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This article is part of the supplement: Semantic Web Applications and Tools for Life Sciences, 2008

Open Access Research

Semantic web data warehousing for caGrid

James P McCusker1, Joshua A Phillips2, Alejandra González Beltrán3, Anthony Finkelstein3 and Michael Krauthammer1*

Author Affiliations

1 Department of Pathology, Yale University School of Medicine, New Haven, CT, USA

2 Semantic Bits, LLC, Reston, VA, USA

3 Department of Computer Science, University College London, London, UK

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BMC Bioinformatics 2009, 10(Suppl 10):S2  doi:10.1186/1471-2105-10-S10-S2

Published: 1 October 2009

Abstract

The National Cancer Institute (NCI) is developing caGrid as a means for sharing cancer-related data and services. As more data sets become available on caGrid, we need effective ways of accessing and integrating this information. Although the data models exposed on caGrid are semantically well annotated, it is currently up to the caGrid client to infer relationships between the different models and their classes. In this paper, we present a Semantic Web-based data warehouse (Corvus) for creating relationships among caGrid models. This is accomplished through the transformation of semantically-annotated caBIG® Unified Modeling Language (UML) information models into Web Ontology Language (OWL) ontologies that preserve those semantics. We demonstrate the validity of the approach by Semantic Extraction, Transformation and Loading (SETL) of data from two caGrid data sources, caTissue and caArray, as well as alignment and query of those sources in Corvus. We argue that semantic integration is necessary for integration of data from distributed web services and that Corvus is a useful way of accomplishing this. Our approach is generalizable and of broad utility to researchers facing similar integration challenges.