Posts Tagged ‘semantic web’

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Semantic Web Applications and Tools for Life Sciences
Berlin, 10th December 2010

http://www.swat4ls.org/2010/

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Overview
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SWAT4LS is a workshop that provides a venue to present and discuss benefits and limits of the adoption of Web based information systems and semantic technologies in life sciences, biomedical informatics and computational biology.

Rationale
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The web is a key medium for information publishing, and web based information systems play a key role in biomedical information exchange and integration. At the same time, the variety and complexity of biomedical information call for the adoption of semantic-based solutions. The Semantic Web provides a set of technologies and standards that are key to support semantic markup, ontology development, distributed information resources and collaborative social environments. Altogether the adoption of the web-based semantic-enabled technologies in the Life Sciences has potential impact on the future of publishing, biological research and medicine. This workshop will provide a venue to present and discuss benefits and limits of the adoption of these technologies and tools in biomedical informatics and computational biology. It will showcase experiences, information resources, tools development and applications. It will bring together researchers, both developers and users, from the various fields of Biology, Bioinformatics and Computer Science, to discuss goals, current limits and some real use cases for Semantic Web technologies in Life Sciences.

Topics
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Topics of interest include, but are not limited to:
• Standards, Technologies, Tools for the Semantic Web
o Semantic Web standards and new proposals (RDF, OWL, SKOS, Linked Data, … )
o Biomedical Ontologies and related tools
o Alternative approaches to integrate semantic representations and web based solutions
o Formal approaches to large biomedical knowledge bases
• Systems for a Semantic Web for Bioinformatics
o RDF stores, Reasoners, query and visualization systems for life sciences
o Semantic biomedical Web Services
o Semantics aware Biological Data Integration Systems
• Existing and prospective applications of the Semantic Web for Bioinformatics
o Semantics aware application tools
o Semantic Wikis
o Semantic collaborative research environments
o Case studies, use cases, and scenarios

Type of contributions
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The following possible contributions are sought:
• Research papers
• Position papers
• Posters
• Software demos
We are also accepting proposals for tutorials, hackathons or other related events to be held on Dec 8th (hackathons) and Dec 9th (tutorials). If interested, please contact info at swat4ls.org

Proceedings
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All accepted communications will be published in the proceedings. Proceedings for the last editions of the workshop have been pubslished via the CEUR-WS.org Workshop Proceedings service (see http://ceur-ws.org/). Best papers will be invited to a journal special issue (probably BMC Bioinformatics).

Special issue
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Authors of accepted contributions to the last editions of SWAT4LS have been invited to submit extended and revised contributions for a special issue in BMC Bioinformatics (dedicated to the SWAT4LS 2008 edition), and for a special issue of the BMC Journal of Biomedical Semantics (dedicated to the SWAT4LS 2009 edition, in preparation). We will continue with this approach and we will announce more detailed infomation as soon as we have reached an agreement with publishers.

Deadlines
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• Submission openinig: 7 September 2010
• Papers submission deadline: 12 October 2010
• Posters and demo submission deadline: 1 November 2010
• Communication of acceptance: 8 November 2010
• Camera ready: 21 November 2010

Instructions
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All papers and posters must be in English, formatted according to LNCS format (http://www.springer.de/comp/lncs/authors.html) and submitted in pdf format.
• Submissions for papers should report original research, and should be between 8 and 15 pages.
• Submissions for position papers should report qualified opinions, recommendations or conclusions, and should be between 3 and 6 pages.
• Submissions for posters should be between 2 and 4 pages.
• Submissions for software demo proposals should also be between 2 and 4 pages.

Submission
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All submissions will be handled via the EasyChair submission system. A link will be provided when registrations open.
To ensure high quality, submitted papers will be carefully peer-reviewed by at least three members of the Scientific Program Committee.

Workshop Chairs
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• Adrian Paschke, Corporate Semantic Web, Freie Universitaet Berlin, Germany
• Albert Burger, School of Mathematical and Computer Sciences, Heriot-Watt University, and Human Genetics Unit, Medical Research Council, Edinburgh, Scotland, United Kingdom
• Paolo Romano, Bioinformatics, National Cancer Research Institute, Genova, Italy
• M. Scott Marshall, Adaptive Information Disclosure Group, University of Amsterdam, The Netherlands
• Andrea Splendiani, Biomathematics and Bioinformatics dept., Rothamsted Research, UK

Program Committee
See website http://www.swat4ls.org/2010/

Natasha Noy and Peter Yim will be our keynote speakers at the 1st International Workshop on Semantic Repositories for the Web (SERES 2010).

