JATS-Con 2010 Schedule with Abstracts

Registration

Welcome and Introduction

Are We There Yet?

Jeff Beck, NCBI, NLM

The Journal Article Tag Suite has had a surprisingly quick acceptance since we released the first version in 2003. In this introduction I review how we got to where we are today, revisit some old controversies, define some terms, explain where "JATS" came from, and at least ask the question, "Is there anything left to do?"

NLM Journal Publishing DTD Flexibility: How and Why Applications of the NLM DTD Vary Based on Publisher-Specific Requirements

Bruce Rosenblum, Inera Incorporated

The NLM Journal Publishing DTD was designed for full-text encoding of journal articles for current publication. More restrictive than the NLM Archive and Interchange DTD, the Journal Publishing DTD nevertheless allows for wide latitude in the application of many elements and attributes. The interpretation of the DTD in a given context may be based on forethought and specific business requirements or may be somewhat arbitrary, depending on the experience level of the DTD user. On the basis of a review of more than 20 implementations of the DTD, this paper will discuss various interpretations chosen by a range of publishers as well as the business or technical requirements that led to those decisions. The implications, pro and con, of this flexibility will be examined. The paper concludes with the suggestion that this flexibility is one factor that has led to wide adoption of the NLM DTD Suite.

Journals and Magazines and Books, Oh My! A Look at ACS' Use of NLM Tagsets

Dan O'Brien, American Chemical Society, Publications Production Systems
Jeff Fisher, American Chemical Society, Publications Production Systems

Over the past several years, the ACS Publishing Division has implemented XML-based publishing processes that make use of the NLM Tagsets. We describe how our chemistry-related Journals, Books, and Magazine publications have all implemented various flavors of the NLM Tagsets in both the production and electronic delivery of our content. We discuss some of the customizations that we made to the tagsets, why we made them, how the tagsets are used within our environment, and some of the successes and mistakes that we have experienced along the way.

Fitting the Journal Publishing 3.0 Preview Stylesheets to Your Needs: Capabilities and Customizations

Wendell Piez, Mulberry Technologies, Inc.

An introduction to the NCBI/NLM Journal Publishing 3.0 Preview XSLT stylesheets, which provide for basic styled display of Journal Publishing 3.0 data, in HTML and PDF, with an emphasis on features enabling extension and customization. With demonstrations.

JATS to EPUB: Unraveling the Mystery

Laura Kelly, NCBI, NLM

It's no great mystery that the increasing support of the EPUB format is making it more and more attractive to publishers. But what does seem to be a mystery is how best to use existing JATS data to generate EPUB content. This paper looks to unravel that mystery by explaining the basics of EPUB and examining how it relates to the Tag Suite. The paper also discusses ways that existing Tag Suite tools can be utilized to make the process of generating EPUB data easier.

eXtyles, Typefi, and the NLM Journal Publishing DTD

Louise Adam, Federation of Animal Science Societies
Chandi Perera, Typefi Systems

The Federation of Animal Science Societies recently implemented an XML-based journal publishing workflow with the eXtyles software and Typéfi Publish at the core. With eXtyles, we export XML (validated to the NLM Journal Publishing DTD) from edited Word files, which is used by the Typéfi Publish system to automatically generate a composed journal article in minutes. This new workflow combines the efficiency of batch pagination with the rich design capabilities and ease of use of InDesign. We are able to supply NLM XML to our online journal hosts, enabling rapid online publication (now within hours instead of days). The new workflow has allowed us to eliminate a labor-intensive, time-consuming, and expensive typecoding process. In this presentation, we will review the eXtyles-Typéfi workflow and the Typéfi-InDesign template and XSLT and discuss some of the challenges encountered in implementing this new composition process for STM journals.

