SWC’s Matthias Samwald contributes to W3C notes

Early June saw the release of two notes drafted by the Semantic Web Health Care and Life Sciences (HCLS) Interest Group within the W3C. One of the contributors, and editor of one note, is Matthias Samwald, a project coordinator at SWC, who is a member of this SIG and who has worked on several Semantic Web projects for the Yale Center for Medical Informatics (USA), Science Commons (USA) and DERI Galway (Ireland).

A Prototype Knowledge Base for the Life Sciences
W3C Interest Group Note 4 June 2008
Editors: M. Scott Marshall, Eric Prud’hommeaux
Contributors: Alan Ruttenberg, Jonathan Rees, Susie Stephens, Matthias Samwald, Kei-Hoi Cheung
Abstract: The prototype we describe is a biomedical knowledge base, constructed for a demonstration at Banff WWW2007 , that integrates 15 distinct data sources using currently available Semantic Web technologies such as the W3C standard Web Ontology Language [RDF]. This report outlines which resources were integrated, how the knowledge base was constructed using free and open source triple store technology, how it can be queried using the W3C Recommended RDF query language SPARQL [SPARQL], and what resources and inferences are involved in answering complex queries. While the utility of the knowledge base is illustrated by identifying a set of genes involved in Alzheimer’s Disease, the approach described here can be applied to any use case that integrates data from multiple domains.

Experiences with the conversion of SenseLab databases to RDF/OWL
W3C Interest Group Note 4 June 2008
Editors: Matthias Samwald, Kei-Hoi Cheung
Contributors: Alan Ruttenberg, Huajun Chen
Abstract: One of the challenges facing Semantic Web for Health Care and Life Sciences is that of converting relational databases into Semantic Web format. The issues and the steps involved in such a conversion have not been well documented. To this end, we have created this document to describe the process of converting SenseLab databases into OWL. SenseLab is a collection of relational (Oracle) databases for neuroscientific research. The conversion of these databases into RDF/OWL format is an important step towards realizing the benefits of Semantic Web in integrative neuroscience research. This document describes how we represented some of the SenseLab databases in Resource Description Framework (RDF) and Web Ontology Language (OWL), and discusses the advantages and disadvantages of these representations. Our OWL representation is based on the reuse and extension of existing standard OWL ontologies developed in the biomedical ontology communities. The purpose of this document is to share our implementation experience with the community.