Maloney, Chris. “JATSPack and JATSPAN, a packaging format and infrastructure for the NLM/NISO Journal
Archiving Tag Suite (JATS).” Presented at Balisage: The Markup Conference 2011, Montréal, Canada, August 2 - 5, 2011. In Proceedings of Balisage: The Markup Conference 2011. Balisage Series on Markup Technologies, vol. 7 (2011). https://doi.org/10.4242/BalisageVol7.Maloney01.
Balisage: The Markup Conference 2011 August 2 - 5, 2011
Balisage Paper: JATSPack and JATSPAN, a packaging format and infrastructure for the NLM/NISO
Journal Archiving Tag Suite (JATS)
NCBI / NLM / NIH (Contractor)
Chris Maloney works as a contractor for NLM/NCBI, on the PubMed Central and Bookshelf
The Author's contribution to this Work was done as part of his official duties as
an NIH employee and is a Work of the United States Government. Therefore, copyright
may not be established in the United States. 17 U.S.C. § 105.
If Publisher intends to disseminate the Work outside the U.S., Publisher may secure
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permit others to do so.
The NISO Journal Archiving Tag Suite (JATS, formerly known as ‘the NLM DTD’) is a
common format used in
publication of scientific literature. JATSPack, a proposal based on the new EXPath Packaging System,
provides a way to package schema customizations and software
libraries associated with any of the JATS schemas, thus making it easier for developers
to distribute JATS-related resources and easier for users to acquire, install, and
JATSPAN (the JATSPack Archive Network) is
a website allowing users to share and collaborate on JATSPacks. A client-side command
line tool, jatspan, interacts with the site and eases the task of
maintaining local repositories of JATSPacks.
JATS was recently released as a NISO standard for trial use. The JATS schemas are downloadable from the NLM site,
and come in several flavors, which have different semantics and use cases. These
include Archiving and Interchange (green), Journal Publishing (blue), and Article
Authoring (pumpkin). They also come in three different formats: DTD, W3C Schema, and
Most publishers who use the JATS choose to use the DTD format (Rosenblum 2010).
Although they are still
often referred to as the "NLM DTDs", this paper will use the terms "JATS" and "JATS
be clear that: A) the standard is now NISO, and is no longer specifically issued by
the NLM; and B) it is not just DTDs, but also other schema formats. One unfortunate
the JATS acronym is that the tag suite is not limited to Journal Articles, but can
be used for
other types of documents (books, for example).
This paper describes JATSPack, which is a packaging format based on the new EXPath Packaging System specification.
JATSPack provides a well-defined way of packaging customizations and libraries associated
any of the JATS schema. JATSPacks are bundled packages of catalog files, schema,
documentation, code, and sample files, all with a coherent purpose. The JATSPack format
primarily designed to facilitate the exchange and reuse of JATS customizations, but
also be used to package and transfer code libraries — for example, XSLT transformations
translate JATS to/from some other format. JATSPack can be thought of as a format for
plugin modules, with each
plugin providing a bundle of new functionality which can be easily installed into
JATSPack and JATSPAN are not part of the NLM/NISO JATS.
JATSPack is a proposed specification that is completely independent of the tag suite.
JATSPAN is a non-commercial web site with no affiliation with
JATSPack specifies a directory structure and a package descriptor file format.
The package descriptor file, similar to a manifest file in other packaging formats,
describes the contents, metadata about the included resources, and the dependencies
Establishing this format will facilitate the automatic installation and
maintenance of libraries and of schema extensions, which should allow easier reuse
interchange of the schema themselves. This, in turn, should allow for easier interchange
of JATS document instances.
JATSPAN, the JATSPack Archive Network,
is a website similar in
concept to the very successful CPAN
(Comprehensive Perl Archive
Network). Its main purpose is to allow users to share and collaborate on JATSPacks.
Authors can upload their customizations or libraries, and can search for and
download JATSPacks produced by
others. Every JATSPack can be downloaded in one of two formats. The contents are
exactly the same, but the download files differ in their filename extension: a .xar
which is the extension used by the EXPath Packaging System, or as a .zip file, so
package can be used stand-alone, without any special infrastructure.
Providing a centralized repository like this will make it easier to discover
packs that might be relevant to one's needs, as well as making it easier to install
them on the local system.
Associated with JATSPAN is a command-line client, jatspan (lowercase),
which runs on a user's machine and
maintains a local on-disk repository. jatspan has a
simple interface and lets users look up and install packages from JATSPAN. One benefit
to this architecture is that dependencies between packs can be resolved automatically.
example, if users want to install packs that depend on others, they don't have to
figure out where to go to get these, and then, perhaps, be frustrated by different
directory structures and installation requirements. Instead, the dependency packs
found, downloaded, and installed automatically.
The following are a few examples of use cases that these specifications are designed
A publisher installs support for a third-party JATS customization
Suppose a publisher wants to integrate support for document instances that conform
some customization of JATS that was not developed in-house. Very often, document instances,
if they even have a document type declaration (doctype decl) at all,
do not include an absolute
system identifier (a URI) to reference the DTD.
So, at a minimum, either an OASIS catalog entry must be
added to a local catalog file to cross reference the formal public identifier
(FPI) to the DTD served somewhere on the Internet, or the DTD
must be downloaded and installed on the local filesystem, and the XML processors be
aware of it. This is not especially difficult, but does require a certain level of
and coordination of system resources.
If the customization were packaged in the JATSPack format, then the
necessary setup would be more automated. It would be as easy as identifying the desired
pack and using the jatspan utility to install it in the local repository.
utility automatically updates the local OASIS catalog file with a <nextCatalog>
point to the new JATSPack. So any tool that is able to use
OASIS catalogs to resolve
identifiers would automatically get access to the new schema files without any additional
The important point here is that, because of the way the JATSPack format incorporates
OASIS catalog files, this system can be used with any XML processing tool, not just
that are JATSPack-aware. This is tested and works right now for both
the oXygen XML editor and the
This use case is described in more detail in the TaxPub
A developer writes a new translator, and shares it with others
In this use-case, suppose that a developer that has written a
transformation from JATS into a new file format. It could be someone who did it for
perhaps, a company has a vested interest in promoting the file format.
