Balisage Paper: A client-side JATS4R validator using Saxon-CE

Background

The National Center for Biotechnology Information of the National Library of Medicine originally created the Journal Archiving and Interchange Tag Suite (JATS)JATS01 with the intent of providing a common format in which publishers and archives could exchange journal content.

It was developed in response to a Document Type Definition (DTD) used by the NCBI/NLM PubMed Central project to archive life science journals from a variety of sources. Input and support from Harvard University Libraries, as well as support from The Andrew W. Mellon Foundation and collaboration with Inera, Inc. and Mulberry Technologies, Inc., allowed the scope of the project to be broadened and resulted in the NLM Journal Archiving and Interchange Tag Suite.

JATS is a NISO standard (Z39.96-2012)NISO01 that defines elements and attributes that describe metadata and full content of scholarly journal articles. The Tag Suite is the complete set of elements and attributes described in the standard. Along with these descriptions, the standard includes three article models or Tag Sets: the Journal Archive and Interchange Tag Set, the Journal Publishing Tag Set, and the Article Authoring Tag Set.

The intent of the Tag Suite is to preserve the intellectual content of journals independent of the form in which that content was originally delivered. It enables an archive to capture structural and semantic components of existing material without modeling any particular sequence or textual format.

JATS is the XML model used for all content stored in PMC.PMC01 All content in PMC is free to read, but the XML versions of the truly open access articles are available through the PMC Open Access Subset.PMC02

The Problem

In 2012, an automated software tool—the Open Access Media Importer (OAMI)OAMI1 started using the articles in the PMC Open Access Subset to find audio and video objects that could be loaded to Wikimedia Commons for use on Wikipedia and elsewhere. The OAMI used several JATS elements and attributes including those for licensing, keywords and media types. This use revealed inconsistencies in the XML available from PMC.

Although JATS is a standard and PMC performs some standardization of the submitted XML during ingest, JATS has had to allow for the fine nuances of publishing and the varying requirements of different types of content and different publishers. As a result, publishers use JATS inconsistently, which leads to problems when reusing the content. These inconsistencies affected how the OAMI software could reuse the material. Inconsistencies and ambiguities in license tagging were exceptionally problematic. This required some algorithms to determine whether the content was compatible with reuse on Wikimedia Commons.

For example, in some instances, the license URI specified a “CC-BY” license, but the human-readable text contradicted it, adding an extra non-commercial clause:

        <license license-type="open-access"
            xlink:href="http://creativecommons.org/licenses/by/2.5/">
            <p>Re-use of this article is permitted in accordance with the Creative Commons Deed,
                Attribution 2.5, which does not permit commercial exploitation.</p>
        </license>

In other examples, articles had license information outside of any <license> element:

        <permissions>
            <copyright-statement> Uosaki et al. This is an open-access article distributed under the
                terms of the Creative Commons Attribution License, which permits unrestricted use,
                distribution, and reproduction in any medium, provided the original author and
                source are credited. </copyright-statement>
            <copyright-year>2011</copyright-year>
        </permissions>

Other articles were found to have different, contradictory license URIs within the <permissions> element.

Similar problems were found whenever it was attempted to automatically extract metadata related to the article and the accompanying media files. In particular, tagging related to subjects, keywords and captions, the media types of those accompanying files, and other areas.

These problems led to a paperMIET01 that was presented at JATS-Con 2014 and triggered a call to action for the development of best practices for tagging in JATS in a way that improves reusability.BECK01

JATS for Reuse—JATS4R

In June 2014, a group of publishers and aggregators met in Cambridge, UK, to discuss JATS reusability issues. The group formed as "JATS for Reuse" and decided to publish best tagging practices recommendations to improve the reusability of JATS-tagged article content. The meeting resulted in a prioritization list of topics (elements). A websiteJ4R01 and a public mailing listJ4R02 soon followed.

The OAMI work revealed that many other JATS tags are used inconsistently, for example those concerned with mathematical formulas, affiliations and contributor roles.

In January 2015, the group was expanded to include more publishers, representation from online hosts, and also other interested parties such as content processing vendors. The group is open to anyone interested in the creation of content in XML format using the JATS DTD. Current JATS4R endorsing parties are listed on the JATS4R website.

As of this writing, the group has issued tagging recommendations in two areas: Permissions and LicensesJ4R03 and Mathematics.J4R04 When the group formalizes a recommendation, we encode the rules in Schematron. The Schematron files are available from the GitHub repository.J4R05

Tool Details

To facilitate checking instance documents against the JATS4R rules without requiring journal production editorial staff to set up their own Schematron validation service, we have implemented a validation tool hosted at http://jats4r.org/validator/. When run against an instance document, the tool parses the XML, validates against the correct NLM or JATS DTD, if one is specified, and then checks it against the JATS4R Schematron rules, and presents a report to the user. The overall data flow of this tool is depicted in Figure 1.

Fig. 1: Tool Data Flow

   
                result = xmllint.validateXML({
                xml: [filename, contents],
                arguments: ['--loaddtd', '--valid', '--noent', filename],
                schemaFiles: [[dtd_filename, dtd_contents]]
                });

Schematron Representation of JATS4R Recommendations

As described above, the JATS4R recommendations are encoded into schema files in Schematron format. The recommendations are broken down by two categories:

• level - either errors, warnings, or info

• topic - math or permissions (currently; more to come)

The Schematron rules for each of the combinations of level and topic are encapsulated in their own files. This is shown schematically in Figure 2. The table in the lower-right shows each of the (six) combinations of level and topic, and each table cell corresponds to a Schematron file.

Fig. 2: Schematron Files

There are two "master" Schematron files which break down the tests in two different ways:

• jats4r-level.sch - phases for “errors”, “warnings”, and “info”

• jats4r-topic.sch - phases for “math” and “permissions”

Another "master" Schematron file, which determines conformance or non-conformance of an instance document, is jats4r.sch. This includes all topics, but only the "error” level tests, and is equivalent to using the “errors” phase of jats4r-level.sch.

Future work