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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2105-10-S10-S2) contains supplementary material, which is available to authorized users.
Highlights
We propose a Semantic Web data warehouse approach that enables users to map data from multiple grid data sources into an ontologically-driven data store, or knowledge base (KB), where they can use data from a semantic perspective. caGrid, a core technology of caBIG® ("Cancer Biomedical Informatics Grid”) [1,2,3,4,5], is a semantically annotated grid sponsored by the National Cancer Institute that provides a consistent framework for grid web services
The information models of the grid services are mapped to concepts from the National Cancer Institute (NCI) Thesaurus (NCIt) [6,7,8,9], a rich, cancerfocused terminology source, through Common Data Elements (CDEs) registered in the Cancer Data Standards Repository [10]
We generated the OWL ontologies for caTissue, caArray, and the NCIt concepts they use from the metadata available from those services
Summary
CaGrid, a core technology of caBIG® ("Cancer Biomedical Informatics Grid”) [1,2,3,4,5], is a semantically annotated grid sponsored by the National Cancer Institute that provides a consistent framework for grid web services. The information models of the grid services are mapped to concepts from the NCI Thesaurus (NCIt) [6,7,8,9], a rich, cancerfocused terminology source, through Common Data Elements (CDEs) registered in the Cancer Data Standards Repository (caDSR) [10]. CDEs represent semantically interoperable “join points” among information models, which provide a basis for data integration. There is no transparent mapping of semantics onto data from grid services. Semantic interoperability is the job of the client and requires the ability to reason over (or interpret) the metadata, including class hierarchies, attributes, associations, and their corresponding annotations to establish equivalencies
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