For whatever reason, let's say that they want to share it with others and try to
get others to adopt it and integrate it into their systems.
Right now, there is no standard way to
present this transformation library to the world. Typically, the library would be
for download on the developer's website, as a Zip file, with a README file that includes
instructions for unpacking and installation. The actual details of packaging the
library, finding a place to put it, and letting others know about it, involve a lot
detailed decisions. Each individual step is not difficult, but taken together, they
present a barrier to this kind of sharing of code libraries.
All this is ripe for standardization. Indeed, this is the main raison d'etre
for the EXPath Packaging specification.
The transformation languages in which these
are usually written, XSLT, XQuery, and XProc, are mature enough that they can be written
a portable, system-independent way.
The JATSPack format is specified and JATSPAN provides many examples, which reduces
burden of making decisions about how exactly to package the bundle.
JATSPAN provides a publically-accessible place to upload packages, so developers
don't have to find places on their own websites for them.
If a library were created as a JATSPack, and were put
on JATSPAN, it would be easier for potential users to discover and install.
library had dependencies on others, then those others would not have to be bundled
this package. The
jatspan client program would take care of resolving these dependencies automatically.
A publisher or a developer who is introduced to the JATS for the first time
can be a bit overwhelmed. To be sure, JATS is extremely well documented,
as one can readily see by browsing the
NLM web site.
Yet the fact that JATS have been in use for a long time, and that there are
now many different branches (flavors) and versions, can make them seem,
to someone who is not familiar with them, complicated.
Someone who wants to evaluate the suitability of JATS for their particular
needs might want to be able to quickly set up a system that can process
any JATS instance document, regardless of what flavor or version that instance
document conforms to. This is difficult to do, because each flavor and each
version of the JATS is distributed as a separate, flattened Zip file which
includes the bundled version of all of the files needed for that particular
set. For example, the books
2.3 DTD Zip file includes all of the
books-specific modules, as well as all of the shared modules, and even
the xhtml and mathml2 library modules.
For each flavor/version of interest, it is necessary to download and extract
the Zip file, and then manually tweak the provided OASIS catalog file for
that set, and then point your XML tool set to use that catalog
Because there are so many different tag set bundles, it would be quite
time-consuming to configure a system that is able to use them all.
This is not seen as a problem, because this is not the primary
use-case that the NLM site is designed to serve.
They provide stand-alone bundles specifically so that a user who
is interested in only, for example, Publishing 2.3, can download that version
and not be confused by all of the others (Jeff Beck, personal communication,
But if someone is interested in configuring a system that can
understand and process any JATS instance document; either for the purposes
of evaluating JATS, or so that they can exchange documents with other
organizations, it would be quite difficult.
To address this use case, and to provide a basis for the JATSPack
architecture, I have repackaged all of the JATS DTD modules as JATSPacks,
put them into a single bundle, and made the
repackaged versions available on JATSPAN.
This base bundle is (optionally) installed automatically when you first
run the jatspan client utility, as part of its setting up the
Existing JATS DTDs are available as JATSPacks below for details.
A publisher develops a new JATS customization
Let's say that a publisher has a need to customize the JATS, in order to include
domain-specific data within the source documents in their database. This is actually
primary use-case that JATSPack was designed to address, and this is the complement
the first use case described above. That use case
described customizations from the user's perspective, and this use case describes
from the author's perspective.
There are a number of concerns that
tend to make people reluctant to define customizations. Among the most prominent
is that a customization to the JATS might make their
documents less portable. This use case is discussed in detail in the
Customizations and Compatibility section, below.
EXPath Packaging - the basis for the JATSPack format
JATSPack is an extension of the
Packaging System (hereinafter EXPath-pkg, written by Florent Georges).
EXPath-pkg is a simple, concise format for the packaging of files of various core
XML technologies, including XML Schema, Relax NG, Schematron, NVDL, XSLT, XQuery,
XProc (Georges 2010).
It also provides a flexible extension mechanism which is exploited by JATSPack to
additional file types, and other requirements specific to its needs.
As defined by EXPath-pkg, a package is a set of files that fulfill a common purpose.
Each package has a globally unique name (which is a URI) and an abbreviated name (hereafter
referred to as abbrev), an NCName.
Abbrev values are case-insensitive, and, by convention,
all lowercase. A component is one file within a package, and can be one of several
A package includes a package descriptor (similar to a JAR manifest file) which lists
the package contents and top-level metadata about the package. This metadata includes
URI name, abbrev, version number, and a list of dependencies.
Finally, all the files of a
package are arranged in a specified directory structure, and used to create a Zip
by convention is given a name based on the abbrev, the version number,
and a ".xar" extension.
EXPath-pkg is an emerging standard which is already supported by several tools,
including the eXist and Qizx XML databases, the Saxon XSLT and XQuery processor and
Calabash XProc processor. (Support in Saxon and Calabash is via third-party plugins.)
also implemented as an open-source Java library, hosted as the
on Google Code.
The goal of JATSPack is to be a forward-compatible extension of EXPath-pkg,
meaning that any system that
is capable of deploying EXPath packages will be able to deploy JATSPacks (although
not all of the features of JATSPacks would be fully exploited). Note that, in fact,
EXPath packages and JATSPacks are forward-compatible extensions of
simple Zip files, meaning that
JATSPacks could be used by anyone, without any special infrastructure at all, just
unzipping them onto the local filesystem.
JATSPack extends EXPath-pkg as follows.
JATSPack-specific extensions to the package
descriptor file. This will include the ability to record the author,
release date, and other
metadata. See Overall structure of
JATSPacks, below, for more information about this.
Sample instances documents. If the pack includes a schema
customization, then it should include a set of sample documents.
See Sample files and automated tests,
More specific directory
structure. EXPath-pkg is very loose about the directory structure of
files within the main
package directory. JATSPack specifies this structure more explicitly.
Requirement for two-part abbrevs. Currently, EXPath-pkg abbrevs
are simple NCNames. In JATSPack, they are two NCNames separated by a slash.
For example, "nlmjats/archiving".
Another source of
inspiration for the JATSPack format was the
Document Does it all (ODD) format of TEI.
