City Research Online

Semantic web data warehousing for caGrid

McCusker, J. P., Phillips, J. A., Gonzalez-Beltran, A. N. , Finkelstein, A. ORCID: 0000-0003-2167-9844 & Krauthammer, M. (2009). Semantic web data warehousing for caGrid. BMC Bioinformatics, 10(10), S2. doi: 10.1186/1471-2105-10-S10-S2


The National Cancer Institute (NCI) is developing caGrid as a means for sharing cancer-relateddata and services. As more data sets become available on caGrid, we need effective ways ofaccessing and integrating this information. Although the data models exposed on caGrid aresemantically well annotated, it is currently up to the caGrid client to infer relationships between thedifferent 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 thetransformation of semantically-annotated caBIG®Unified Modeling Language (UML) informationmodels into Web Ontology Language (OWL) ontologies that preserve those semantics. Wedemonstrate 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 queryof those sources in Corvus. We argue that semantic integration is necessary for integration of datafrom distributed web services and that Corvus is a useful way of accomplishing this. Our approachis generalizable and of broad utility to researchers facing similar integration challenges.

Publication Type: Article
Additional Information: © 2009 McCusker et al; licensee BioMed Central Ltd.This is an open access article distributed under the terms of the Creative Commons Attribution License (,which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Subjects: Q Science > QA Mathematics
Q Science > QA Mathematics > QA75 Electronic computers. Computer science
R Medicine > RC Internal medicine > RC0254 Neoplasms. Tumors. Oncology (including Cancer)
Departments: Presidents's Portfolio
Text - Published Version
Available under License Creative Commons: Attribution 2.0.

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