XML output across multi-journal portfolios.
• Outsourcing JATS conversion to specialists with JATS, DTD validation, and editorial QC expertise is now standard practice for mid-to-large STM publishers.

Why Are Open Access Journals Moving to XML-First Production?

Open access journals are moving to XML-first production because repositories, aggregators, and funder compliance systems are built to ingest structured XML not PDF. PDF remains the human-readable “version of record” for most readers, but it is not machine-actionable. XML is.

Three forces are driving this shift:

1. Funder mandates. Plan S (backed by cOAlition S, which includes many European national funders) requires that publications resulting from funded research be machine-readable and properly tagged with persistent identifiers, licensing metadata, and structured references.
2. Repository requirements. PubMed Central, Europe PMC, and DOAJ all require JATS-conformant XML for full-text deposit. Without it, articles may be indexed with incomplete metadata or excluded entirely.
3. Discoverability and citation tracking. Crossref’s citation-matching and reference-linking infrastructure depends on accurately tagged XML. Poorly structured XML leads to broken DOI links, missed citations, and lower visibility in scholarly search.

For journals based in the EU including the Netherlands, where Elsevier maintains its global headquarters and where open access policy is closely tied to national funder requirements this isn’t optional. It’s becoming the baseline expectation from funders, institutions, and readers alike.

What Does a Typical JATS XML Production Workflow Look Like?

A typical JATS XML workflow for an open access journal follows six stages, moving from manuscript intake to final repository deposit.

Stage

What Happens

Common Output

1. Manuscript Intake

Author manuscript received in Word, LaTeX, or PDF; structural elements identified

Cleaned source file

2. Copyediting & Pre-editing

Language editing, reference formatting, terminology consistency checks

Edited manuscript

3. XML Tagging & Conversion

Content converted to JATS-compliant XML (Archiving, Publishing, or Authoring DTD)

Validated JATS XML file

4. Typesetting & Composition

Parallel PDF/HTML generation from or alongside the XML

Print-ready PDF, HTML

5. QC & Validation

DTD/schema validation, reference linking checks, accessibility checks

QC report, corrected XML

6. Repository Deposit

XML and metadata pushed to PubMed Central, Crossref, DOAJ, institutional repositories

Indexed, discoverable article

The most efficient workflows run steps 3 and 4 in parallel generating XML, PDF, and HTML from a single structured source rather than treating XML as an afterthought derived from a finished PDF. This “XML-first” approach is what allows publishers to hit faster turnaround times without sacrificing accuracy.

Which JATS DTD Should an Open Access Journal Use?

The right JATS DTD depends on where the XML will be deposited and how it will be reused.

• JATS Archiving and Interchange DTD the most comprehensive tag set, required by PubMed Central and most repositories for long-term archiving. This is the default choice for most OA journals.
• JATS Publishing DTD a streamlined subset used by some publishers for their own production systems before converting to the Archiving DTD for deposit.
• JATS Authoring DTD designed for use earlier in the workflow, when authors or editors are tagging content before full production.

For most open access STM journals, the Archiving and Interchange DTD is the safest default, since it’s the version PubMed Central, Europe PMC, and most aggregators expect on ingest.

How Long Does JATS XML Conversion Typically Take?

JATS XML conversion timelines vary by article complexity, but for a standard 8,000–10,000 word STM research article with tables, figures, and 40–60 references, typical turnaround is:

• Simple articles (minimal tables/equations): 1–2 business days per article
• Moderate complexity (multiple tables, figures, supplementary files): 2–4 business days
• High complexity (heavy mathematical notation, large datasets, multimedia): 4–7 business days

Batch processing converting an entire issue or backlog at once typically reduces per-article turnaround by 20–30% due to shared style sheet setup and validation scripts across the batch.

What Are the Most Common JATS XML Errors That Delay Publication?

The most common errors that cause JATS XML to fail validation or repository ingest are:

1. Incorrect or missing DOI and ORCID tagging leads to broken links in Crossref and author disambiguation failures.
2. Malformed reference lists inconsistent citation styles converted incorrectly, breaking citation-matching.
3. Improper table and equation encoding tables converted as images instead of structured XML tables; equations not encoded in MathML.
4. Missing or incomplete metadata funder information, licensing (CC BY, CC BY-NC, etc.), and article history dates omitted or incorrectly tagged.
5. DTD validation failures XML that doesn’t conform to the declared schema, often caught only at the repository deposit stage, causing rejection and rework.