The ODD has very clean structure, which encourages literate programming (documentation
and code in the same source document), examples of usage, clear separation of concerns,
best of all, encapsulation of all the relevant data into a single document with a
standardized structure (Lou Burnard et al 2005).
The JATSPack format strives to be similar to ODD, and could even be
thought of as encapsulating the library or customization in one document,
if one expands the
definition of "document" to include "Zip file" (which is quite reasonable).
As already mentioned, every JATSPack must have an
abbrev and a version number. In JATSPack, in order
to help ensure that the abbreviated names will be unique, they are composed of
two parts, each of which is an NCName (by convention, all lowercase, and the underscore
character should not be used in either part).
These are separated by a forward slash in the package descriptor file, for example,
The name of the package file is specified to be
When the two part abbrev is used in the package
filename, the forward slash is translated into an underscore. For example,
The actual low-level format of the file is that of a
Zip file, and the directory structure within that archive is as shown here.
At the top two levels are directories corresponding to the two parts of the
Within the package contents directory are the EXPath-pkg descriptor file expath-pkg.xml,
and optionally a README.txt file. Also in this
directory are an OASIS catalog file and one
subdirectory for each of the main file types of the package.
The expath-pkg.xml file format is described in Georges 2010. Extensions to the file format, as
allowed by the extension mechanism, allow us to include metadata specific to JATSPacks.
The 'jp' namespace prefix is used for this.
The following is an example of what the package descriptor file would look like
for a hypothetical customization of
the base Archiving and Interchange Tag Set, version 3.0, designed to add elements
and attributes to describe filesystems.
<title>Filesystem customization of JATS Archiving 3.0</title>
This customization of the Archiving and Interchange Tag Set, version 3.0,
adds filesystem-related elements and attributes, for describing computer
filesystems within instance documents.
<dc:rights>This work is in the public domain.</dc:rights>
<!-- Package contents. -->
The top-level <package> element includes
attributes that give the abbrev,
the package name (a URI), and the version of this package.
The @spec attribute indicates the version of EXPath-pkg
that this package descriptor conforms to. The <title> element
gives a human-readable title of the package.
The @jp:spec attribute is a JATSPack extension to the
EXPath-pkg package file format. This attribute is required for all JATSPacks,
and its value gives the version of the JATSPack specification that this
package conforms to.
Another JATSPack extension is the addition of the
<rdf:Description> metadata section, which uses the XML
vocabulary defined by the Dublin Core
Metadata Initiative (DCMI) to allow authors to describe the package
in more detail.
EXPath-pkg allows zero-to-many <dependency> elements,
each of which indicates a
dependency of this package. In this example, we see that the
filesystem package depends on
the JATS Archiving 3.0 base JATSPack.
The <jp:catalog> element specifies the location of the
OASIS catalog file that
accompanies this package. Finally, the <xslt> element
specifies the location of an
XSLT module, and the URI which is used to import it from other modules.
OASIS Catalog files
Note that there are no individual entries in the package descriptor for the top-level
DTD files of this filesystem
customization. That's because these DTD modules are specified in the OASIS catalog
following the principle of DRY,
are not duplicated in the
descriptor. Resolution of public identifiers (FPIs) and system identifiers (URIs)
DTD modules within
this package is delegated to the catalog file mechanism.
An elided view of the OASIS catalog file accompanying this package is the following.
This catalog file uses the @uri attribute with a relative URI value
to specify the location of the main DTD included
with this package. An important point here is that there is nothing special about
catalog file. It is usable by any system that can read OASIS catalog files, and does
depend on those systems' understanding the JATSPack format.
Existing JATS DTDs, and selected Relax NGs, are available as JATSPacks
The existing set of 34 complete DTDs of the JATS, as downloadable from the NLM
jats FTP sites, has been
repackaged as JATSPacks. In addition, the latest NISO trial versions of the
Relax NG schemas have been included in those JATSPacks. (The older NLM JATS versions
of the JATSPacks only include the DTDs.) These can all be downloaded
from JATSPAN as a single bundle.
The DTDs include all seven flavors, and
up to seven versions of each, going all the way back to version 1.0, and all the
way up to the recently released NISO trial versions.
As described in the use case "A publisher evaluates JATS for the first time"
above, each DTD version on the NLM FTP site is downloadable as a single Zip file which
includes all of the
files required for that version, including all the core files that the version
depends on. As mentioned, this is very suitable for, for example,
a publisher or author who is interested in configuring a system
capable of dealing with a specific flavor and version (for example, Article
Authoring 3.0) of JATS.
Unfortunately, however, this method of distribution makes it difficult to implement
single system that's capable of processing instance documents that conform to
any of the many different versions of JATS.
Because each Zip file on the FTP site is a complete set of all of the files needed
an instance of the DTD, among the complete set of all flavors and versions, there
is a lot
of duplication of files.
This leads to some ambiguity when many of these sets coexist on the
same system at the same time. If the same public identifier is used in multiple catalog
files on the
system, and point to document instances which are not identical,
it is difficult for someone
configuring the system to sort out whether the differences are substantive, and if
which is the canonical instance.
The JATSPack base bundle eliminates this redundancy, factors shared modules out into
core package, and cleans up a few inconsistencies.
The result is a well-defined directory
structure, with well documented dependencies. Each individual package comes with an
catalog file that only has entries for the file in that particular module. A top-level
catalog file is provided that uses the <nextCatalog>
element to include all of the others.
These JATSPack versions of the schema are 100% compatible with those on the NLM site,
because of this, the JATSPack versions of the NISO DTDs are fully compliant implementations
the NISO standard.
The Relax NG Zip files downloadable from the NLM site do not include OASIS catalog
and so to include these files in the JATSPacks, it was necessary to create entries
for them. This is discussed in more
detail in Namespaces and Relax NG, below.
Journal Publishing 3.0 Preview Stylesheets as a JATSPack
These are a set of preview stylesheets for the
Publishing tag set, version 3.0, that are available for download from the
They are authored by Wendell Piez, and are described very nicely in
Piez 2010, from the
These were repackaged into the JATSPack format. This was very straightforward, and
involved the following steps:
Assigning an abbrev:
"html/publishing-3.0-preview"; a name, which is a URI:
"http://jatspan.org/jatspacks/html/publishing-3.0-preview", and a version: "1.0".
