JATS-Con 2015 Schedule with Abstracts

Registration

Welcome and Introductions

JATS Diversity—A Content Management Perspective

Evan Owens, Cenveo Publisher Services

Standards can be rigid or they can have built-in flexibility…and any standard can have to change over time as business needs evolve. So variation in standardized encoding in the past, present, and future are highly likely and can present challenges for content management processes. This talk will begin by summarizing the diversity of the JATS landscape as described in the papers at the last four JATS-CONs and then speculate about content management strategies for coping with the diversity of implementations and the evolution of standards.

Automating Complex High-Volume Technical Paper and Journal Article Page Composition with NLM XML and InDesign

Becky Fadik, SAE International
Brian Trombley, Data Conversion Laboratory

SAE International is a global association of more than 138,000 engineers and related technical experts in the aerospace, automotive and commercial-vehicle industries. Annually, SAE organizes and manages an industry conference, its World Congress and Exhibition, where thousands of technical papers and journal articles are presented as part of the conference program. Leading up to the Word Congress, the technical papers and journal articles are reviewed for compliance to SAE publishing requirements and published for print and made available online in a very short time-frame. This paper describes how SAE evolved the production cycle from a less than efficient XSL-FO based process to a highly automated process leveraging NLM XML, XSLT and Adobe InDesign resulting in productivity gains and higher quality output. This paper will take you through the evolution of this project and talk to future enhancements aimed at driving additional benefits.

The Public Knowledge Project XML Publishing Service and meTypeset: Don't call it "Yet Another Word to JATS conversion kit"

Alex Garnett, Simon Fraser University
Juan Pablo Alperin, Simon Fraser University
John Willinsky, Stanford University

The Public Knowledge Project's Open Journal Systems, which provides a robust workflow and interface for editing, publishing, and indexing scholarly journal content, has always been somewhat agnostic as to the format of the content itself. Most authors, unsurprisingly, use Microsoft Word for its familiarity and ubiquity during the actual writing process, and the act of getting content from Word format into something that can be easily consumed on the web after that has always been something of a mystery among publishers. Those who have the means will typically outsource or partially automate the markup of an article in XML or an XML-like format, and this XML can then be transformed into HTML on the fly for viewing (OJS does include some stylesheets for this purpose); others, including many smaller open source journals, convert directly to the printable PDF format as a path of least effort, leaving them with something that looks nice on a printed page but potentially not so nice and not too flexible otherwise. For the past two years, PKP has been working on a web service (which integrates into OJS' workflow via a provided plugin) to fully automate the conversion of Word/compatible documents into the National Library of Medicine's standard JATS XML format (the same format which underlies PubMed Central), using fuzzy parsing and machine learning heuristics, and transform documents from there into matching human-readable HTML and PDF. This development, broadly speaking, takes two parts: one, the core OpenOffice/Word 2007 "docx" XML to JATS XML conversion engine, called "meTypeset" developed jointly with Martin Eve of the Open Library of the Humanities, and two, the web service pipeline, which unites meTypeset and other open-source libraries (including LibreOffice, ParsCit, ExifTool, and others). This service provides citation parsing, XMP metadata, and other industry-standard features. Improvement of various parsing features and automated evaluation is ongoing.

All Aboard! Round-tripping JATS in an HTML-based online CMS and editing platform

Wendell Piez, Piez Consulting Services

In a project just starting up, we are endeavoring to convert JATS (or actually near-NLM-Book) data into HTML for an HTML-based CMS, where the documents (structured reference material in short articles) will be edited (in the usual sort of web-based HTML editor) -- and then must be siphoned back up into the JATS-like textbase, for further processing using JATS-based tools.

Going both ways presents many interesting theoretical and technical challenges. This paper will describe the design principles we are following, with our solutions and findings by next April.

Creating JATS XML from Japanese language articles and automatic typesetting using XSLT

Hidehiko Nakanishi, Nakanishi Printing Co. Ltd.
Toshiyuki Naganawa, Antenna House, Inc
Soichi Tokizane, University of Tokyo

As multi-lingual JATS evolved from NLM DTD, J-STAGE, a Japanese e-journal platform, adopted JATS 0.4 in May 2012. As a result, increasing number of publishers began publishing their journals in JATS XML. This article discusses challenges and solutions to creating JATS XML for multi-language articles.

Improving the reusability of JATS

Jeff Beck, NCBI/NLM/NIH
John Chodacki, PLoS
Alf Eaton, PeerJ
Michael Evans, F1000
Rupert Gatti, Open Book Publishers
James Gilbert, eLife
Melissa Harrison, eLife
Christopher Maloney, NCBI/NLM/NIH
Daniel Mietchen, Museum für Naturkunde Berlin; NCBI/NLM/NIH
Tom Mowlam, Ubiquity Press
JATS4R Working Group,

Despite a fair degree of standardization, JATS is still not used consistently across publishers, which inhibits harvesting and reuse of JATS-tagged materials. To address these issues, a working group has been formed to evaluate existing flavours of JATS and to harmonize them by issuing recommendations on how reuse-relevant tags should be used and on how documentation and guidelines can be clarified. Besides establishing communication channels and working out procedures, the group has already tackled some specific tagging issues, most notably the machine readability of license statements and of mathematics in journal articles.

Using BITS for Non-Standard Content

Dana Wheeles, Silverchair

Many objects published in a codex format in print do not easily translate as "books" online. After adopting BITS as its core model for traditional book content, Silverchair has created an initiative to leverage the same tag library and expand its implementation to load other book-like objects, non-standard content objects, and born-digital content onto a shared platform.

