Robin Cover

XML Daily Newslink. Thursday, 05 June 2008
A Cover Pages Publication http://xml.coverpages.org/
Provided by OASIS http://www.oasis-open.org
Edited by Robin Cover

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This issue of XML Daily Newslink is sponsored by
IBM Corporation http://www.ibm.com
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HEADLINES:

* FDA Issues Structured Product Labeling Guidance: No Delays
* A Prototype Knowledge Base for the Life Sciences
* Archival Information Package: Cornerstone of the OAIS Implementations
* A DSRL Script for Mapping from Schematron 1.n to ISO Schematron
* Toward Integration: Multilanguage Programming
* Describe REST Web Services with WSDL 2.0: A How-To Guide

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FDA Issues Structured Product Labeling Guidance: No Delays
Angie Drakulich, Pharmaceutical Technology

The US Food and Drug Administration issued a new guidance on indexing
structured product labeling (SPL). The Center for Biologics Evaluation
and Research (CBER) and the Center for Drug Evaluation and Research
(CDER) will begin indexing SPL in the product labeling for human drug
and biologic products. SPL became a requirement in October 2005 when
FDA stated that SPL in Extensible Markup Language (XML) was the only
electronic format for content of labeling that CDER could process,
review, and archive, according to the guidance. The agency is now
recommending that content be submitted in SPL. SPL enables the
electronic exchange of the content of labeling and other regulated
product information. It also enables the inclusion of indexing elements
with product labeling. Indexing is made possible by machine-readable
tags that are inserted into the label, but that do not appear on the
actual printed label (consumers cannot see them). With these tags,
individuals using clinical-decision support tools and electronic
prescribing systems can more easily and rapidly search and sort
product information in product labeling... The change also will help
to decrease prescribing errors and enhance the safe use of medical
products. For example, says the guidance, a full-text search of the
content of labeling for hepatoxicity will miss labelings that use
the term liver toxicity. New indexing elements based on standards
adopted for use in the healthcare setting will address this problem.
The new guidance comes upon the completion of a six-month FDA pilot
project that evaluted how best to add indexing elements to products.
It also comes approximately two months after FDA issued a draft
guidance on structured product labeling. The new guidance addresses
some of the suggestions received from industry based on the draft,
including more concrete advice on how applicants can recommend
indexing terms to the agency and how indexed terms will be identified
and shared...

http://tinyurl.com/4jwnz4
See also Structured Product Labeling (SPL) Guidance: http://xml.coverpages.org/healthcare.html#GuidanceSPL-2008

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A Prototype Knowledge Base for the Life Sciences
M. Scott Marshall and Eric Prud'hommeaux (eds), W3C Interest Group Note

Members of the W3C Semantic Web in Health Care and Life Sciences Interest
Group (HCLS) have published a Note describing "A Prototype Knowledge
Base for the Life Sciences." The document explains how one can use
the Semantic Web to express and integrate scientific data. These
techniques can be used for modeling any data, and the benefits of
integration and model consistency apply to other diverse, distributed
data domains. It is hoped that this document will inspire further
contributions to the ongoing work at Neurocommons and the Health Care
and Life Sciences Interest Group, as well as inspire those in other
domains to exploit the Semantic Web. The prototype is a biomedical
knowledge base, constructed for a demonstration at the Banff WWW-2007
Conference. It integrates fifteen (15) distinct data sources using
currently available Semantic Web technologies such as the W3C standard
Web Ontology Language (OWL) and Resource Description Framework (RDF).
This report outlines which resources were integrated, how the knowledge
base was constructed using free and open source triple store technology,
how it can be queried using the W3C Recommended RDF query language SPARQL,
and what resources and inferences are involved in answering complex
queries. While the utility of the knowledge base is illustrated by
identifying a set of genes involved in Alzheimer's Disease, the approach
described here can be applied to any use case that integrates data from
multiple domains... Many health care and life sciences organizations
are interested in the data integration abilities promised by the Semantic
Web. More specifically, the benefits include the aggregation of
heterogeneous data using explicit semantics, and the expression of rich
and well-defined models for data aggregation and search. Semantic Web
technologies enable one to more flexibly add additional data sets into
the data model, and more easily reuse data in unanticipated ways. Once
data has been aggregated, a Semantic Web reasoner computes implied
relationships among the aggregated data resulting in tighter integration
and the possibility of additional insights.

