Lecture: Unifying Ontology Services for Functional Genomic Annotations by Dr. Tomasz Adamusiak on 12/13/2011

Unifying Ontology Services for Functional Genomic Annotations

Brown Bag Lecture by Dr. Tomasz Adamusiak | 12/13/2011 11AM-12PM | 7th Floor Conference Room, Bldg 38A

Abstract: The focus of this talk is the application of semantic web technologies and linked open data principles to gene expression data.

The Functional Genomics Group at the European Bioinformatics Institute in Cambridge, UK hosts the second largest resource of public transcriptomics data in the world. A subset of this data is semantically annotated with the Experimental Factor Ontology (EFO) in order to provide condition-specific gene expression queries.

Working with the W3C Semantic Web for Health Care and Life Sciences Interest Group (HCLSIG) BioRDF task force I made this data available via a public SPARQL endpoint (http://www.ebi.ac.uk/efo/semanticweb/atlas) for everyone to reuse and integrate in their semantic web applications, and a number of ontology-related tasks has been abstracted in an integrated programming toolkit for Common ONTOlogy Application Tasks (http://www.ontocat.org) in order to prevent unnecessary replication of this effort across different research groups and to lower the barrier to building semantically-enabled applications.

James Malone at the EBI laid the groundwork for the transformation of gene expression data into RDF. The OntoCAT project was a collaboration with Morris Swertz group at the University Medical Center Groningen, the Netherlands.

Bio: Tomasz Adamusiak is a Postdoctoral Fellow in Clinical Informatics in the Cognitive Science Branch of the Lister Hill National Center for Biomedical Communications at the U.S. National Library of Medicine. His research interests include development of biomedical ontologies, genotype-to-phenotype modelling, and application of semantic web technologies to life science data.

Tomasz studied medicine at the Friedrich-Alexander-University of Erlangen-Nuremberg in Germany and at the Medical University of Lodz in Poland from which he received an MD degree in 2006 and a PhD in Clinical Immunology in 2008. Before joining NLM in 2011 he was a bioinformatician in the Functional Genomics Group at the European Bioinformatics Institute in Cambridge, UK, and earlier a system manager in the Medical Image Knowledge Management department at Siemens Healthcare in Erlangen, Germany.

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