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JATS-Con 2016 Schedule with Abstracts

April 12, 2016




Welcome and Introductions


Integrate to Innovate: Using Standards to Push Content Forward

Angela Cochran, ASCE

While many of the traditional publishing tasks remain intact, new tasks that are much more technical in nature have changed the skill sets required to be scholarly publishers. Overseeing peer review now also means similarity searches, keyword tagging, maintaining large reviewer databases, and collecting ORCID and funder information. Production now includes stringent XML tagging, multiple deliverables, and the creation of structured metadata. Publishing technology departments, which barely existed 8 years ago, are an absolute must. Even licensing issues become more complicated with text and data mining requests and piracy issues. As new and developing standards and services such as Funder Identification, ORCID, CHORUS, and more come online, publishers and their vendors must integrate when they would rather innovate. The trick is in realizing where integration allows more innovation.


Identifying and Standardizing Funding Information in Scholarly Articles: A Publisher's Solution

Alexander B. Schwarzman, OSA—The Optical Society
M. Scott Dineen, OSA—The Optical Society

Increasingly, funding agencies require public access to journal articles reporting on research they sponsor, and requirements for public-access compliance vary greatly among agencies. At a time when the publisher role comes into question, the journal publisher is in a unique position to leverage specialized knowledge and mature production techniques to properly identify and standardize the funding information that is now so critical to meeting funder, author, and publisher obligations. In theory, capturing an article's funding information should be easy. Publishers ask authors to declare funders in the acknowledgements. At manuscript submission, authors choose from a funder dropdown list. But in practice it isn't easy. In fact, the Optical Society (OSA)—a publisher of 17 scholarly journals—achieved only moderate improvement of funding capture by prompting authors with the FundRef registry, establishing a dedicated funding section in each paper (distinct from the acknowledgments), and querying authors to check funding information accuracy at final proof corrections. Even after heavy investment in new workflow processes and staff training, our database of NLM 3.0 journal articles—which are used for critical reporting and content fulfillment—revealed significant gaps in agency DOI coverage and lacked uniformity. It was only by introducing an innovative Schematron-based solution that we were able to significantly improve funder identification and standardization. This paper will highlight the logical underpinning of OSA's solution, along with various other procedural changes, to ensure both consistency and completeness of funding metadata. Even though the solution has been largely successful in improving funding metadata quality, challenges remain; and we conclude with lessons learned, such as taking an incremental approach to implementation.


Coffee Break


A Quality Assurance Tool for JATS/BITS with Schematron and HTML reporting

Martin Kraetke, le-tex publishing services GmbH
Franziska Bühring, De Gruyter

De Gruyter adopted the JATS/BITS schema for journal content and established De Gruyter specific XML guidelines for creating XML metadata and full text data. Together with le-tex, De Gruyter developed a submission checker to validate the data quality of book and journal packages delivered from their service vendors. The tool is based on the Open Source software Talend and Transpect.

The submission checker verifies the consistency of metadata, validates against the JATS schema and De Gruyter's business rules, which are specified with Schematron. An HTML report provides a rendering of the source files with the error messages. The messages are displayed at the error location and are grouped by their severity. Content passing the check is forwarded for archiving and publication. It guarantees a technically correct rendering of the content on degruyter.com and facilitates the retrieval and processing for future purposes.


So You Want to Adopt JATS. What Decisions Do You Need To Make?

B. Tommie Usdin, Mulberry Technologies, Inc.

Newcomers to JATS need to make decisions about which tag set to use (Authoring, Publishing, or Archiving), which table model to adopt, and how to handle math. In addition, they should consider citation model and style, contributor names and affiliations, alternative languages and encodings, and adoption of tagging guidelines from PMC, JATS4R, and/or their publishing partners.




Focused Talks


ORCID iD Throughput in Publishing Workflows

Laurel Haak, ORCID
Paul Donohoe, SpringerNature
Véronique Kiermer, PLOS
Helen Atkins, PLOS
John Lees-Miller, Overleaf
Craig Raybould, Hindawi Publishing Corporation

ORCID iDs are unique persistent identifiers for authors and other contributors in the research community, part of a community effort to support authenticated connections between authors and their works and thereby address the name ambiguity problem in scholarly communications. In this paper, we will examine use cases from early adopters of ORCID, all of which have an ORCID throughput to CrossRef; each of these use different publishing platforms and manage XML flows differently. Our goal in this paper is to identify and improve community awareness of effective metadata management practices.


Collecting XML at article submission at eLife: Two steps forward, one step back?

Melissa Harrison, eLife

When eLife was launched in 2012, almost all article metadata was collected from what the corresponding author entered into the submission form. These data were converted to JATS XML at acceptance. We will describe the benefits and limitations of this approach, and how and why we have reverted to a more traditional method of using an author's Word file to generate elements of the XML metadata within the production process for the final full-text XML/HTML version of record. However, we also publish the accepted manuscript PDF for approximately 60% of accepted articles, and this process still relies on the metadata entered via the submission system to generate the HTML heading and metadata information online. We will discuss aspects of the peer-review process and submission system that affect the acquisition and conversion of article metadata for both accepted article PDFs and the final version of record, and the challenges we encountered in our efforts to streamline the production process and improve the end-to-end author experience. We will describe our new production process and the conversion of Word to HTML at the point of acceptance, and how we could extend this to the peer-review workflow to minimise duplication of effort in the process of metadata acquisition.


Data Citations

Timothy W. Clark, Harvard University


Coffee Break


Challenges in implementing a multi-lingual JATS publishing workflow

Chandi Perera, Typefi Systems

There are a number of issues that need to be addressed when implementing a multi-lingual publishing process. Some of these are present across all publishing processes while some are specific to JATS. This paper will specifically focus on issues such as selecting the optimum point in the publishing process for content translation, difficulties with inline text styling, and treatment of translated and generated content with specific reference to JATS and BITS. The paper will also look at addressing the limitations of fonts that cover a limited number of languages in a multi-lingual environment. Finally the session will recommend some best practice approaches in implementing a multi-lingual publishing process.