http://www.w3.org/TR/2008/NOTE-hcls-kb-20080604/
See also the W3C news item: http://www.w3.org/News/2008#item105

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Archival Information Package: Cornerstone of the OAIS Implementations
Guy Marechal, Conference Presentation

This presentation was given at the Sun Preservation and Archiving Special
Interest Group (Sun PASIG) Conference held May 27-29, 2008. The event
focused upon repositories, preservation, digital asset management,
tiered storage architectures, and longterm data management. Summary:
"In the Open Archival Information System (OAIS) standard, the Archival
Information Package (AIP) is embedded in the system and not an interface
of the system like the Submission Information Package (SIP) or the
Dissemination Information Package (DIP). Many important projects sponsored
by the European Union came to the conclusion that the key for concrete
implementations of OAIS is to focus on the AIP as external interface and
to merge the AIP, SIP and Persistent-DIP concepts. With that approach,
the AIP are exchanged between systems and so the persistence and the
interoperability are solved by the same constructs: indeed, the
persistence is in fact the temporal interoperability of an evolving
"Enterprise repository" and "Federated Archiving" requires space
interoperability. It means that the approach offers a high degree of
flexibility in the practical implementation of the full chain of the
construction to the exploitation of the information assets. Each of the
functional elements of the OAIS model is simply assumed existing in one
or more occurrences. This allows of exploding the 'System' (the "S" of
the OAIS acronym) into independent functional blocks that could be
delivered by independent suppliers and managed by independent parties;
it allows also operating as a federation of organisations. The AXIS
architecture proposes an open and customised specification of constructs
for implementing the AIP in the form of 'Autonomous eXchange Entities'.
The AXE's are structured through a three levels wrapping system fitting
perfectly with the Object oriented and Honeycomb repositories like the
ST5800 but also allows directly the adoption of powerful retrieval
through constructs (like XAM or OAI) and of powerful Package Wrappers
(like ZIP, METS and MXF). The AXIS architecture is planned to be made
available in open source on the Web site of the UNESCO..." Note: the
PASIG collection of online presentations contains many papers of
interest; see, for example, Raymond Clarke's "ZFS: The Last Word in
File Systems."

http://events-at-sun.com/pasig_spring/presentations/GuyMarechal_FedArchivesAIP.pdf
See also the PASIG online presentations: http://events-at-sun.com/pasig_spring/presentations/

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A DSRL Script for Mapping from Schematron 1.n to ISO Schematron
Rick Jelliffe, O'Reilly Articles

ISO Document Schema Renaming Language (DSRL) is one of Martin Bryan's
contributions to the ISO Document Schema Description Languages project
at JTC1 SC34 WG1. This brings together various technologies by Murata
Makoto, James Clark, Martin Duerst, Jenni Tennison, and others
(including me) to try to build a layered solution to validation using
a variety of 'little languages'... DSRL is now at a very late draft
stage, and I expect it will be finalized over this year. DSRL is
declarative: it provides mappings, and even though it could be used
to rename items in schemas, Martin Bryan's open source XSLT
implementation of it takes the more direct route of renaming the
document... My vision is that in the near term, with DSRL completing
the base DSDL quartet of RELAX NG, NVRL, DSRL and Schematron, that
standards developers will start to take them on board as a package:
(1) ISO NVDL selecting the particular schemas for different namespaces
and culling foreign elements as desired; (2) ISO DSRL renaming,
localization and providing default values to handle common evolution
cases; (3) ISO RELAX NG performing grammar-based validation, extended
with its XSD data types; (4) ISO Schematron performing more complex
and detailed validation. A couple of years ago we finally arrived at
the point where people had come to pretty realistic apprehensions about
the proper limits of XSD functionality, and I think we are now arriving
at the same kind of level of maturity with RELAX NG. As these limits
become commonplace, I think the need for NVDL and DSRL (for XSD and
for RELAX NG) will similarly become more well-know. My prediction is
that it will increasingly occur to community standards bodies that
their standards have quite a number of constraints or gotchas which
are poorly expressed in English but much clearer (and machine verifiable)
when expressed using DSRL (and NVDL and Schematron.)