Creating the requisite directory structure.
Moving files around. The files in this library comprise 14
XSLT files, nine files of documentation, a CSS resource, and a readme.txt file.
Reimplementation of all of the shell stylesheets as individual steps defined within
XProc pipeline. At the top level of the preview stylesheets are seven "shell" XSLT
which are basically pipelines. One of the seven should be used depending on choices
citation style, desired output format, and content filtering (print only). Unfortunately,
these shell stylesheets use Saxon-specific extensions and depend on one of the non-free
versions of Saxon. It makes sense to implement these as an XProc pipeline, with three
parameters for the choices described above.
Writing the package descriptor file. This
involved assigning absolute import URIs to the outward-facing XProc and XSLT modules.
Zipping it into the file html_publishing-3.0-preview-1.0.xar, and uploading it to
By itself, repackaging this library in this way could
not be considered an improvement over the current deployment of this tool,
as a Zip file.
However, there are a few advantages. Since this package is on JATSPAN, it can be searched
for and discovered on JATSPAN. The documentation can be browsed by anyone from the
site, without downloading and extracting the package. Anyone using the jatspan client
utility could install it automatically with the following simple command.
jatspan install html/publishing-3.0-preview
Anyone with an EXPath-pkg enabled system would have instant
programmatic access to the XProc stylesheets and XSLT modules, through their import
Normally this would require some integration effort, but with JATSPack, it is automatic.
Furthermore, there are no disadvantages to packaging this way. The JATSPAN site allows
anyone to download this package as a .zip file (exactly the same file as the .xar,
a different extension), which can then be unzipped on the filesystem and used just
Another advantage is that other JATSPacks, written by other authors, could
declare a dependency on this package. This would simplify the installation and
integration of those later packages. And this point makes a good segue to the next
At the JATS-Con last year, Laura Kelly gave
an excellent presentation
on the EPUB format and a set of
transformations for converting JATS documents into EPUB (Kelly 2010).
She wrote the transformations in standards-conforming, system independent, XSLT 2.0
XProc. The effort to repackage this as a JATSPack was quite minimal, and involved
the same steps as above. The abbrev assigned to this JATSPack is
This set of transformations uses the preview stylesheets described above. The original
Zip file distribution of this library includes a copy of the XSLT files from the preview
stylesheets that are used.
In the JATSPack, those have been removed, and replaced with a
dependency declaration in the package descriptor file. The advantage of this is
that users can avoid having two copies of the same library (the preview stylesheets)
on their system at the same time. In this simple example, it would not be
a big problem. But the problem of multiple copies of the same resources
can get severe as the number of packages and libraries increases.
Accessible Tables Stylesheet
The next example is not a JATSPack at all; it is an EXPath-pkg.
My colleague Martin Latterner wrote a very nice XSLT stylesheet which takes as
input an XHTML table. The stylesheet computes, for each table cell, which horizontal
vertical headers correspond to that cell. The stylesheet then adds classes to the
headers to explicitly encode the associations.
This is necessary so as to properly code tables for compliance with Section 508 of
U.S. Rehabilitation Act of 1973, providing for accessibility to the disabled, in particular
the visually impaired. With tables marked up like this, screen readers can assist
impaired users by reading, for any given table cell, the headers associated with that
Figure 1 illustrates the result of this transformation.
Given that tables can have very complicated structures, with multiple
@rowspan cells in different places, this is not a trivial algorithm.
header cells to be highlighted with a different background color, as shown in
This stylesheet provides a very specific bit of functionality,
and is something that other users could benefit from, so it is suitable for
packaging and putting on a public repository.
However, since it operates on XHTML tables, and is not JATS specific, it is more
appropriate to package it as an EXPath-pkg and to put it on CXAN
(the Comprehensive XML Archive Network),
so that is what we did.
The reason this is included as an example in this paper is to illustrate the
important fact that JATSPack systems are backwards-compatible with EXPath-pkg.
Any system set up to use JATSPacks will also be able to install and use any of the
EXPath-pkgs on CXAN.
To use this particular accessible tables stylesheet, one would install the EXPath-pkg,
and then simply import the stylesheet using the import URI defined in the package
descriptor. It could be wrapped in an XProc step, or the template could be invoked
from another stylesheet.
TaxPub is a customization of JATS in DTD form, which was described
in a paper presented at last year's JATS-Con (Catapano 2010).
allows for the encoding of literature of biological taxonomy, and in particular, taxonomy
treatments, which are blocks of well-structured markup with very specific semantics.
open-source project on SourceForge, with
documentation on the
project home page.
The TaxPub customization comprises a set of DTD files, which defines a set of
new element names with a "tp:" pseudo-namespace-prefix (e.g. "tp:taxon-treatment").
This has been repackaged as a JATSPack and put on the JATSPAN website. The following
a summary of the steps involved:
Assigned a unique abbrev: "taxpub/schema",
and version: "0.1".
Created the specified directory structure:
Moved the TaxPub DTD-specific .dtd and .ent files into the dtd directory. There
are five of these.
Removed the no-namespace-prefix versions of the DTD. These have been deprecated.
Fixed the relative system identifiers in each of the TaxPub modules so that they
reflect the fixed directory structure of a JATSPack installation. This is similar
what was done for the base JATS modules. It is not strictly necessary, but has the
benefit that the same modules can be used on systems that don't support OASIS catalog
Fixed the DOCTYPE declarations of the sample files. As downloaded, the included
sample files' DOCTYPE declarations did not use formal public identifiers (FPIs),
and used only relative system
identifiers. For example:
<!DOCTYPE article SYSTEM "../tax-treatment-NS0.dtd">
These were changed to use FPIs, and the relative system identifier was changed to
reflect the new directory structure. For example:
<!DOCTYPE book PUBLIC
"-//TaxonX//DTD Taxonomic Treatment Publishing DTD v0 20100105//EN"
This allows these sample files to be used in the automated tests. They also now serve
as examples of the proper DOCTYPE declaration to use for instance documents of these
types. If it is desired that documents of this type be easily exchangeable between
systems, then it is crucial that document instances be properly self-identifying.
