JATS-Con 2021 Schedule with Abstracts

Welcome and Introductions

Lazy guide to managing

Patricia Feeney, Crossref

The dream of many (journal publishers at least) is for everyone to agree enough on standards and specifications like JATS to make content easy to distribute with limited conversion. That's not the reality we live in―publisher and platforms have their own specific needs, and funneling metadata through Crossref and other distribution platforms requires planning and maintenance. We have a system that works (sort of) but things are changing rapidly and it's no longer enough to link journal articles to citations―we need to connect funding to research outputs, researchers with licenses, and make all of the content surrounding research identifiable and discoverable.

How do we stay (or become) nimble while also sorting out how to manage emerging types of content and the metadata we need to create a rich research nexus? There's no perfect solution, but the Crossref—JATS relationship can go a long way towards making things easier for us all.

MECA and JATS Compatibility: A case study utilizing the JATS Compatibility Meta Model

Laura Randall, NCBI/NLM/NIH
Sally Ubnoske, Aries Systems Corporation

The NISO Manuscript Exchange Common Approach (MECA) project is a cross-organization industry initiative to develop a common approach to manuscript transfer that can be adopted across the scholarly publishing industry. MECA establishes a vocabulary set that includes transfer, review, and manifest models. These models are designed to work with different article XML schemas, including the latest NISO JATS standard (v1.2). In order to avoid conflicts between these project vocabularies and the JATS, we reviewed the MECA vocabularies against the NISO JATS Compatibility Meta Model (v0.7).

This paper describes the review and analysis of the MECA schemas against the JATS Meta Model, how we documented the analysis, and the recommendations we made to resolve issues revealed by the analysis. It includes the documentation we produced to communicate the results of the analysis and what actions we took to move forward with the project, including both changes to the schemas and requests to changes in the JATS.

We hope sharing our experiences with this process will help others who are trying to do the same.

Upgrading a Production System to JATS 1.2: Throw out your old food containers

Vincent Lizzi, Taylor & Francis Group
Joanna Czerepowicz, Taylor & Francis Group

Following the release of JATS 1.2 in March 2019, the Digital Production team within the Journals Production department of Taylor & Francis began a project to modernize our article XML based on JATS 1.2. This upgrade from a customized version of JATS 1.0 to JATS 1.2 would be the first major upgrade since transitioning from a proprietary DTD in 2012. This project began with a number of inter-dependencies, which increased as the project went on and became aligned with other projects to significantly improve our digital foundation. The Digital Production team has worked closely with the Taylor & Francis Global Supplier Management Team, prepress vendors, contractors, and development teams for internal content management systems to complete this upgrade. This paper and presentation give a progress report in which we share some of the experiences and lessons we have learned from this upgrade.

Change Tracking in the XML-Based LiXuid Production Workflow Using Fonto’s Document History

Bert Willems, Fonto
Charles O’Connor, Aries Systems

When Aries was looking for an XML editing platform to build on for the LiXuid XML workflow, a top priority was change tracking that was robust and usable to satisfy the needs of journal production staff. The solutions available at the time, based on using processing instructions, either did not capture the full range of possible changes or were unreliable in their behavior. Aries also wanted to avoid having to superset JATS to add change tracking elements. Fortunately, Fonto, one of the candidate XML editors, was working on a solution based on DeltaXML called Document History. What sets Document History apart is its ability to display changes made across different revisions of an XML document. This principle is called a changelog and it is different from A/B comparisons typically employed in change tracking solutions. A changelog is a comparison between multiple, subsequent revisions of an XML document merged back into one annotated XML document which is then visualized. This changelog contains the necessary information to attribute changes to specific users and moments in time, something that is typically only offered by active change tracking systems. Another property of this changelog is its ability to show overlapping and conflicting changes. Both textual and XML changes are displayed in Document History as a redlined version of the document. Through the UI, users have the ability to determine what range of revisions they want to look at, and the application provides the ability to navigate quickly to the associated XML editor as well as to mark change as seen.

Leaping the Field: On Being an Early Adopter and Jumping from PDF to NISO STS

Mark Gross, Data Conversion Laboratory, Inc.
Daniel Berger, American Water Works Association

The American Water Works Association (AWWA) was one of the first Standards Associations to convert content to NISO STS XML. Data Conversion Laboratory (DCL) worked with AWWA to transform its standards content and provide a platform for interchange and interoperability.

