Preprint Server: Journal of Web Semantics

The emergence of the Internet and of high-throughput technologies in the biomedical area have led to an explosion of online accessible biomedical data and tools. The intelligent integration of such data is vital for progress in many biomedical applications. Yet, current technologies are not sufficient to address this problem. Therefore, we are witnessing today the first steps of biomedicine moving towards the establishment of a next generation web, a *semantic* web. Biomedical researcher are at the forefront of publishing data in XML formats, which are often standardized. They actively develop ontologies as common reference points to facilitate the annotation of data. They start offering their tools as web services. Thus, the foundation of a semantic web for the life sciences are laid. Yet, much research needs to be done to make the semantic web an every-day reality:

The design, maintenance and evolution of biomedical ontologies is a practical open problem. Formal and informal guidelines and technologies for the development of ontologies need to be investigated. Automated integration and creation of ontologies will be an important step in this process.
The Integration of current Data Sources should also be considered as part of the semantic web strategies through both biomedical ontologies and local data semantics. How to best do this needs to be addressed through approved practices.
The semantic web will not replace the current web, but there will be a transition from the current web to a semantic web. This transition needs to be facilitated by textmining, natural language processing, and modelling technologies which enrich free text with ontological concepts and which structure unstructured text.
Web services need to be transparently integrated into a semantic web. Web service discovery and deployment need to be supported with security, privacy, quality-of-service and provenance appropriately addressed.
If the semantic web transparently links data and tools, it will be possible to reason over such knowledge networks. Suitable logics and rule engines need to be developed to draw conclusions from these knowledge networks.
Novel methods and algorithms need to be implemented to improve searching and browsing by operating on a semantic level rather the keyword-based approaches currently used
The next generation browsers and views for such complex information need to be defined in terms of how users wish and need to interact with such a rich semantic environment.
New applications need to be developed which make use of the richer data representation. Currently, online tools are limited in the type of queries they support. A semantic web should demonstrate the capability of flexibly considering user constraints in query answering.

As documented by a recent W3C workshop on Semantic Web for the Life Sciences the life sciences can play an important role in realizing the semantic web. This special issue will give an opportunity to researchers in the area to demonstrate how far we have moved already towards the next generation web.

Topics of Interest should combine Semantic Web technologies with Life Science applications. These include but are not limited to:

Semantic Web Technologies...

Ontologies
Web technologies such XML, RDF, OWL
Web services
Data and system integration
Semantic browsers and visualizations
Rules and reasoning on the web
Intelligent Agents
Textmining and natural language processing

...for Life Science Applications

Representing biomedical knowledge
Extracting biomedical knowledge from free text
Integrating distributed biomedical data sources and tools
Reasoning over biomedical knowledge
Searching and browsing the biomedical text
Biomedical applications
Applications in Drug Discovery and Development

Important Dates:

Deadline for submission : 15 November 2005
Notification of acceptance: 15 February 2005
Final Papers due: 15 March 2006
Special issue's publication: May 2006

Guest Editors:

Eric Neumann, Sanofi-Aventis
Michael Schroeder, TU Dresden

Submissions: ------------ Authors are invited to submit a full paper with original unpublished work in English to ms@biotec.tu-dresden.de

Further information and guidelines are available from the Elsevier author portal:
authors.elsevier.com/JournalDetail.html?PubID=671322&Precis=DESC and
www.websemanticsjournal.org

In case of any questions do not hesitate to contact the guest editors.

Contact: ms@biotec.tu-dresden.de and Eric.Neumann@sanofi-aventis.com

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