Created a catalog.xml file in the base "taxpub" directory. This cross references
each of the defined FPIs in this customization to it's correct module in the
package. For example:
Created a new README.txt file, adapted from the existing one, and adding a bit of
information about the new structure.
Zipped the result, gave it the name
taxpub_schema-0.1.xar, and then uploaded it to the
To see the advantages of this packaging format, let's consider a very specific
use-case. Suppose that I am a user who works with the oXygen XML editor, and
I find that I have a need to read, edit and validate TaxPub files.
If TaxPub were not packaged in a JATSPack, the process of adding support to oXygen
would not be difficult, but would require a little bit of expertise and some time.
have to download the Zip file, unpack it, and read the README file to see if there
specific instructions I needed to worry about. Then I would find a place for it to
my filesystem and move the files there. The tricky bit is then to set up oXygen to
understand the public identifer, and have it retrieve the correct DTD. I could either
add an entry to my
own personal catalog file (if I have one), add it to oXygen's master catalog file,
or set up a "document type association" inside oXygen.
Now let's suppose instead that I will use the JATSPack version of TaxPub.
Of course, there is a bit of
up-front configuration required, to set up a JATSPAN repository and point
oXygen to it. But that is a one-time operation, which then allows me instant access
to any number of JATSPacks. Also, this one-time setup is
actually quite trivial, and easier than installing the support for the single TaxPub
document type as described above. The setup involves two steps:
Installing the JATSPAN software, and running it for the first time.
This establishes a JATSPAN repository on the local filesystem.
Telling oXygen where to find the master catalog file of the JATSPAN repository,
by adding an entry in the "XML Catalog" preferences box. Note that
any tool that is
able to use OASIS catalog files could be pointed to this JATSPAN master catalog
file, and would have the automatic ability to reference all of the schema files
of all of the installed JATSPacks.
After the initial setup is done, to install support for TaxPub as a JATSPack,
I need to enter one command:
jatspan install taxpub/schema
That is it — everything else is done automatically. When the TaxPub JATSPack is
downloaded, a <nextCatalog> entry is added to the JATSPAN repository master catalog
file, so oXygen instantly resolves any public identifiers defined by TaxPub. After
entering the above
command, I can validate and process TaxPub documents in oXygen.
Customizations and Compatibility
The original motivation for developing
the JATSPack specification was to devise a means to package schema
customizations together with software libraries that allow users to transform documents
from the new schema. This is still, perhaps, the primary use-case.
There is an ongoing sea change in the way that scientific research is published and
presented. The lines between traditional definitions of media types, such as journal
books, wikis, blog posts, presentations, etc., are continually getting blurred
(Owens 2010). This implies
that the number of different types of content included with scientific publications
rapidly. Often it is most appropriate to include disparate types of data with the
source documents, and that means either customizing the JATS schema, or providing
means of including it, such as (for example) using the flexible
elements, and adding appropriate layer validation.
The TaxPub example illustrates that the JATSPack/JATSPAN infrastructure can facilitate
interchange of documents and data between organizations. A common theme overheard
year's JATS-Con was that often, individual publishers' versions of their JATS DTDs
are not interchangeable. In other words, PMC's version of JATS is not the same as
Highwire's, even if they nominally use the same flavor and version of the tag
suite. With a small amount of up-front work to resolve discrepancies and repackage
customizations, this interchange problem can be helped, if not solved.
The TaxPub example also serves to illustrate that the cost of doing compatible
customizations need not be high. This can lead to easier reuse of existing XML
vocabularies. The XML
landscape is vast, and vocabularies have been defined for wide array of specialized
topic domains — biological taxonomy is just one example.
As mentioned previously, and as TaxPub illustrates, often it is very
appropriate and beneficial to mix markup from other vocabularies directly into
the instance documents. If the customization is deployed as a JATSPack, then one
could make the customization without having to worry quite so much about breaking
compatibility with existing systems, and the ability to exchange documents.
But often one wants to do more with a document than just validate it, and that
is where the true power of EXPath-pkg, and by extension JATSPack, lies.
Customizations can also be packaged
with software libraries in XProc, XQuery, and XSLT, that allow users to transform
and from the new schema. This would facilitate making forwards-compatible schema
First, let's review what is meant by backwards and forwards compatibility, in the
context of document schemas. For this, I highly recommend
Orchard 2004. In a nutshell, backwards compatibility means that existing
(version A) documents can be used by new XML processing systems, and forwards
compatibility means that newer documents (version B) can be
used by existing processing systems.
A very successful model of forwards compatibility, that we are
all familiar with, is the "must ignore" pattern of extensibility of HTML.
This stipulates that HTML renderers must ignore any tags that they don't understand.
effect, this is a forwards-compatibility extension substitution rule. It allows future
designers to customize the HTML schema, adding elements and attributes, while being
predict how document instances in the new schema will be processed by old systems.
ignore" rule is one substitution rule, but it is very limited. If designers could
set of transformations with the new schema, then those designers could define their
TaxPub as an example of customization
TaxPub serves as a good example of this type of customization. It includes many new
elements that deal specifically with taxonomy treatments, and thus introduces
the problem of forwards compatibility:
TaxPub, as an
extension, provides semantics beyond what is available in the base DTD through creating
newly named elements - thus lending itself to domain-specific application. However,
instances may not be easily processed by applications already familiar with the Publishing
This problem could be addressed by writing a set of XSLT stylesheets and including
with the TaxPub JATSPack. These stylesheets would transform the new elements into
plain-old-JATS. This would make it easier for third-party systems to install meaningful
useful support for TaxPub documents. Unlike the "must ignore" rule, the substitution
written in XSLT could provide for richer markup in the result document, displaying
content in visually distinctive ways, and perhaps even preserving the semantic content
means of special attribute keywords (for example).
Designing a customization that is both forwards and backwards compatible, and
compatible with other already-existing schema, is not trivial.
