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Briefings in Bioinformatics Advance Access published online on January 16, 2009
Briefings in Bioinformatics, doi:10.1093/bib/bbn051
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© The Author 2009. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Moby and Moby 2: Creatures of the Deep (Web)

Ben P. Vandervalk, E. Luke McCarthy and Mark D. Wilkinson

Corresponding author. Mark D.Wilkinson, Department of Medical Genetics, The Providence Heart + Lung Research Institute at St Paul's Hospital, University of British Columbia, Vancouver, British Columbia V6Z 1Y6, Canada. Tel: +1-604-628-7807; Fax: +1-604-806-9274; E-mail: markw{at}illuminae.com

Facile and meaningful integration of data from disparate resources is the ‘holy grail’ of bioinformatics. Some resources have begun to address this problem by providing their data using Semantic Web standards, specifically the Resource Description Framework (RDF) and the Web Ontology Language (OWL). Unfortunately, adoption of Semantic Web standards has been slow overall, and even in cases where the standards are being utilized, interconnectivity between resources is rare. In response, we have seen the emergence of centralized ‘semantic warehouses’ that collect public data from third parties, integrate it, translate it into OWL/RDF and provide it to the community as a unified and queryable resource. One limitation of the warehouse approach is that queries are confined to the resources that have been selected for inclusion. A related problem, perhaps of greater concern, is that the majority of bioinformatics data exists in the ‘Deep Web’—that is, the data does not exist until an application or analytical tool is invoked, and therefore does not have a predictable Web address. The inability to utilize Uniform Resource Identifiers (URIs) to address this data is a barrier to its accessibility via URI-centric Semantic Web technologies. Here we examine ‘The State of the Union’ for the adoption of Semantic Web standards in the health care and life sciences domain by key bioinformatics resources, explore the nature and connectivity of several community-driven semantic warehousing projects, and report on our own progress with the CardioSHARE/Moby-2 project, which aims to make the resources of the Deep Web transparently accessible through SPARQL queries.

Keywords: Semantic Web, Semantic Web services, data integration, distributed SPARQL, OWL, RDF

Submitted: August 4, 2008. Received (in revised form): October 17, 2008.


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