JATS-Con 2011 Schedule with Abstracts

Registration

Welcome and Introduction

Best Practices or Common Practice?

Jeff Beck, NCBI, NLM

The JATS is pretty big. And there is some documentation — and some examples. But when you come across a tagging question, the easiest thing to do is to solve it like someone else solved it. You want to know how THEY do it over there, or how THAT GUY who wrote this software that we use does it. Not all Practices are "Best Practices", and even if they are they might not be right for you.

JATS and Electronic Deposit at the Library of Congress

Erik Delfino, Library of Congress
Jane Mandelbaum, Library of Congress

This presentation will describe the current state of the Library of Congress effort to collect digital materials for our national collection through Copyright mandatory deposit. The Library is actively working with publishers to develop standards and workflows for the deposit of e-serials content in the NLM DTD and other formats.

Article vs Issue XML: Capturing the Table of Contents under the NLM DTD

Nikos Markantonatos, Atypon

Article XML captures not only article-specific metadata such as the article title and the abstract, but lots more information about the issue, the volume, and the journal that this article is published under. There are advantages in extracting all this non-article specific information in one place: the issue XML. We have built a separate issuexml.dtd on top of the JATS Tag Set and ported our entire hosted content, which includes hundreds of thousands of issues, to use that. We view the issue XML as the natural next step which helps us build a layered structure of articles and issues, much like these are encountered in the real world.

In practice, the issue XML helps us eliminate journal and issue metadata redundancy from the article XMLs, and allows for a more natural encoding of the Table of Contents, complete with its issue title, section headings, redefined article metadata, cover image and its associated caption.

Variations in XML Reference Tagging in Scholarly Publication

Bruce Rosenblum, Inera, Inc.

From the earliest days of markup languages, tagging of references has presented unique challenges. References to journals are relatively easy to tag, once a publisher has settled on a consistence structure - for example, with or without the loose text and punctuation between elements (sometimes called boilerplate text). References to non-journal content such as books, conference proceedings and gray literature, however, can present unexpected or awkward situations, and even journal references can occasionally prove idiosyncratic. This paper will provide a brief history of reference tagging in SGML and XML and will discuss specific reference markup structures in JATS, from the common to the arcane. The evolution from citation and nlm-citation to the newer element-citation and mixed-citation elements in 3.x will be reviewed, including a discussion of the workflow implications of each model. The author will conclude with some observations about the intersection among reference markup, online reference linking, and the true meaning of references in the world of electronic publishing.

JATS Implementation Panel Discussion

Cindy Maisannes, CFA Institute
Lynn Murdock, Public Library of Science
John Nickerson, Emory University
Jeffrey Boatright, Emory University
Paul Reekie, CSIRO Publishing

Introduction to Multi-language Documents in JATS

Deborah Aleyne Lapeyre, Mulberry Technologies, Inc.

The current JATS includes several structures that support encoding documents in which (some) metadata or text is provided in more than one language. In addition to the practically ubiquitous xml:lang attribute, there are elements specifically designed to contain multiple languages. Many metadata elements have been made repeatable and given an xml:lang language attribute, so that they can be present in the metadata once for each language. This introduction will explain the mechanisms for marking up multi-language content as well as examples of their use. You will learn how to encode an author's name in several languages (or language/script combinations) without creating the false impression that these variations represent additional authors. You will learn how to encode a table or a figure in several languages. Tagged metadata examples will illustrate the use of translated abstracts, titles and subtitles, keywords, and journal titles. Citation examples will illustrate multiple sources, reference authors in several scripts, and more.

Creating XML-based, peer reviewed, scientific publications on the Web

Carl Leubsdorf, Jr., Solvitor, LLC

This paper, presentation, and demo will describe Annotum, a new open-source journal authoring and publishing system. Among the topics covered:

The inspiration for and growth of rapid-process scientific publications, with near-instantaneous review and publishing of important scientific information.

How freely-available open-source tools and software can form the basis of an entire "ecosystem" of authors, publishers, designers, and coders.

A call to action for scientific researchers and publishers to take control of their own destiny by using a freely-hosted publishing system to create XML-compliant content for scientific repositories.