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CALL FOR PAPERS
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1st International Workshop on Semantic Repositories for the Web (SERES 2010)

http://www.ontologydynamics.org/od/index.php/seres2010/

at the 9th International Semantic Web Conference

http://iswc2010.semanticweb.org

November 7, 2010, in Shanghai, China
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Ontologies and Linked Data vocabularies are being actively developed and used by numerous applications. Several domains are making their vocabularies available for others to reuse. In addition, good practices when developing ontologies are often followed, particularly for producing reusable modules. The Semantic Web is a modular and highly federated environment of reusable knowledge sources; these provide the meaning so that SW applications change our experience of the web. Within this context, the need for repositories delivering the added value that makes the SW a concrete step beyond our current experience of the web is palpable. SERES addresses issues around semantic repositories within the context of the SW.

The number of ontologies being built and made available for reuse has increased steadily in the last few years. Semantic Web search engines such as Swoogle and Watson currently index several tens of thousands of them; there are also systems specifically designed to support the publication of ontologies, e.g. Cupboard, NCBO Bioportal, and ONKI. Some tools also support editing features, e.g. Neologism, Knoodl. While being a foundation for the Semantic Web, this new environment where ontologies are shared and interlinked online also poses new challenges; fostering thus a number of research projects aiming to understand, amongst others, ontology reuse, storage, publication, versioning, quality control, evaluation, retrieval and modularization. For instance, as part of the EU NeOn project new tools supporting Knowledge Engineering in the age of “networked ontologies” have been developed, while in the EU OASIS project approaches from software engineering and formalization are now also being applied to inter-connect ontologies. Moreover, despite initial efforts, ontology repositories are hardly interoperable amongst themselves. Although sharing similar aims (providing easy access to Semantic Web resources), they diverge in the methods and techniques employed for gathering these documents and making them available; each interprets and uses metadata in a different manner. Furthermore, many features are still poorly supported; for instance, modularization, versioning, and the relationship between ontology repositories and ontology engineering environments (editors) to support the entire ontology lifecycle.

By the same token, there are several domains making available knowledge resources; for instance, digital libraries such as Pubmed Central offer a large collection of biomedical abstracts and, in some cases, open access to the full document. Some researchers are starting to bridge the gap between clinical and experimental data and literature; such connection is being built via ontologies, some approaches have had BioPortal as their ontology repository. Linked Data is also being explored as a means for publishers to expose their content. Knowledge management over documents is actively aiming to make real the notion of self-descriptiveness; being this intrinsically related to various resources over the web providing meaning for atomic component in documents –words, tables, figures, maps, etc. In order for these systems to be successful, it is necessary to provide a forum for researchers and developers to discuss features and exchange ideas on the realization of repositories providing semantics. In addition, it is now critical to achieve interoperability between these repositories, through common interfaces, standard metadata formats, etc. SERES10 intends to provide such a forum.

Questions addressed by SERES10:

· How can semantic repositories support the realization of the SW?

· Semantic repositories, ontology repositories, knowledge repositories, where are the boundaries? How are they interacting? Are they changing our experience of the web?

· How are domain specific knowledge repositories, such as biomedical digital libraries, interconnecting knowledge in meaningful manners?

· How are e-government initiatives using and delivering semantics and knowledge repositories?

· How can ontology repositories support novel semantic applications?

· How can ontology repositories encourage the development of high quality ontologies that are used routinely by relevant communities?

· How can ontology repositories provide semantics for applications?

· How can ontology repositories contribute to the reuse of ontologies across different domains and applications?

· How can ontology repositories interoperate with one another to support scalability, availability and distributed reasoning?

· How can provenance and intellectual property information be managed in and across ontology repositories?

· How can the abundant and complex knowledge contained in relevant ontology repositories be made comprehensible for users?

· How can branching, versioning, mappings, dependencies and configurations/compositions be managed in and across ontology repositories?

· How can ontology repositories interoperate with related applications such as ontology editors, automated reasoners, and rule engines?

· How can modularity be better supported in and across ontology repositories; similarly, how could modularization be formalized?

· How can ontology repositories support distributed reasoning?

· How can ontology repositories support corporate, national and domain specific metadata/semantic infrastructures?

· What measurements for describing and comparing ontologies can we use? How could ontology repositories use these?

Workshop Audience

We want to bring together researchers and practitioners active in the design, development and application of semantic web technology, semantic registries and repositories, knowledge management systems, knowledge repositories, repository editors, modularization techniques, versioning systems and issues around federated ontology systems. As some repository-related tools are already under development, and repositories are a crucial part of business infrastructure, we also address progressive Chief Technology Officers interested in using these technologies.

