JATS-XML: The Emerging Standard in Academic Publishing for Everyone?

Introduction

In the evolving world of academic publishing, structured formats are essential for efficiently creating, preserving, and distributing research. Researchers, publishers, and funding agencies rely on consistent metadata to access and track scientific contributions and funding compliance.

One format (besides PDF) that has gained widespread adoption is JATS-XML (Journal Article Tag Suite XML). JATS-XML has become the backbone of modern academic publishing, supporting open-access mandates, long-term archiving, and seamless integration with repositories. But what makes JATS-XML so crucial, and how is it being adopted across different sectors? How do smaller publishers implement advanced technology like JATS-XML?

What is JATS-XML?

JATS-XML is an XML-based standard for encoding scholarly articles. It was developed by the National Information Standards Organization (NISO) to provide a structured way to store, share, and archive academic research.

There are several JATS variants, each designed for different use cases:

• JATS Blue (Publishing Tag Set) – Used by publishers to format journal articles for publication.

• JATS Green (Archiving Tag Set) – A flexible format for long-term digital preservation.

• JATS Orange (Authoring Tag Set) – A stricter format for writing academic articles directly in XML.

• PubMed JATS – The version PubMed Central uses to store biomedical research articles.

Why JATS-XML is Becoming the Standard

1. Interoperability Across Platforms

JATS-XML allows seamless integration with major publishing platforms, repositories, and indexing services such as PubMed, CrossRef, Redalyc, and OpenAIRE. This ensures that articles are easily discoverable and correctly indexed.

2. Support for Open-Access Mandates

Funders and organizations like the NIH, Wellcome Trust, and cOAlition S (Plan S) demand that research outputs be openly accessible. JATS-XML simplifies compliance by structuring metadata, licensing information, and funding details in a machine-readable format.

3. Automation and Efficiency

With JATS-XML, publishers can automate production workflows, converting articles into multiple formats (HTML, PDF, ePub) from a single source. Tools like SciFlow Publish and OS-APS are helping streamline the adoption of JATS-XML.

4. Long-Term Archiving and Preservation

Repositories like PubMed Central, Europe PMC, and CLOCKSS rely on JATS-XML to archive research articles. By storing content in JATS, publishers ensure their articles remain accessible for future generations.

Who is Using JATS-XML?

1. Open-Access Publishers

PLOS, eLife, Frontiers, and SciELO widely use JATS-XML to structure and disseminate their research outputs. These publishers provide full-text JATS-XML versions of their articles, ensuring machine-readability and accessibility.

2. Academic Repositories

Major repositories, including PubMed Central (PMC), mandate JATS-XML for article deposits. University libraries and institutional repositories also adopt JATS-XML to improve metadata quality and integration.

3. Journal Platforms and Tools

Platforms like Open Journal Systems (OJS), Scholastica, and HighWire Press have integrated JATS-XML into their workflows. This allows smaller journals to generate JATS-XML automatically, making their content more discoverable and reusable.

Challenges in Adopting JATS-XML

Despite its advantages, JATS-XML adoption comes with challenges:

• Technical Complexity – Publishers need XML expertise or automated tools to convert manuscripts into JATS-XML.

• Legacy Workflows – Many journals still rely on PDF-first or Word-based production, making the transition to JATS-XML difficult.

• Standardization Across Variants – Different JATS flavors (Blue, Green, Orange) can create formatting and metadata tagging inconsistencies.

The Future of JATS-XML

As open-access mandates grow and automated publishing tools improve, JATS-XML adoption will only increase. Future developments may include:

• AI-assisted JATS-XML conversion tools to simplify adoption for smaller publishers, like SciFlow Publish.

• Better integration with funding databases to streamline compliance tracking.

• Expansion beyond journals into books (further adoption of BITS-XML), conference papers, and datasets.

Conclusion

JATS-XML has established itself as the standard for structuring academic research. Enabling interoperability, automation, and long-term preservation ensures that scholarly content remains accessible and machine-readable. As more publishers, funders, and institutions adopt JATS-XML, it will continue to play a critical role in the future of academic publishing.