JATS-Con 2022 Schedule with Abstracts

Welcome and Introductions

Accessible Publishing

Chandi Perera, Typefi, Inc.

An Incomplete Guide to Creating Accessible Content

Joni Dames, Inera | An Atypon Company

What are the obstacles preventing people from accessing your content? Are you creating content that people can interact with easily? Is your content more than just 508-compliant? Or: how to stop worrying and incorporate some basic steps in your workflow to help make sure your content is accessible to everyone.

JATS from Markdown: developer friendly single-source scholarly publishing

Albert Krewinkel, Pandoc development team
Arfon Smith, Openjournals
Juanjo Bazán,

Research software has become an integral part of doing science in many disciplines. As a consequence, it is becoming increasingly important to publish. The Journal of Open Source Software (JOSS) is a developer friendly, open access journal for research software packages. Article authors are generally comfortable with tools commonly used by software developers. The JOSS production pipeline is considerate of this, supporting submissions to be written in Markdown, a lightweight markup-language.

Here we present the single-source publishing pipeline developed for JOSS, especially the conversion of articles authored in Markdown into PDF and XML formats, including JATS. We describe how we built on, and extended, the document converter "pandoc", how metadata is processed and integrated into the publishing artifacts, and which advantages and challenges we see in enriching plain-text inputs into structured documents.

The source code for the updated publishing system is available at https://github.com/openjournals/inara

Identifying XML Issues that Impact Content Interchange

Mark Gross, Data Conversion Laboratory (DCL)

Publishers' content collections are complex, often spanning decades, during which time standards have evolved. JATS XML from 2006 is significantly different from JATS XML 2022. Errors and issues with content structure have serious impact on downstream discoverability and content interchange. This presentation demonstrates how Content Clarity, by Data Conversion Laboratory, analyzes an entire corpus of XML to identify missing DOIs, bad xrefs, duplicate IDs, invalid assets, and other issues in the JATS XML that do not necessarily invalidate the files but do contribute to interoperability issues.

Improving content structure to take full advantage of JATS XML 1.3 benefits the entire journal publishing ecosystem. Publishers may be missing out on functionality if content is not consistent and up to date with the latest DTD. This session dives deep into the clarity checks DCL performs on publishers XML files and will demonstrate suprising findings that linger in both legacy and even current content:

• DOI conflicts
• Invalid XML/Parsing errors
• Duplicate IDs within an article
• Missing self uri PDF
• Incorrect dates
• Vol/issue/ppub differences
• Missing doctypes
• And more strange but true JATS findings!

Enemies, Frenemies, or Allies? The JATS Standing Committee and JATS4Reuse

Jeffrey Beck, NCBI/NLM/NIH

What is the difference between the JATS Standing Committee and JATS4Reuse? Why are there two groups? Who should I pay attention to? What happens if they don't agree?

Improving JATS for Multilingual Articles

Vincent Lizzi, Taylor & Francis

The scenarios for journal articles that contain more than one language are no longer (and never really were) limited to having an article's title, abstract, and keywords translated to additional languages. JATS currently has a variety of structures for tagging articles that are in multiple languages or have substantial amounts of the content in more than one language. However, these structures are not all coherent and are not up to the tasks of handling some common use cases. A subcommittee of the NISO JATS Standing Committee (with participation from members of the STS and BITS committees and some other invited experts) was formed, in 2021, with the goal of recommending changes to JATS to enable it to usefully encode multilingual articles. The subcommittee has recommended a set of changes that introduce new structures that can be available to JATS users who need them while not burdening JATS users who rarely deal with multilingual content. Most of these changes are backward compatible with earlier versions of JATS. These changes are currently a work in progress and may become available in a future version of JATS. This paper presents a proposal for improving JATS to better support tagging multilingual articles with the hope of garnering feedback and suggestions from the JATS community.

Kotahi: a new JATS production system

Dan Visel, CoKo Foundation

Kotahi is a new open source journal production system in active development by the Coko Foundation. Designed to accommodate a number of different work flows, it's built around Wax, a configurable editor based on React. Articles can be exported from the system as HTML (via a GraphQL API), PDF, and JATS. Internally, metadata is collected through document parsing and a form; on export to JATS, the document is transformed from the internal format of HTML to JATS and front matter and back matter are constructed from metadata. A component-based editor, Wax, allows for more sophisticated composition of structural entities that otherwise might be hard to represent in an HTML-based system.

• https://kotahi.community
• https://waxjs.net

Naming content as requirements in standards―the Standards Norway approach

Dorothée Stadler, DOST Consult

What are requirements? And why is everyone talking about them? Do I need this in my organisation as well? And how can I do this in NISO STS?

More and more standards customers and standards authors are asking for markup of requirements in standards, and Standards Development Organizations (SDOs) are struggling to find a solution that integrates seamlessly with NISO STS. Many initiatives are on the way, many discussions are being had, and still only a handful of SDOs are addressing this need to date.

As an independent consultant, I have worked with Standards Norway to clarify the business needs and to design a practical solution to service the needs of the Oil & Gas Industry that is now implemented in their instance of Fonto XML. This presentation will walk you through the business problem, how we've solved it and what challenges we faced (and are still facing).

JATS Open Session

A JATS XML comparison algorithm for scientific literature

Milos Cuculovic, IRIMAS, University of Haute-Alsace
Frédéric Fondement, IRIMAS, University of Haute-Alsace
Maxime Devanne, IRIMAS, University of Haute-Alsace
Jonathan Weber, IRIMAS, University of Haute-Alsace
Michel Hassenforder, IRIMAS, University of Haute-Alsace

JATS is nowadays the de-facto standard for the XML representation of journal articles. Academic publishers convert articles from tex, docx and odt to JATS with the benefit of carrying article information in a machine readable and typesetter tool independent format. Following recent growth in higher education, the number of scientific, peer-reviewed articles has increased exponentially for more than a decade. Each of these articles has to go through a laborious process, from the initial screening through peer review, author revision rounds and the final decision made by the Editor in Chief. The decision is made by analyzing and comparing reviewer comments to the revisions made by the authors, which is a manual process that requires a lot of time, attention and rigor. We describe within this article a new JATS comparison algorithm, called jats-diff. The algorithm is usable to the final decision makers allowing them to compare different article versions using bijection between author modifications on one side and the detected differences on the other. Moreover, jats-diff calculates the similarity index between the two articles.

Using BITS for 10 Years and Counting

Cindy Maisannes, CFA Institute

In 2011, CFA Institute was an experienced user of the green Journal Archiving tag set for scholarly journals, conference proceedings, and white papers. But when we made the decision to insource the production of our flagship organizational publication―a set of equation- and table-heavy curriculum textbooks that had to be reproduced in their entirety from scratch on an annual basis―we knew there was no way we could tag that content simply as a journal. We evaluated different book tag sets before adopting the NLM Book Tag Set Version 3.0.

More than 10 years out from that decision, many things have changed. XML tagging meant to support the production of print books has been repurposed and extended to a greater number of products in a variety of different formats. The structure and the content of the curriculum has become increasingly complex. The content management systems and associated workflows by which the content moves in and out of XML have exploded. Tag sets have been updated and modernized. Our commitment to and appreciation for single-source publishing workflows grows.