IMPORTANT DATES
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Paper Submission Deadline August 20, 2010, 23.50 Hawaii time
Acceptance Notification September 17, 2010
Camera Ready October 7, 2010
SERES Workshop (tentative date) November 7, 2010

SUBMISSION AND PROCEEDINGS
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Research papers are limited to 12 pages and position papers to 5 pages. For
system descriptions, a 5 page paper should be submitted. All papers and system
descriptions should be formatted according to the LNCS format

http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0

Proceedings of
the workshop will be published online. Depending on the number and quality of
the submissions, authors might be invited to present their papers during a
poster session.

Please submit your paper via EasyChair at

http://www.easychair.org/conferences/?conf=seres10

Submissions that do not comply with the formatting of LNCS or that exceed the
12 page limit (research papers) or 5 page limit (position papers and systems descriptions) will be rejected without review.

We note that the author list does not need to be anonymized, as we do not have
a double-blind review process in place.

Submissions will be peer reviewed by three independent reviewers. Accepted
papers have to be presented at the workshop and they will be included in the

workshop proceedings that are published online at CEUR-WS.

Program Committee

Natasha Noy, Stanford University, USA.

Li Ding, Rensselaer Polytechnic Institute, USA.

John Bateman, Universität Bremen, Germany.

Michael Kohlhase, Jacobs University, Germany.

Raul Palma, Poznan University, Poland.

Oscar Corcho, Universidad Politecnica de Madrid, Spain.

Fabian Neuhaus, University of Maryland, USA.

Aleman-Bonarges Meza, Universidad Politecnica de Victoria, Mexico

Christoph Lange, Jacobs University, Germany.

Sandro Hawke, W3C.

Christopher Baker, University of New Brunswick, Canada.

Nigam Shah, Stanford University, USA.

Peter Haase, Institute of Applied Informatics and Formal Description Methods, Germany.

Michael Gruninger, University of Toronto, Canada

Leyla Garcia, Bundeswehr University, Germany.

Benjamin Good, USA

Matthew Horridge, University of Manchester, UK

Organizing Committee

Alexander Garcia, University of Bremen
Mathieu d’Aquin, Knowledge Media Institute of the Open University
Mike Dean, Principal Engineer at Raytheon BBN Technologies
Kenneth Baclawski, College of Computer and Information Science, Northeastern University

Biography

Peter Mika is a researcher and data architect at Yahoo! Research in
Barcelona. He received his BS in computer science from Eotvos Lorand
University and his MSc and PhD in computer science (cum laude) from
Vrije Universiteit Amsterdam. His interdisciplinary work in social
networks and the Semantic Web earned him a Best Paper Award at the 2005
International Semantic Web Conference and a First Prize at the 2004
Semantic Web Challenge. He has been co-chair of the Semantic Web
Challenge since 2007. Mika is the youngest member elected to the
editorial board of the Journal of Web Semantics. He is the author of the
book ‘Social Networks and the Semantic Web’ (Springer, 2007). In 2008
he has been selected as one of “AI’s Ten to Watch” by the editorial
board of the IEEE Intelligent Systems journal.

Abstract

“Year of the Monkey: Lessons learned from the first year of SearchMonkey”

In this presentation we reflect on the experiences we have gained since
the launch of SearchMonkey, Yahoo’s groundbreaking Semantic Web
application platform in May, 2008. For most publishers, SearchMonkey
provided the first occasion to learn about semantic technologies and
reflect on the costs and benefits of providing data in semantic formats
such as RDFa. For developers inside and outside Yahoo, it often meant
having to learn the somewhat peculiar knowledge representation paradigms
of the Semantic Web. As a summary of these experiences, this
presentation provides key insights to those interested in what the
Semantic Web looks like in action and at a large scale, viewed from the
perspective of a search engine provider. It also highlights critical
bottlenecks in the adoption of semantic technologies on the Web and
therefore should be also of interest for Semantic Web researchers and
developers.

I have just found a very interesting paper titled “A user-centred evaluation framework for the Sealife semantic Web browsers”.

Abstract: Semantically-enriched browsing has enhanced the browsing experience by providing contextualised dynamically generated Web content, and quicker access to searched for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife’s main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure.

Definitely, Life Sciences is a domain where semantic annotation can be very valuable.

You can get the whole paper at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755822/pdf/1471-2105-10-S10-S14.pdf

In case you do not have time to read the paper, I recommend you to have at least a look at http://www.gopubmed.org/web/gopubmed/