Semantic Web Application and Tools 4 Life Science

domenica 5 settembre 2010

Jonas Almeida to Keynote at SWAT4LS

Jonas Almeida will give a keynote at SWAT4LS.

Title: Development of Integrative Bioinformatics Applications using Cloud Computing resources and Knowledge Organization Systems (KOS).

Summary: In response to the increasingly data intensive and increasingly heterogeneous sources involved in large scale biomedical initiatives, such as The Cancer Genome Atlas (TCGA), NCI's Specialized Programs of Research Excellence (SPOREs) and NHLBI's Proteomics Centers, we have had to move to abstract logical frameworks to develop applications that make use of more distributed computational resources. As a result, we embarked on a 6 year effort to increase the abstraction level of our data structures by relying on the diadic predicated nature of RDF (Wang 2005) to facilitate both our ability to represent fast changing biological data and to let the domain experts themselves participate in its constant re-definition (Almeida 2006). Fast forward to 2010 and a Knowledge Organization System, S3DB (Almeida 2010) is in place as a logical framework for a computational ecosystem assessable via SPARQL endpoints, such as http://tcga.s3db.org. In the process we found out, like many others, that the collaborative involvement of domain experts puts peculiar pressures on the software development environment. Specifically, that it clashes with the conventional stand alone executable application model we were used to. In response we moved to use code injection (javascript) and other distributed features of the modern web browser as a development platform, as in clinical trial initiatives such as http://aguia.googlecode.com and visualization of biomolecular data as in http://cnviewer.googlecode.com, and distributed computing in http://quanah.googlecode.com.

Wang X, R Gorlitsky, and JS Almeida (2005) From XML to RDF: How Semantic Web Technologies Will Change the Design of ‘Omic’ Standards. Nature Biotechnology, Sep;23(9):1099-103 [PMID:16151403].

Almeida JS, C Chen, R Gorlitsky, R Stanislaus, M Aires-de-Sousa, P Eleutério, JA Carriço, A Maretzek, A Bohn, A Chang, F Zhang, R Mitra, GB Mills, X Wang, HF Deus (2006) Data integration gets 'Sloppy'. Nature Biotechnology 24(9):1070-1071. [PMID:16964209].

Almeida JS, Deus HF, Maass W. (2010) S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics. 2010 Jul 20;11(1):387. [PMID 20646315]

martedì 31 agosto 2010

A special issue in BMC Bioinformatics will be dedicated to the SWAT4LS 2010 workshop

We are planning to edit a special issue in BMC Bioinformatics dedicated to the 2010 edition of the workshop. The call for this special issue will be open to all authors of accepted contribution to SWAT4LS.

venerdì 20 agosto 2010

Franz Inc. to sponsor SWAT4LS 2010

Franz Inc. is sponsoring SWAT4LS 2010

venerdì 13 agosto 2010

Christopher Baker to present a keynote at SWAT4LS 2010

Christopher Baker: A renaissance for the point mutation: from legacy data to semantic web service

Christopher Baker is currently the Innovatia Research Chair and Associate Profesor at the University of New Brunswick, Canada. Up until 2008 he was the head of the Semantic Technology Group at the Data Mining Department, I2R, (A-STAR) where his team developed KnowleSuite, now licensed from I2R by Knorex Pte Ltd, in Singapore. Chris has considerable experience in Biomedical Informatics and Semantic Technologies and was co-editor of the book Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences published by Springer in 2007. In 2005, his team won the Semantic Web Challenge (2nd prize) at the International Semantic Web Conference. He now serves on the Editorial Board of the Journal of Biomedical Semantics and is an invited expert for the W3C's Semantic Web in Health Care and Life Sciences Interest Group (HCLSIG). Chris holds PhD in Microbiology from the University of Wales, Cardiff (1996).