This paper is a case study of how BITS was adapted for our system to encode a library of defined "types" of non-standard content.

The Long Road to JATS

Paul Donohoe, Macmillan Science and Scholarly
Jenny Sherman, Macmillan Science and Scholarly
Ashwin Mistry, Macmillan Science and Scholarly

Nature Publishing Group/Palgrave has over a million articles, 180 journals, three in-house DTDs, numerous workflows and production systems, as well as teams based across the world. The challenge: How do we move to using JATS as our single DTD, introduce a streamlined production process and increase the number of journals we publish? This paper describes our journey so far, the challenges we faced, the XML tools we have used, the decisions we made and the reasons for them, and the work still to be done.

Adapting JATS to support data citation

Daniel Mietchen, Museum für Naturkunde Berlin; NCBI/NLM/NIH
Johanna McEntyre, EBI
Jeff Beck, NCBI/NLM/NIH
Christopher Maloney, NCBI/NLM/NIH
Force11 Data Citation Implementation Group,

Data are often not cited in a consistent fashion. To address this, Force 11 have developed the Data Citation Principles. JATS 1.1d1 has provisions for citing articles and other sources, but does not offer straightforward ways of expressing some of the concepts needed for data citation. In order to facilitate the citation of data in JATS-tagged documents in a way that is compliant with the Data Citation Principles, the Force11 Data Citation Implementation Group held a meeting in June, at which several new elements, attributes and values for attributes have been suggested to be added to JATS. These have since been submitted to the JATS Standing Committee, which largely accepted them, so they are now included in JATS 1.1d2. This talk will explain the decision criteria behind the elements that were proposed, and how they were selected for JATS 1.1d2. It will in addition provide suggested examples for use of the new tags.

Superimposing Business Rules on JATS

Tommie Usdin, Mulberry Technologies, Inc.
Debbie Lapeyre, Mulberry Technologies, Inc.
Carter Glass, Mulberry Technologies, Inc.

Publishers are stuck between a rock and a hard place. They want to use JATS for interchange but they want their model to help them maintain consistency and enforce their business rules, which JATS does not. We suggest a Schematron layer so they can have it both ways without having multiple models (a notion many publishers find confusing) or needing to transform their content on export (which many content creators find terrifying).

JATS for Ejournals and BITS for Ebooks—Adopting BITS for Scholars Portal Ebook Repository

Wei Zhao, OCUL—Scholars Portal
Ravit H. David, OCUL—Scholars Portal
Sadia Khwaja, OCUL—Scholars Portal
Qinqin Lin, OCUL—Scholars Portal

Scholars Portal (SP) is a service available to faculty and students at Ontario's 21 universities in Canada. After the success of adopting JATS in SP ejournal repository, SP team decided to adopt BITS as the standard format for SP ebook repository. SP ebook repository contains more than 600,000 ebooks from 28 publishers. The current platform is a PDF based platform running on Ebrary's ISIS system. Our ultimate goal is building a new book application based on BITS XML in Mark Logic. At the current stage, we will be transforming the publisher's native data into BITS format and begin populating a new BITS XML database in Mark Logic while feeding the BITS data into ISIS. This article will discuss why BITS DTD is chosen, examine the workflow, the process of data transforming and loading, analyze the benefits and challenges and make the recommendations of improving BITS DTD.

Building an Automated XML-Based Journal Production Workflow

Charles O'Connor, Dartmouth Journal Services
Stephen Haenel, Dartmouth Journal Services
Antony Gnanapiragasam, Dartmouth Journal Services
Michael Hepp, Dartmouth Journal Services
Tina Fleischer, Dartmouth Journal Services

The biggest challenge of single-source publishing has been capturing changes during the page proof stage. Until now, direct XML editing in composition has required a high-end system (such as 3B2) and trained operators. Even then, PDF-based proofing places a barrier between the actors---authors and editors---and the source XML file, leading to inefficiency and increased chance of error. The key to creating a robust, automated XML-based workflow is an XML proofing and editing environment that requires little to no learning for the author and has comprehensive change tracking for the editor. The PDF can then be created by a lights-out composition system at any point in the correction cycle. Here we describe creating an XML-through journal production workflow that takes early JATS XML from copyedited manuscripts through layout and PDF generation, author and editor correction cycles, and delivery of assets, all controlled by a task-driven production management system.

Open Session

A complete end-to-end publishing system based on JATS

Kaveh Bazargan, River Valley Technologies

JATS is fast becoming the de facto standard in scholarly publishing. We describe a web-based platform that handles the complete publishing process from authoring to publication, where the file being worked on is always a native JATS XML. This method minimizes the risk of errors in format conversion, and in addition speeds up the publication process.

The software used is primarily PHP and MySQL with other free software to allow visual formatting. During the authoring process, the file is saved as HTML, but upon submission it is converted to JATS. Thereafter, all conventional stages of production, e.g. peer review, copy editing and author proof correction are carried out on the JATS file directly. Any data (e.g. editor queries to author) that are not to be held in the final delivered file, are saved as processing instructions.

Once author corrections are approved, the XML is automatically converted to a LaTeX file which is immediately typeset in the server using PDFTeX to produce the final PDF. If any fine-tuning is required, this is done by the typesetter, or even by the publisher, through a graphical user interface which embeds the relevant TeX commands using PIs, and then recreates the PDF file. We will give a live demonstration of the system.

Smoke Screens of Impossibility

Bruce Rosenblum, Inera, Inc.