Catching these errors before deposit through automated DTD validation combined with manual editorial QC prevents costly rejection cycles with repositories, which can delay publication by days or weeks.

Wordium vs. In-House XML Production: A Quick Comparison

Factor

In-House Production

Outsourced JATS Workflow (Wordium)

Setup time

Weeks to months (hiring, training, tooling)

Immediate existing trained teams

Cost

Higher (salaries, software licenses, infrastructure)

40–60% lower than Western in-house costs

Scalability for backlog/issue spikes

Limited by headcount

Flexible capacity for batch and peak loads

JATS/DTD expertise

Requires ongoing training as standards evolve

Specialist teams working across multiple DTD versions daily

QC and validation

Often manual, inconsistent

Automated DTD validation + AI-assisted QC + manual editorial review

Parallel output (XML + PDF + HTML)

Often sequential, slower

Built into XML-first workflow

How Can Open Access Publishers Prepare for Stricter XML Requirements?

Publishers can prepare for tightening XML and accessibility requirements by taking four practical steps:

1. Audit current XML output against the latest JATS version your target repositories require, since DTD versions are periodically updated.
2. Standardize metadata capture at submission funder IDs, ORCID, and licensing information should be collected structurally at manuscript submission, not reconstructed later.
3. Move to XML-first or XML-parallel production rather than converting from finished PDFs, which is slower and more error-prone.
4. Pair XML conversion with accessibility compliance since EPUB and HTML outputs derived from JATS XML must also meet WCAG 2.1 AA standards under the European Accessibility Act for any EU-distributed digital content.

This last point matters particularly for publishers operating in or distributing into the EU, including the Netherlands, where accessibility compliance and open access XML requirements now overlap a journal’s XML isn’t just for indexing anymore, it’s also the source for accessible digital formats.

Frequently Asked Questions

What is the difference between JATS and NLM DTD? JATS (Journal Article Tag Suite) is the NISO-standardized successor to the earlier NLM DTD. JATS is now the actively maintained standard, while NLM DTD versions are considered legacy. Most repositories now require JATS-conformant XML, though many systems still accept NLM-tagged files for backward compatibility during transition periods.

Do all open access journals need JATS XML, or only those depositing in PubMed Central? While PubMed Central explicitly requires JATS XML for deposit, other repositories and aggregators including Europe PMC, Crossref, and many institutional repositories also expect JATS-conformant XML for full functionality, including accurate citation linking and metadata harvesting. Journals that only produce PDF risk reduced discoverability even outside PubMed Central.

Can JATS XML be generated automatically without manual tagging? Partial automation is possible using AI-assisted conversion tools, particularly for well-structured manuscripts with consistent formatting. However, manual editorial QC remains essential for reference accuracy, table/equation encoding, and metadata validation fully automated conversion without review carries a high risk of validation failures at deposit.

How does JATS XML relate to EPUB and accessibility compliance? JATS XML can serve as the structured source from which EPUB files are generated, since both formats rely on tagged, semantic content rather than visual layout. When JATS XML is properly tagged including alt text for figures, table headers, and reading order the resulting EPUB is better positioned to meet WCAG 2.1 AA requirements under regulations like the European Accessibility Act.

How Wordium Can Help

Wordium provides end-to-end JATS XML conversion for open access journals from manuscript intake and copyediting through DTD validation, parallel XML/PDF/HTML production, and repository-ready deposit packages. Our teams work across JATS Archiving, Publishing, and Authoring DTDs, with AI-assisted QC layered on top of manual editorial review to catch the errors that cause repository rejections before they happen.

If your journal’s XML workflow is creating bottlenecks or if you’re preparing for stricter funder and accessibility requirements get in touch with Wordium’s XML production team to discuss a workflow audit.

Related Wordium Services: XML Conversion | Copyediting & Indexing | Accessibility (WCAG/EPUB) | Typesetting & Composition