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RKB: a Semantic Web knowledge base for RNA.

Cruz-Toledo J, Dumontier M, Parisien M, Major F

Department of Biology, Carleton University 1125 Colonel By Drive, K1S5B6, Ottawa, Canada . jctoledo@connect.carleton.ca.

ABSTRACT : Increasingly sophisticated knowledge about RNA structure and function requires an inclusive knowledge representation that facilitates the integration of independently -generated information arising from such efforts as genome sequencing projects, microarray analyses, structure determination and RNA SELEX experiments. While RNAML, an XML-based representation, has been proposed as an exchange format for a select subset of information, it lacks domain-specific semantics that are essential for answering questions that require expert knowledge. Here, we describe an RNA knowledge base (RKB) for structure-based knowledge using RDF/OWL Semantic Web technologies. RKB extends a number of ontologies and contains basic terminology for nucleic acid composition along with context/model-specific structural features such as sugar conformations, base pairings and base stackings. RKB (available at http://semanticscience.org/projects/rkb) is populated with PDB entries and MC-Annotate structural annotation. We show queries to the RKB using description logic reasoning, thus opening the door to question answering over independently-published RNA knowledge using Semantic Web technologies.

J Biomed Semantics 2010;1 Suppl 1:S2.

Pubmed ID: 20626922

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