August 2006
Trends and Tools in Bioinformatics and Computational Biology
Wilfred W. Li, University of California, San Diego (UCSD), San Diego Supercomputer Center (SDSC)
Nathan Baker, Washington University in Saint Louis
Kim Baldridge, UCSD, SDSC
J. Andrew McCammon, UCSD
Mark H. Ellisman, UCSD, Center for Research In Biological Systems (CRBS)
Amarnath Gupta, UCSD, SDSC
Michael Holst, UCSD
Andrew D. McCulloch, UCSD
Anushka Michailova, UCSD
Phil Papadopoulos, UCSD, SDSC
Art Olson, The Scripps Research Institute (TSRI)
Michel Sanner, TSRI
Peter W. Arzberger, California Institute for Telecommunications and Information Technology (Calit2), CRBS, UCSD

3.7. Networks, pathways, ontologies and graph query engines

PathSys is a general-purpose, scalable, graph data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism, and a generic data-importing mechanism through schema-mapping. The client software, named BiologicalNetworks, supports the navigation and analyses of molecular networks (Figure 9B). As systems biology integrates information from many data sources, distributed or integrated, there is an increasing demand for managing, querying and automated reasoning using ontology concepts and description logic. OntoQuest is developed to provide the extended mapping schemes for storing OWL (web ontology language) ontologies into backend databases (Figure 9A). It is aimed to guide a user to explore ontological datasets and eventually make non-preconceived, impromptu discoveries.

Both PathSys and OntoQuest take advantages a new semantic-aware RDF (resource description framework) algebra, which supports the inference of complex relationships represented in ontological hierarchies. OntoQuest is being developed using the Cell Centered Database (CCDB) and neuroscience ontology, whereas PathSys is driven by research in yeast signaling pathways. The technology is extensible to the data integration between distributed data and computation services described with appropriate semantics and ontology terms (Figure 9). The technology being developed under OntoQuest may also be used to provide additional semantic annotations to Opal based web services to improve automated service discovery and utilization.

Figure 9A
Figure 9B
Figure 9. A) OntoQuest architecture: ontology based query engine and database environment. B) BiologicalNetworks is a client interface to the PathSys database warehouse, with support for many xml data formats.

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Reference this article
Li, W. W., Baker, N., Baldridge, K., McCammon, J. A., Ellisman, M. H., Gupta, A., Holst, M., McCulloch, A. D., Michailova, A., Papadopoulos, P., Olson, A., Sanner, M., Arzberger P. W. "National Biomedical Computation Resource (NBCR): Developing End-to-End Cyberinfrastructure for Multiscale Modeling in Biomedical Research," CTWatch Quarterly, Volume 2, Number 3, August 2006. http://www.ctwatch.org/quarterly/articles/2006/08/national-biomedical-computation-resource/

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