Aggregating E-Journals: Adopting the Journal Archiving and Interchange Tag Set to Build a Shared E-Journal Archive for Ontario

Wei Zhao, OCUL Scholars Portal
Vidhya Arvind, OCUL Scholars Portal

Ontario Scholars Portal (SP) is a digital repository containing almost 20,000,000 articles from over 8400 full text journals of 16 publishers which covers every academic discipline. Starting in 2006, SP began adopting NLM Journal Archiving and Interchange Tag Set v2.3 for its XML based E-journals system using MarkLogic. The publishers native data is transformed to NLM Tag Set in SP in order to normalize data elements to a single standard for archiving, display and searching. The data transformation is processed in two steps—the crosswalk done by the librarian and the coding by the programmer. Although not all the elements from the Tag Set have been used, additional customized tags have been added to capture the loading information. Local rules and policies are applied to tag the document in addition to those imposed by NLM Tag Set. Decisions for multiple options for transforming the publishers' tag, developing the schemato construct the journal and issue table of content structures on our own, evaluation the consequences of moving all our content to version 3.0 are the challenges of using this Tag Set.

Portico: A Case Study in the Use of the Journal Archiving and Interchange Tag Set for the Long Term Preservation of Scholarly Journals

Sheila Morrissey, ITHAKA
John M. Meyer, ITHAKA
Sushil Bhattarai, ITHAKA
Sachin Kurdikar, ITHAKA
Jie Ling, ITHAKA
Matthew Stoeffler, ITHAKA
Umadevi Thanneeru, ITHAKA

This paper explores the experience of Portico (www.portico.org), a not-for-profit digital preservation service providing a permanent archive of electronic journals, books, and other scholarly content, as both an implementer and a partner in the on-going development of the National Library of Medicine's Journal Archiving and Interchange Tag Set. It reviews the shared origin of both entities in the 2001-2002 Mellon Foundation funded study of e-journal archiving projects, and the process by which Portico has attempted to distill and share with the larger JATS community the experience which we have gained over the course of converting approximately 70 e-journal formats (adumbrating approximately 170 distinct variants such as versions and provider-usage-profiles) into the Journal Archiving and Interchange Tag Set. It briefly details the challenges encountered by the authors of this paper (who comprise the technical team who create the transformations of publisher-supplied content to NLM) in normalizing these many formats to a single one. It describes the profile of the NLM Journal Archiving and Interchange Tag Set employed by Portico (which is fully convertible to that tag set), the rationale behind the usage choices it enforces, and its use in normalization of input, some of which itself is NLM (albeit reflecting usage profiles, whether implicitly or explicitly documented and declared, of different publishers). Finally, it discusses possible additional refinements that might be desired, particularly in relation to the <named-content> and <custom-meta-group> elements, to ensure consistent and lossless transformation from various publisher formats to the Journal Archiving and Interchange Tag Set.

TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions

Terry Catapano, Columbia University Libraries

TaxPub is an extension of the NLM/NCBI Journal Publishing DTD (Version 3.0) for the encoding of the literature of biological taxonomy. A key feature of this literature is the taxonomic description: publications or sections of publications, which name and describe species and other taxonomic. Given that it is estimated that the majority of all species have yet to be described, and that some 15-20,000 new species are described each year, and that markup might be applied prior to publication at less expense than applying markup to existing publications, TaxPub aims at providing a tagset for the encoding new taxonomic literature. TaxPub extends the Publishing ("Blue") DTD parsimoniously. A few phrase level elements are available at the relevant places throughout the entire DTD. Most of the extension, however, occurs in a single section-level element <tp:taxon-treatment>. The development of the extension has proceeded smoothly but several challenges have been encountered: lack of consensus on the components of taxonomic descriptions; relationship and alignment of TaxPub to other related schemas in the field; decisions on creating new elements or using existing NLM DTD elements and how to document and validate the usages; resistance to DTD as the XML schema language, and the efficiency of creating a superset extension rather than utilizing other simpler profiling mechanisms.

Accessible Publishing Using the Journal Article Tag Suite

Melanie Lauckner, World Health Organization
Chandi Perera, Typefi Systems

An estimated 10% of the world's population — approximately 650 million people, of which 200 million are children — experience some form of disability. This is a significant audience, which has a right to access information. The accessibility of information is required of governments and international organizations by the United Nations Convention on the Rights of Persons with Disabilities, as well as by the Disability Discrimination Act (Australia and United Kingdom) and Section 508 of the Rehabilitation Act (USA).

Many governments and international organizations use the Journal Article Tag Suite (JATS) to publish journal content. The World Health Organization (WHO) uses JATS to publish the monthly peer-reviewed Bulletin of the World Health Organization and will jointly publish with the World Bank the World report on disability later in 2010. To make publications accessible, WHO is leveraging its single-source XML to create a number of products, including clear print, accessible PDF, large print and the conversion of JATS to the DAISY DTD (dtbook).