With the JATSPack format, and a set of examples and detailed how-to
instructions, some of the work required can be made
The definition of "customization" can be
broad. A customization does not necessarily include a new DTD (or Relax NG or XSD
Customizations are often implemented as the addition of layered validation implemented
in, for example, Schematron, that imposes a set of style rules that are more specific
particular organization's use of the JATS. Sometimes these validation rules are coded
simply as XSLT stylesheets that are applied to instance documents, and return a predefined
According to Beck 2010, the results of a survey of publishers indicated that,
"Half of the respondents said that they impose rules other than schema validation
Since JATSPack supports Schematron, XSLT, and other formats, there is no reason that
these sorts of style checkers couldn't also be packaged as JATSPacks and made available
to third parties. Since JATSPack/JATSPAN imposes rules on versioning and the uniqueness
of identifiers, it can help to safeguard against incompatibilities that can result
from ad-hoc sharing of these sorts of libraries.
Namespaces and Relax NG
JATSPack can also ease the migration away from DTDs and
towards Relax NG for JATS schema. There are several reasons why this
is desirable. DTDs do not properly support XML namespaces, and so hamper
interoperability. Using namespaces will allow third parties to create customizations
having to worry so much about name clashes that can result from mixing vocabularies.
"The major design point of XML namespaces is to allow decentralized extensions."
That decentralized customizations and extensions occur is a fact.
I don't think anyone would argue that
decentralized customizations is a bad thing, or should be prohibited (even
if that were possible).
Yet, an inherent problem is that
they can be difficult to manage and control.
The JATSPAN infrastructure is designed to adapt to
this decentralization, while at the same time providing specifications and imposing
requirements, such that the proliferation of new schema doesn't become a problem.
It does this by requiring that the formal public identifiers (FPIs) and URIs used
to identify resources are
well defined and unique, and also by virtue of its fixed directory structure, ensuring
that separate individual JATSPacks fit together on the same system without clashing.
Invoking the TaxPub customization as an example again, in the paper given at JATS-Con
last year, the author describes some of the inherent difficulty of working with DTDs:
The lack of robust namespace support in DTD removed the option of importing external
schemas into TaxPub. This would make synchronization less onerous, for example, were
decided to include Darwin Core elements in TaxPub. It also would enable the inclusion
data in TaxPub instances themselves rather than on linking to them as external documents.
There are other reasons for recommending the use of Relax NG over DTDs, and an
entire paper could be written on just that topic.
However, there are two problems that must be overcome before Relax NG schemas
can be used easily for JATS documents.
The first is the lack of URI names for these
Relax NG resources, and the second is that there is no standard way for documents
identify the Relax NG schema to which they conform.
The first problem, the lack of URI names, is inherent in the current JATS
infrastructure. Relax NG schema are identified by URIs,
and not FPIs. In other words, URIs are used as the names of
these resources, and there is no other name. That this is a problem was
eloquently described by Norman Walsh in his blog post from 2004 titled,
"On the Web, My Name
is 266 North Pleasant Street" (Walsh 2004). The current
of the W3C lead inexorably to the choice that new resources, such
as Relax NG files, should be identified by absolute, canonical, persistent,
and stable HTTP URIs.
NLM has declined to issue such URIs for these resources. They are worried about
the potential for excessive server traffic driven by automated tools that
process these URIs, similar to the
experience of the W3C.
Without these URI identifiers, the Relax NG schema cannot be referenced in the
instance documents in a clear, unambiguous way. And as mentioned before,
crucial to interchange of document instances is that they identify themselves.
With the JATSPack/JATSPAN architecture, I have attempted to address this problem
in the following ways.
First of all, JATSPack, since it is based on EXPath-pkg, supports the
inclusion of Relax NG XML and compact-notation files. These should reside
in the "rng" and "rnc" subdirectories of the package root, respectively.
Every JATSPack is assigned a name, which is an absolute URI. This includes
the base JATS packages. For these, I assigned HTTP URI names that use the
"jatspan.org" domain. For example, the JATSPack implementation of the NISO
trial version of the Article Authoring schema, version 0.4, has the name
The OASIS catalog files included with each JATSPack includes a
<rewriteURI> entry which allows the identification of
any resource within the JATSPack by using an absolute URI starting with
the URI of the JATSPack.
This provides a de facto canonical absolute URI
name for each of these resources.
JATSPAN may serve these resources from these absolute URIs, but may not.
That decision is TBD.
Regardless, that URI can be safely used to identify these resources
within instance documents.
While repackaging this as a JATSPack, I assigned a URI name to this package
of "http://jatspan.org/jatspacks/nisojats/articleauthoring/0.4". I added the following
<rewriteURI> entry to the OASIS catalog
file for this package.
In effect, this assigns a URI name to the master Relax NG schema
file of this package, and that name is
Please feel free to use this name in any context, to refer to this resource.
As mentioned above, JATSPAN might serve this resource at that URL, but might not;
it is not guaranteed.
The second problem is that there is no standard, agreed upon way for instance
documents to identify themselves as conforming to a particular Relax NG
schema. The philosophy behind this fact is that schema validation should
be a separate process that is not specified by the instance documents. In
other words, the idea is that the system, and not the document, should
decide what schema to apply, and that for a given document, any of a number
of schema might be applied, depending on the context.
This is a nice theory, but in practice it has impeded the adoption of
Relax NG in this particular domain.
The oXygen XML editor defines a processing instruction (PI) that can be used
within an instance document. For example, given the URI described above,
an instance documents could now use this PI to identify itself as a document
conforming to this Relax NG schema:
This is very processor-specific, and therefore is not a good general solution.
Perhaps the most straightforward way of making the association is by using
a namespace on the root node of the document. But the immediate problem
with this is that the NISO-JATS Relax NG schemas will fail if any non-null
namespace is given on the root node of any document.
Solving this particular problem is out of the scope of this paper, but I
would like to suggest that the Relax NG schema files delivered with JATS
be modified to specify a canonical namespace for each of the document types.
Failing that, this could always be done as an independent customization, in
a separate JATSPack.
More JATSPack features and recommendations
It is recommended that each JATSPack includes documentation, including structured
documentation of any schema extensions. The exact format of this documentation is
TBD, but the goal is that it should seamlessly integrate with existing JATS
documentation. That is, the documentation should simply "plug in" to the documentation
provided by the JATSPacks that come before it in the dependency tree. For example,
hyperlinks to element or attribute descriptions, between the documentation for the
packs and between packs and the base JATS documentation, should resolve correctly.
aspect of the format is still under exploration.