PMC Tagging Guidelines: A case study in normalization

Abigail Elbow, NCBI, NLM
Breena Krick, NCBI, NLM
Laura Kelly, NCBI, NLM

In 2003, when the NLM Tag Suite was being introduced, PMC was developing a new production system that would use XML data tagged in the NLM DTD. Since the DTD was new, there were no modeled examples and we were constantly asking ourselves how things should be tagged. That made us realize that we needed more consistent tagging than the DTD required—we needed our own subset. The decisions we made while developing the current PMC software became the foundation of what is now the PMC Tagging Guidelines—a set of rules that describe the normalized XML used in PMC.

This presentation will take a broad look at those early decisions, and how they developed into the Guidelines we use today. We'll also cover the various components that make up the Guidelines—from the HTML pages to the PMC Style Checker. Lastly, we will show demonstrations of the Style Checker, both the web-based tool and the XSL stylesheets.

NISO/NFAIS Supplemental Journal Article Materials Working Group - A Progress Report

Alexander ('Sasha') Schwarzman, American Geophysical Union

A joint NISO/NFAIS working group on supplemental materials to a journal article began its work in the early Summer of 2010. Its mission is to develop Recommended Practices for managing supplemental materials. The Practices will address many aspects of handling supplemental materials, such as their selection, review, editing/markup, identification, discovery, linking, packaging, accessibility, preservation, and rights managements, etc. Two working groups have been formed: the Business Working Group deals with the semantic and policy issues, while the Technical Working Group addresses the technical and implementation issues. This paper and presentation will demonstrate the progress the joint group has made and illuminate the challenges that lie ahead.

Reality Check: What to expect from automated conversion to NLM XML

Devorah Bloom, Data Conversion Laboratory, Inc.
Beth Friedman, Data Conversion Laboratory, Inc.
Gitty Kupferstein, Data Conversion Laboratory, Inc.

When looking to convert legacy content to the NLM Journal Publishing DTD, there is always concern of how well automated tools can give quality results with minimal post-conversion clean-up. This presentation will look at what an automated approach can (and can't) do, issues that are best dealt with pre-conversion, issues that are best dealt with post-conversion, and an examination of the kinds of tools that can help to ensure consistency and accuracy in delivered documents. This presentation is based on lessons learned in converting over 2 million pages to the NLM Journal Publishing DTD.

Taming the Beast: JATS data, non-JATS data, and XML Namespaces

Wendell Piez, Mulberry Technologies, Inc.

An introduction to basic concepts, gotchas, and rules of thumb for working with namespaces in JATS documents and processing systems, addressing questions including the following: What are namespaces in XML, why do I need them, and why am I so confused? What can I do about this? Can I avoid namespaces altogether? (Yes, sometimes, but mostly no, not in the real world.) If I can't avoid them, how do I work with them, and what practices do I follow so as to understand what's going on in my data, recognize and fix problems when they arise, and prevent them from ever arising? What are the rules of good namespace hygiene?

For all users of JATS, especially if you have links (XLink is in a namespace), tables (OASIS/CALS/Docbook tables are in a namespace), MathML (in a namespace), or SVG (in a namespace), or if you intend to work with or convert documents to or from XHTML (in a namespace), XSL-FO (in a namespace), other namespaced XML formats, or any format at all when using a namespace-aware technology like XSLT or XQuery.

Journal Article Tag Suite Update and Open Discussion

Book Publishing with JATS

Chandi Perera, Typefi Systems

JATS is gaining in popularity as a viable tag set for book publishing. Number of publishing organizations has adopted the NLM Book tag set as their core publishing DTD. This paper will present a series of case studies from not-for-profit and commercial organizations who have adopted the NLM Book DTD for titles ranging from reports, reference material to higher education text books.

This paper will examine why the NLM Book DTD was chosen, benefits and challenges post implementation. This paper will further detail how the more complex design requirements were reconciled and achieved within the NLM Book ecosystem. Finally the paper will touch on how the content changes within the layout environment were reconciled back to the NLM source and the challenges faced in such a process.

The future of the JATS: the probable, the possible, and the unlikely

B. Tommie Usdin, Mulberry Technologies, Inc.

In the year since JATS-Con 2010 the JATS has made one major step (becoming a draft NISO Standard) and many small steps (changes to the Tag Suite itself). This is a good time to think about the future of the JATS. Will it, and should it, be basically stationary from now on? Will it be gracefully and gradually extended? What sorts of changes are probable? Are there revolutionary changes we should be thinking about?