First International Workshop on Semantic Applied Technologies on Biomedical Informatics (SATBI 2011)

In conjunction with ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB)

Chicago, IL, U.S.A. August 1-3, 2011

Confirmed keynote speakers

Dr. Jesualdo Tomas Fernandez Breis

Jesualdo Tomas Fernandez-Breis, PhD; Associate Professor at the Department of Informatics and Systems, University of Murcia (Spain), where he is also serving as Web Coordinator. He is member of the International Association of Ontologies and its Applications, and the International Society for Computational Biology.

His research is mainly focused on the application of Semantic Web Technologies in biomedical domains. He has led research projects which have produced significant contributions in the formalization and enrichment of biomedical ontologies, the semantic integration of biomedical resources and the semantic interoperability of healthcare records.

His paper 'Enriching the Gene Ontology via the Dissection of Labels using the Ontology Preprocessor Language' was recently awarded with the Best Research Paper Award at EKAW 2010

Talk: Enrichment of biomedical ontologies: challenges and possibilities

Dr. Christopher Baker

Dr. Christopher Baker is currently the Innovatia Research Chair and Associate Professor at the University of New Brunswick, Canada. He is Co-PI on the C-BRASS Project - Canadian Bioinformatics Resources as Semantic Services initiative that is mandated to provide semantic service descriptions to bioinformatics resources and to leverage the SADI Framework. Until 2008 he was the head of the Semantic Technology Group at the Data Mining Department, I2R, Singapore.

Dr Baker 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).

Talk: Deployments of SADI Semantic Web Services in Genomics, Lipidomics, Toxicology and Healthcare

Abstract:Operationalizing web-based bioinformatics databases and algorithms for meaningful knowledge discovery continues to pose significant technical challenges for scientists. The need to identify relevant links across database records and review the compatibility of input and output formats limits the reuse of existing online resources. Moreover, the subsequent interpretation of integrated Omics-data in the context of the state of the art methodologies and contemporary knowledge accessible through a single query platform, using explicit semantics, is yet to be fully realized.

Core to such a discovery paradigm is the nascent SADI Semantic Web Services framework which comprises of (i) a set of conventions for creating web services, namely that service interfaces are defined using OWL-DL classes and associated predicates to represent the service inputs and output sand that services consume and return OWL Individuals of classes; (ii) a client tool, SHARE, which exposes SADI Web Services as if they were a virtual, distributed SPARQL endpoint through which workflows are automatically designed and executed to resolve the end user queries.

To address the proliferation, adoption and validation of this framework the C-BRASS* Initiative was mandated to address resource integration through the large scale deployment of SADI web services across multiple research disciplines in Biomedicine. This talk will outline the creation and use of clusters of distributed SADI services deployed to expedite common bioinformatic tasks, namely extraction of genomic annotations from the scientific literature, gene ontology annotation of probes on a custom microarray - for toxicology studies in fish, classification of small molecules in lipidomics, and the surveillance of hospital acquired infections in health informatics.

The merits of the SADI framework; as a medium for publishing data and resources on the web for reuse by a variety of stakeholders, as well as the realization of ad-hoc knowledge discovery through a single interface to a registry of services, freeing scientist from learning details of tool interfaces or semantic idiosyncrasies of databases, will be outlined.

* C-BRASS: Canadian Bioinformatics Resources as Semantic Services is funded by CANARIE - Canada's Advanced Research and Innovation Network.