This project was particularly interesting and challenging as AWWA had no prior XML and the conversion process was from PDF to NISO STS. After 1 year of working with NISO STS, this paper reviews how it has improved AWWA's publishing process and what the larger standards community should understand about the specification.

Mark Gross, President of Data Conversion Laboratory, and Daniel Berger, Senior Manager of Production at AWWA, will discuss

• Content structure: tips and best practices that ensure the free flow of standards content. Discussion around XML as well as workflow processes that enforce the NISO STS XML standard.
• Content conversion: critical components of analysis, specification, conversion, QA/QC, timeline, and budget. The content included some challenging situations that required some non-perfect decisions in terms of MathML, images, tables, and footnotes.
• Content interchange: how the new format helps with indexing and searching and supports improved discoverability of AWWA's content.
• Tag suite: nuances of the tags during conversion and desired enhancements after 1 full year in production.

JATS to JATS with Eddie 2

Liam Quin, Delightful Computing

When faced with the task of writing XSLT transformations to make from one version of JATS to another, often with proprietary (in-house) extensions at one end or both, developers may find the size of the vocabulary intimidating.

Eddie 2 is a tool that implements a systematic methodology for writing XSLT transformations that convert between broadly similar DTDs such as two versions of JATS. Using this tool can make development both faster and more robust. The paper describes the analysis-first methodology and how the tool supports it.

Learn more at Delightful Computing.

A full text collection of COVID-19 preprints in Europe PMC using JATS XML

Audrey Hamelers, EMBL-EBI (European Bioinformatics Institute)
Michael Parkin, EMBL-EBI (European Bioinformatics Institute)

In March 2020, in response to a call from the White House Office of Science and Technology Policy, more than 50 publishers agreed to openly share articles related to the COVID-19 pandemic via PMC (and through PMC International, Europe PMC). As a complement to this effort, and in recognition that many researchers were publishing their results rapidly via preprints, a project was launched in July 2020 to collect as many full-text preprints relating to COVID-19 as possible and make them available via Europe PMC alongside peer-reviewed COVID-19 articles. By various means, preprints in PDF format are retrieved from a number of preprint servers (including medRxiv, bioRxiv, arXiv, ChemRxiv, Research Square, and SSRN) and converted to JATS XML. The Europe PMC plus manuscript submission system is used to manage the processing of preprint conversions and communications with authors. To date, around 25,000 COVID-19 preprints have been made available in this way. In this paper we will share what we’ve learned about using JATS XML for preprints and how this aligns or deviates from using JATS XML for peer-reviewed articles.

A Deep Dive into JATS Documentation

B. Tommie Usdin, Mulberry Technologies, Inc.

JATS use is supported by a wide variety of information resources. The JATS Standing Committee maintains the JATS Standard and the JATS Tag Libraries. In addition, there are recommendations, conference proceedings, user guidelines, and discussion lists. Similar resources support users of BITS and NISO STS.

The Standards are the de jure definition of the tag sets. Their value to users is mostly in the fact that they exist!!

The Tag Libraries are the de facto definition of the tag sets. They are the information resources users should turn to with questions about structure, usage, and definitions. The tag libraries are a rich and complex reference source. I believe that even regular users will be surprised by some of the information content and navigation tools provided in the tag libraries. The design of the tag libraries has recently been updated to make them more accessible and more responsive to the needs of frequent users.

Other resources include the proceedings of several conferences including JATS-Con, JATS4R Recommendations, the archive of JATS-List, Guidelines provided by major recipients of JATS articles, and tagged articles provided on the web sites of several JATS users.

JATS Open Session

WYSIMTWYG ―What you see is more than what you get when using XML

Ken Holman, Réalta Online Publishing Solutions Limited

Authoring standards documents in XML provides publishing options not available when using traditional word-processing-based desktop publishing. Organizations not having used XML yet may be unaware of the opportunities to tailor back-room renditions of standards documents that are augmented to be useful to authors and editors yet remain unpublished and are never seen by users of the final result. This is a case study about meeting a client's requirements to convert existing standards to NISO STS, update them, and add semantic markup. It reveals the use of a tailored rendition of standards documents to expose and review markup not visible to the end user. Agreement on the semantic markup is critical to the use of the content from the published document in downstream processes. Tailored augmented renditions are important tools to support the review of hidden markup, and are not available as readily when not using XML as the basis for publishing.

An Unprecedented Pivot to the New Normal

Jeffrey Beck, NCBI/NLM/NIH