Code libraries in XSLT, XQuery, and XProc
JATSPacks can include library functions that pull out specific data from instance
documents, so that the data is easily accessible from any JATSPack-enabled system.
This is a
way to provide different "views" on instance documents that could be appropriate for
different purposes. JATSPacks that import and customize others could also extend the
functions defined in the imported packages. This is analogous to the object-oriented
programming paradyme of creating a derived class from a parent class, and overriding
extending certain methods.
As described above under "Customizations and Compatibility", in order to facilitate
interchange of document instances, authors of JATSPacks that customize the schema
encouraged to provide a stylesheet for conversion to and from the "standard JATS".
Also, for these customization JATSPacks, authors are encouraged to supply XSLT
stylesheets that import and extend the Journal Publishing Preview Stylesheets. In
a complete preview stylesheet for the new JATS customization would be available for
instantly upon installation of the new JATSPack. If the stylesheet which converts
"standard JATS" is provided, then the implementation of this preview stylesheet is
— it is just the baseline preview stylesheet applied to the output of the "standard
Sample files and automated tests
In order to enable interchange of documents and of the software that processes them,
instance documents must be self-identifying. Among the recommendations for proper
which supply DTD customizations, sample files should be included which have the appropriate
DOCTYPE declaration for that customization, which use the correct formal public identifer
(FPI). The jatspan client
utility, when installing a new JATSPack, performs automatic tests, which include validation
of each of the sample files. In addition to validating them in place, this step includes
test in which each sample file is copied to a separate temporary directory and then
validated. This ensures that the FPI is used to resolve the DTD, not the system identifier,
and guarantees that instance documents modeled after the JATSPack sample files can
exchanged between different systems.
Additionally, any type of JATSPack can include its own predefined test in the form
an XQuery function which returns a boolean true (pass) or false (fail). Since all
resources inside a JATSPack are addressable by using URIs relative to the "name" URI
JATSPack itself (given in the package descriptor), these test could operate on the
sample files, to verify the integrity of the package as a whole, and that the software
library operates correctly on the target system.
As mentioned in the introduction, JATSPAN is a website at
jatspan.org, and is based on the
concept of the CPAN website,
providing a place where users can upload and share JATSPacks.
There are three complementary, interlocking faces of the JATSPAN site.
A repository of JATSPacks, and a website allowing users to upload and
download from that repository.
A client application jatspan, which enables users to
maintain a local installation of JATSPacks.
A set of RESTful web services (these are envisioned for the future).
The "phase 2" implementation of JATSPAN will copy the Servlex/eXist architecture
of the CXAN site as described in Georges 2011.
jatspan.org web site
Here is a list of some of the features of the JATSPAN website:
Anyone can browse the list of JATSPacks, see their descriptions (which are
extracted automatically from the package descriptors) and download those of interest.
JATSPacks can be downloaded in one of two forms (that differ only in the filename
extension): XAR files (which have the .xar extension) or Zip files (which have the
Users can also browse the JATSPack documentation on the JATSPAN site, without
having to download the package.
Authors of JATSPacks can use the JATSPAN site to check that their preferred
abbrev is not already in use.
Registered users can upload JATSPacks. These are unpacked on the server,
automatically checked for consistency (for example, that the package descriptor file
is valid) and instantly made available to other users for browsing and download.
The site automatically runs the automated document-generation tools XSLStyle and
xqDoc over the XSLT and XQuery JATSPack components, respectively, and makes the
generated documentation instantly available on the site.
The site, in its alpha incarnation, is implemented as a set of Perl CGI scripts
based on the Catalyst web
jatspan client program
I would like emphasize again that JATSPacks are usable on any system without any
special infrastructure. Downloading the package as a Zip file and extracting it to
filesystem could be done exactly the way it is done now, and the included schema,
documentation, and library files are just as usable.
However, there are additional advantages to setting up a local repository and using
jatspan client program to manage it.
The jatspan client is a simple program that users can download
and install. The interface is through the command line, and it is
implemented as a Perl script.
When it is run for the first time, it will ask for a location to create the local
jatspan repository. This is a directory on the local filesystem, which is the root directory
to which downloaded JATSPacks are extracted. The client program then creates this
and writes a jatspan master OASIS catalog file to it, as well as performing
a few other setup tasks.
The master OASIS catalog file can be used by tools, such as oXygen, to resolve
identifiers defined within JATSPacks. These XML tools should be set up to point to
catalog file. As described above, this only needs to be done once, and from that point
those tools will be able to resolve any identifiers defined by any JATSPack that is
installed on the local system.
Also as part of setup, the user can choose whether or not to download and install
repackaged base JATS bundle, described in
Existing JATS DTDs are available as JATSPacks above.
The advantage to choosing to install it is
that all of the flavors and versions of JATS will then be available immediately.
But it is
also possible to use the system without installing the base JATSPacks.
Because of the system of
resolving dependencies automatically, the required base JATS DTD files will be available
soon as the first JATSPack is installed. In other words, they could also be installed
one-by-one, as the need arises.
After setup, the client can install any desired JATSPack by entering the command
jatspan install abbrev
This will install the
latest version of the JATSPack indicated, along with all of its dependencies. It will
update the master catalog file with <nextCatalog> entries,
pointing to the catalog
file provided with each new installed JATSPack.
As an implementation detail, note that the JATSPAN server uses many of the same Perl
functions as the jatspan client, to perform many of the same sorts of tasks.
when a user uploads a JATSPack to the server, the server "installs" this JATSPack
repository, in a manner quite complementary to the operation performed when users
JATSPacks to their client machine.
The next-phase implementation of JATSPAN will copy the Servlex/eXist architecture
the CXAN site as described in Georges 2011.
Besides the obvious
advantage that this is a more flexible architecture, it can take advantage of the
resources that the site is designed to serve, it can also provide a model for how
to set up
a flexible, extensible XML processing toolchain for organizations that need to develop
This architecture is dubbed the JATSPack Application Framework, or JATSPAF. The following
figure shows the relationships among all of these entities.