This paper presents approaches that can be taken to make information accessible to persons with disabilities, beyond the web environment. It shares findings on how accessible products are created using JATS and gives details on approaches taken to mitigate some perceived limitations of JATS. Finally, the paper points out opportunities for implementing JATS to enable the creation of fully accessible content.

These opportunities are:

1. Consistent and exclusive use of alternative text tags within fig, display-equation, inline-equation and other image elements
2. Alternative text for tables <table-wrap>
3. Accessible text for text (for example, replacing abbreviations with full text)
4. Decorative but informative content
5. Conditional content

Bookshelf: Leafing through XML

Martin Latterner, MA, National Center for Biotechnology Information
Marilu Hoeppner, PhD, National Center for Biotechnology Information

Bookshelf is a digital collection of texts in life sciences and healthcare, at the National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM). It currently includes roughly 700 titles, mostly textbooks, government or technical reports, and electronic publications. Content is submitted to Bookshelf by publishers and authors wishing to participate in the Bookshelf project. Supported by the PubMed Central (PMC; NCBI's digital archive of full text articles) infrastructure for publishing and archiving and NCBI's powerful Entrez system for search and retrieval, users can freely gain access to the content, which is closely integrated with other databases at NCBI such as PubMed and Entrez Gene, allowing discoverability of important clinical and scientific information.

Bookshelf maintains its content in XML conforming to the Book DTD of the NLM Journal Article Tag Suite . Several workflows exist to handle the conversion from various input formats to the Bookshelf XML standard. This paper discusses how the NLM Book DTD is used in Bookshelf within the context of PMC, the various workflows in Bookshelf, and mechanisms to integrate content at NCBI.

Why Create a Subset of a Public Tag Set

Deborah Aleyne Lapeyre, Mulberry Technologies, Inc.

The Journal Article Tag Sets were designed as translation targets; they are permissive, descriptive rather than prescriptive, and use escape hatches to preserve as many semantics as possible in born-digital XML content that originates in another tag set. This means that the Tag Sets can describe "almost" anything for "almost" anybody, but they may fail to hit the sweet spot for XML production.

The Journal Article Tag Sets can be used right out of the box, and many users do just that. But for a publisher (particularly a publisher looking to move XML to earlier stages in a workflow) or for an archive with requirements to regularize archival content, the advantages to subsetting can be substantial. A subset leaves all the documents valid to one of the original NLM Tag Sets at the same time it enables business-specific reporting, Quality Assurance, and XML tool use.

Subsetting can eliminate unimportant and meaningless variation that makes all work with a tag set more difficult and time-consuming. An organization can tighten loose models; eliminate elements and attributes that are the twenty percent of the 80/20 rule that they do not need; and provide specific attribute values where the Tag Sets permit any data characters. There are advantages to a leaner tag set for controlling conversion vendors and interchanging with aggregators and business partners. But the largest gains may be in ease-of-use for XML copy-editors and faster ramp-up for the developers building web applications.

Subsetting makes the most sense for XML-first workflows when copy-editing is performed in XML; when a publisher or archive relies on non-subject-matter-expert conversion vendors; and when there are more than a handful of complex output products produced from the XML.

Journal Article Tag Suite Update and Open Discussion

Superset Me—Not: Why the Journal Publishing Tag Set Is Sufficient if You Use Appropriate Layer Validation

Alexander ('Sasha') Schwarzman, American Geophysical Union

This paper relates the experience of a publisher who chose to create a superset of the NLM Journal Publishing Tag Set in order to enforce business rules, data types, and house style and, having done just that, realized that a subset could have been sufficient to meet the publisher's needs if it were used in conjunction with the appropriate layer validation technology, such as Schematron.

The Evolving Information Ecostructure of Publishing

Evan Owens, American Institute of Physics

It has been nearly 25 years since the invention of SGML and the appearance of the first journal article DTD standard and 15 years since the first online journals appeared on the web. A lot has changed in the landscape of publishing in that time...and not just in publishing technology and journal article markup. This paper presents a brief historical overview followed by observations on current trends and speculation as to what will come next in the information management requirements of scholarly and scientific publishing.