JATS Tools for Scholarly Publishing and XML Workflow
The Journal Article Tag Suite (JATS) is the gold standard for the creation, preservation, and distribution of scholarly content. To manage this complex XML standard, a diverse ecosystem of tools has emerged, ranging from simple conversion forms to fully automated enterprise pipelines. These tools allow publishers and researchers to transform raw manuscripts into structured, machine-readable data.
Key Facts
- JATS is a technical standard used to tag scholarly articles for interoperability and long-term archiving.
- Conversion from Microsoft Word to JATS is widely automated via tools like Typeset and eXtyles.
- PDF to JATS conversion remains a significant technical challenge, heavily dependent on the consistency of the source document's structure.
- WYSIWYM (What You See Is What You Mean) editors allow authors to edit content without needing to write raw XML code.
- PubReader provides a specialized web presentation optimized for mobile and tablet devices.
Conversion to JATS
Converting scientific documents into JATS XML often requires a combination of automated software and human oversight to ensure accuracy.
From Word and OpenOffice
Several tools specialize in transforming processed text documents into structured XML:
- Typeset: Offers an automated suite of converters for MS-Word to JATS XML.
- OxGarage: Converts various formats into the National Library of Medicine (NLM) DTD 3.0.
- meTypeset: A fork of the OxGarage stack specifically designed for Microsoft Word .docx to NLM/JATS-XML conversion.
- eXtyles: Automates document editing within Microsoft Word and exports to JATS XML and other DTDs (Document Type Definitions).
From Markdown and PDF
For non-Word formats, the tools vary in complexity. Pandoc 2.0 is a versatile tool capable of converting Markdown and other input formats to JATS.
PDF conversion is notably more difficult. Success depends on how well-structured the source PDFs are. Current solutions and ongoing developments include:
- Shabash Merops and Typeset's PDF to JATS XML Converter.
- CERMINE Content ExtRactor and MINEr.
- The Public Knowledge Project, which is developing a pipeline utilizing pdfx.
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Conversion from JATS
Once a document is in JATS format, it can be rendered into various output formats for distribution.
Web and Digital Formats
- HTML: JATS Preview Stylesheets provide canonical XSLT (Extensible Stylesheet Language Transformations) conversion. Additionally, eLife Lens converts NLM XML to JSON for display via HTML and Javascript.
- PDF and EPUB: Some JATS Preview Stylesheets utilize XSLT and XSL-FO (XSL Formatting Objects) to generate PDFs, while other tools facilitate EPUB creation.
Generic Analysis
DtdAnalyzer serves as a generic tool to compare JATS with other DTDs, assisting in the creation of XML representations, Schematron generation, and XSLT.
JATS Editors
To avoid the steep learning curve of raw XML, various editors provide user-friendly interfaces for scholarly content.
Specialized XML Editors
- Typeset: A WYSIWYM editor supporting NISO and NLM JATS standards, primarily used by publishers to convert author manuscripts into XML, PDF, HTML, and ePub.
- oXygen XML Editor/Author: Through the JATS Framework, oXygen detects JATS documents via DOCTYPE declarations to provide specific stylesheets and utilities.
- FontoXML for JATS: A WYSIWYS (What You See Is What You See) editor for reviewing and editing content.
Web-Based and Integrated Editors
- PubRef "Pipeline": A browser-based editor with real-time previews.
- Annotum: A WordPress theme integrating JATS (Kipling subset) authoring, peer-review, and editorial management.
- Xeditor: Offers a dedicated JATS edition for web-based XML editing.
- Texture Editor: Developed by the Substance Consortium, this was the first "born to JATS" online editor.
- Libero Editor: Developed by eLife, this interface is designed for publishing staff and authors to produce high-quality JATS XML.
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Preview and Customization
Rendering JATS XML into a human-readable format is essential for quality control and final publication.
Rendering Tools
- JATS Preview Stylesheets: A collection of .xsl, .xpl, .css, and .sch files that render NISO Z39.96-2012 JATS 1.0 files into HTML or PDF.
- Typeset: Enables one-click HTML generation from JATS XML, with options for custom journal requirements.
- PubReader: An alternative web presentation designed to enhance readability on tablets, small screens, and desktops.
Customization Documentation
Jatsdoc, integrated with NCBI's DtdAnalyzer, is used to produce documentation for specific JATS customizations.
| Category | Primary Purpose | Example Tools |
|---|---|---|
| Conversion to JATS | Transforming Word/PDF/Markdown to XML | Typeset, eXtyles, Pandoc, CERMINE |
| Conversion from JATS | Transforming XML to HTML/PDF/EPUB | eLife Lens, JATS Preview Stylesheets |
| Editors | Authoring and reviewing JATS content | oXygen, Libero, Texture, FontoXML |
| Preview/Customization | Rendering and documenting JATS | PubReader, Jatsdoc |
Frequently Asked Questions
What is the difference between NISO JATS and NLM JATS?
While both are based on the same foundation for scholarly tagging, NLM (National Library of Medicine) refers to the original DTD standards, while NISO (National Information Standards Organization) represents the formalized industry standard (such as Z39.96).
Why is PDF to JATS conversion considered difficult?
PDFs are designed for visual presentation rather than structural data. Conversion success depends heavily on how consistently the source PDFs are structured; inconsistent layouts make automated extraction unreliable.
What does WYSIWYM mean in the context of JATS editors?
WYSIWYM stands for "What You See Is What You Mean." Unlike a standard word processor, these editors allow users to define the semantic meaning of the content (e.g., marking a section as an "Abstract") without needing to manually code the XML tags.
How does PubReader improve the reading experience?
PubReader is a specialized web presentation layer that optimizes JATS content for readability across various devices, particularly tablets and small screens, providing a more flexible alternative to static HTML.
Can I convert Markdown files to JATS?
Yes, Pandoc 2.0 is capable of converting several input formats, including Markdown, into JATS XML.