The following is a list of features that could be implemented in a future release
the JATSPAN website, that would enhance its usefulness. These are listed primarily
illustrate the benefits that this architecture and this infrastructure could provide.
Faceted search on uploaded JATSPacks, with facets defined for element and
attribute names, authors, dependencies, documentation, etc. When JATSPAN is
implemented in eXist, this is a logical next step.
JATSPacks could be usable directly off of JATSPAN, without installing them to a
local machine. This would involve pointing an XML tool at the master OASIS catalog
file on JATSPAN, which includes <nextCatalog> entries for all
of the JATSPacks
uploaded to date. This would allow users to run tests and use a JATSPack without
installing it locally, for evaluation purposes, in the same way that they now can
browse the JATSPack documentation before downloading the package.
JATSPAN could provide instance document tools, such as a validator and document
previewer. This would let anybody upload a document that purports to conform to any
the JATS schema (including any customized version implemented as a JATSPack), and
validate it and/or preview it. These are similar to the services
provided by the PMC style
checker and article
JATSPAN can be configured to do more thorough checking of uploaded JATSPacks. For
example, when a new pack is uploaded, checking that system ids and public ids are
unique, and that resources identified by system ids and/or public ids are not changed
(it could issue warnings if they are). Also verifying that there are no circular
JATSPAN could implement RSS feeds, allowing users to subscribe to see when new
JATSPacks, or new versions of JATSPacks of interest, are uploaded, for example.
JATSPAN could be configured with a discussion forum, or an issue tracker, such
that users could comment on, rate ("like"), or issue trouble tickets about uploaded
A "Roma for JATS" could be developed and served from JATSPAN.
Roma is a web-based GUI tool
for building customizations to the TEI schema. The output of the "Roma for JATS" would
be a complete JATSPack.
Throughout this paper, I have touted the potential benefits of the JATSPack format
and the JATSPAN site. These benefits include:
making it easier to deploy
systems that support a wide variety of XML formats;
facilitating the creation,
distribution, and maintenance of schema customizations and libraries of code that
would be associated with them;
allowing developers to easily exchange these customizations and libraries; and
facilitating the exchange of scientific documents and data, while preserving their
rich semantic content.
To fully realize the possible benefits, much more work would
be required. However, I
believe that establishing this specification and web site is a good step in the
One of the goals of this proposal is to help publishers and digital repositories
to produce XML systems that are more open. Sharing of schema customizations and
libraries would reduce the amount of duplicated
effort that is expended when adapting systems to different XML document types.
In order to acheive this goal,
this format will have to obtain some measure of support within the publishing
The challenge lies in persuading
systems architects that this format would benefit them,
so that they will expend the effort to adapt their systems to support it.
By providing a "starter set" of JATSPacks, as described in the examples section,
I hope that I've shown that: A) creating JATSPacks is easy, and B) sharing JATSPacks
will benefit everybody.
Of course, there is nothing inherently JATS-specific in the JATSPack format.
The ways in which JATSPack extends EXPath-pkg, as described
above, are primarily to add schema of various formats,
sample documents, documentation, and OASIS catalog files. It would be nice if
these extensions could be rolled into the EXPath-pkg specification itself. That might
eventually obviate the need for the JATSPAN website; it could be merged with CXAN.
Whether that would help or hurt the cause of getting the format adopted is
"Flavor" is my term, which I haven't heard used anywhere else. I will use it throughout
this paper to describe one of the main categories of JATS. One "flavor" roughly
to one top-level DTD file, which might itself have several versions. In a detailed
there are currently seven flavors:
Archiving and Interchange Tag Set - green
Same as archiving but with the OASIS table model
Article Authoring Tag Set - pumpkin
NCBI Book Tag Set - purple
A historical version of the books DTD
Journal Publishing Tag Set - blue
Same as publishing but with the OASIS table model
This is somewhat complicated by the fact that the NISO standard versions of JATS
use a different version numbering scheme, and so should also be considered
separate flavors, even though they are really just newer versions of the existing
 At the time of this writing, there are a few areas of incompatibility between
the JATSPack format and EXPath-pkg. Effort is underway to reconcile these.
The specific incompatibilities are called out in footnotes which follow.
 JATSPack two-part abbreviations are incompatible with the existing
 As described above, some of the
requirements for the JATSPack format derive from the fact that it is an extension
of EXPath-pkg, and some are JATSPack-specific.
 The internal directory structure of JATSPack differs from that specified
for EXPath-pkg, and is another area of incompatibility. The main difference is the
location of the package descriptor file, which is in the root directory for
EXPath-pkg packages. In JATSPack, it was moved to the package's content directory.
This way, it is possible to unzip the packages directly onto the filesystem, without
shuffling of the file locations.
 Note that the conventions for the abbreviated names have yet to be worked out.
 When doing this work, I faced a question, and reached a conclusion, which
might be controversial.
Because I moved files into a different directory structure,
but I wanted them to remain usable by systems without OASIS catalog files,
using the relative system identifiers, I had to change these identifiers in the
modules that reference the moved files. I also made other minor edits to reconcile
cases where, for example, two different instances of a document were referred to by
the same public identifier (FPI). I made these changes,
without changing the FPIs, for those files that
were changed. I think this is the right decision, for the following reason. The
significance of an FPI is that any tool that resolves it correctly will get
identical results. The FPI specifies a logical resource –- a
DTD or an external parsed entity — not a specific byte
sequence. With this change, the resolution of any given FPI will still
result in the exact same entity replacement text,
when all of the sub-entities are correctly resolved.
Piez, Wendell. (2010).
Fitting the Journal Publishing 3.0 Preview Stylesheets to
Your Needs: Capabilities and Customizations.
Proceedings of the Journal Article Tag Suite Conference.http://www.ncbi.nlm.nih.gov/books/NBK47104/
Rosenblum, Bruce. (2010).
NLM Journal Publishing DTD Flexibility: How and Why Applications of the NLM DTD Vary
Based on Publisher-Specific Requirements.
Proceedings of the Journal Article Tag Suite Conference.http://www.ncbi.nlm.nih.gov/books/NBK47101/