NISO STS Project Overview and Update

Robert Wheeler, ASME (American Society of Mechanical Engineers)
Bruce Rosenblum, Inera, Inc.
Lesley West, ASTM International

In August 2015, NISO announced the approval of a work item and a call for participation in the development of NISO STS, a standard tag set for the publication of standards. This work is based on the ISO Standard Tag Set (ISOSTS), which is based on JATS and is already used by ISO and many national standards bodies. The NISO STS project will broaden ISO STS for use by Standards Development Organizations (SDOs) and other organizations in the standards ecosystem. This paper will give an overview history of the ISO and NISO STS projects and a status update on the work of the Policy/Steering and Technical Workgroups. Discussion will include issues to be considered in keeping STS aligned with JATS and BITS, and the logistics for referral of appropriate issues between the three working groups.

April 13, 2016


An implementation of BITS: The Cambridge University Press experience

Mike Eden, Cambridge University Press
Tom Cleghorn, Cambridge University Press

Cambridge University Press's history of using mark-up for academic book content resulted in a proprietary model, loosely based on NLM DTDs. With new requirements and new types of content, the DTD and related business rules were added to. These changes became frequent and unpredictable, creating pain-points in production workflows and resulting in a heavy burden, both internally, in keeping automated processes up-to-date, and externally, in maintaining suppliers' knowledge.

A decision was taken to review the situation. Outside consultants were engaged to perform the review. It became clear that the choice of model and its manner of use constituted only one part of the picture, and that a review of the entire process would be beneficial.

BITS was chosen as the DTD to use, rather than redefining proprietary DTDs. As an emerging industry standard, it is closely aligned with the Journals NISO standard (NISO Z39.96-2012), already in use at CUP. It was also felt that as the standard grew, benefits would arise from the input and requirements of other publishers.

During implementation, consideration was given to, among other aspects:

  • control of use (sub-setting or Schematron)
  • use of MathML and other similar standards
  • schemes for persistent element identification
  • approaches to metadata encoding
  • output intentions and specifications

Workflows were amended from copy editorial through to final delivery, with an emphasis on control of mark-up throughout. This resulted in a considerably better-defined and predictable process for external providers and internal stakeholders, and has resulted in the creation of a robust foundation for book production into the future.


Wrangling Math from Microsoft Word into JATS XML Workflows

Caitlin Gebhard, Inera, Inc.
Bruce Rosenblum, Inera, Inc.

Mathematics is a fundamental building block of modern technology, research, and industry, and yet the technological means of communicating mathematics is still surprisingly primitive. As a result, anyone involved in producing, publishing, or reading mathematical equations electronically knows that it is not a simple process.

The majority of scholarly papers are authored today in Microsoft Word. Some of those papers include simple and/or complex math. Authors have multiple means at their disposal to insert equations in Word documents including several of Word's native equation editors and third-party applications like Design Science's MathType. Building workflows that smoothly and accurately transform all of these formats into the appropriate XML markup for use in multiple rendering environments has many challenges.

This paper will clarify the different forms of equations that can be encountered in Word documents, and discuss the issues and idiosyncrasies of converting these various forms to MathML, LaTeX, and/or images in the JATS XML model. It will also touch on workflow alternatives for handling of equations in various rendering environments and how those downstream requirements may affect the means of equation extraction from Word documents.


Coffee Break


Write once, use everywhere — making an oXygen Framework accessible on the Web

Gerrit Imsieke, le-tex publishing services

An oXygen XML editor framework for checking JATS articles according to business rules and building journal issue packages for Atypon Literatum is presented. In addition, re-use of the framework's unaltered Schematron, XProc, and XSLT in the context of a Web-based service are presented. This demonstrates the power of the standards-based XML stack in conjunction with diverse runtime platforms such as oXygen XML editor and the le-tex transpect.


JATSKit: An oXygen framework for JATS, BITS, and kindred XML formats

Wendell Piez, Piez Consulting

JATSKit is the newly improved oXygen XML Editor framework supporting NISO JATS and now NLM/NCBI BITS XML. With support for conversions of JATS and BITS data into HTML, EPUB and PDF. In addition to one-button publication, new features in the oXygen Author user interface include fielded entry for structured data elements, Schematron validation and QuickFixes, collapsible display of structural elements, more button controls and more. Everything is customizable and extensible.




JATS Open Session


Coffee Break


Jatdown: a markdown language for writing JATS

Paul Johnston, PubRef

Markdown is a great writing syntax based on it's simplicity, readability, and wide-range of support and tooling. Despite it's massive popularity, the utility of plain markdown in a scholarly publishing is limited by markdown's simple document model. In short, plain markdown alone is too simple to support the constructs required in a scholarly publishing context.

The scholarly article document model is precisely which JATS addresses. JATS has a large and somewhat complex feature set and wide range of flexibility. This complexity and flexibility comes as a price of cognitive burden and potential incompatible interpretations of the tag set.

In this article we will explore **Jatdown**, a markdown variant that supports embedded structured content in the form of YAML. Jatdown provides an easy way to write JATS using a Markdown+YAML syntax and a well-defined mapping to a subset of the JATS-XML model.

In summary, Jatdown makes it easy for normal people to author JATS-XML and generate a predictable XML output.


Nobody Hitchhikes Anymore

Jeffrey Beck, NCBI/NLM/NIH

Technology has has a profound effect on nearly all industries. Information can be processed and distributed quickly and cheaply, and everyone has a voice. That's a good thing, right?