http://www.oreillynet.com/xml/blog/2008/06/a_dsrl_script_for_mapping_from.html
See also DSRL resources at the DSDL web site: http://www.dsdl.org/

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Toward Integration: Multilanguage Programming
Steve Vinoski, IEEE Internet Computing

Multilingual programmers embrace the diversity of programming languages,
enabling them to apply different languages to different integration
problems to produce... Many developers simply put up with the mismatch
and slog their way through, eventually reaching what is, at best, a
mediocre solution. To help with productivity issues, they often resort
to code generation, mapping XML constructs to statically typed
programming language constructs to try to ease the impedance mismatch.
Unfortunately, that approach can be extremely brittle as a result of
converting highly flexible XML constructs into rigid static data types
that are difficult to version adequately. Any changes to the XML
document then require new code generation to reflect those changes,
even if the application doesn't use the specific modified XML entities.
The newly generated code can, in turn, require changes to the application
code that uses it, so that any application using the generated code must
undergo full build, test, and redeployment cycles. Any minor productivity
gains achieved through code generation are quickly lost in the noise
when compared to ongoing maintenance costs. Contrast this story of XML
development -- unfortunately, repeated quite often in
enterprise-integration scenarios -- with simply using a programming
language that's better suited to the task. For example, the Python
'language xml.etree' module makes XML handling almost trivial (even with
versioning), and Perl has XML packages that are equally easy to use.
Erlang's xmerl module is quite good as well. Better still, though, are
languages that support literal XML, such as ECMAscript for XML (E4X)
and Scala, which both let developers write XML directly within the
language's syntax. Literal XML effectively eliminates the impedance
mismatch between XML and the programming language, letting the developer
write just a few lines of code versus what might require hundreds or
thousands of lines in a combination of generated and manually written
brittle Java or C++ code...

http://dsonline.computer.org/portal/pages/dsonline/2008/06/w3tow.xml

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Describe REST Web Services with WSDL 2.0: A How-To Guide
Lawrence Mandel, IBM developerWorks

This article provides an introduction to REST and WSDL 2.0, and walks
you through creating a WSDL 2.0 description of a REST Web service. The
term Web services is typically associated with operation- or
action-based services using SOAP and the WS* standards, such as
WS-Addressing and WS-Security. The term REST Web services generally
refers to a resource-based Web services architecture that uses HTTP
and XML. Each of these architectural Web service styles has its place,
but until recently, the WSDL standard didn't equally support both styles.
The WSDL 1.1 HTTP binding was inadequate to describe communications
with HTTP and XML, so there was no way to formally describe REST Web
services with WSDL. The publication of WSDL 2.0, which was designed
with REST Web services in mind, as a World Wide Web Consortium (W3C)
recommendation means there is now a language to describe REST Web
services... REST is an architectural style that treats the Web as a
resource-centric application. Practically, this means each URL in a
RESTful application represents a resource. The URLs are also easy to
understand and remember... Like (X)HTML, REST Web services make use
of hyperlinks in XML. Traditional Web applications access resources
using HTTP GET or POST operations. In contrast, RESTful applications
access resources following the create, read, update, and delete (CRUD)
style using the full range of HTTP verbs (POST, GET, PUT, and DELETE).
There's one more key component of a REST application: RESTful
applications should be stateless. This means in a REST application no
session state is stored on the server. All of the information needed
to satisfy the request is carried in the request message itself. A
client can therefore cache a representation of a resource, which can
significantly improve the application's performance, where a service
explicitly allows it... One significant reason why REST Web services
have to this point not made use of WSDL is that the WSDL 1.1 HTTP
binding was inadequate to describe them. WSDL 2.0 was declared a W3C
recommendation in June 2007. This second version of WSDL was created
to address issues with WSDL 1.1, many of which had been identified
by the Web Services Interoperability (WS-I) organization. In addition,
WSDL 2.0 has good support for HTTP bindings...

http://www.ibm.com/developerworks/webservices/library/ws-restwsdl/

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XML Daily Newslink. Thursday, 05 June 2008