title: RKB: a Semantic Web knowledge base for RNA.
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.
authors.affiliation: Department of Biology, Carleton University 1125 Colonel By Drive, K1S5B6, Ottawa, Canada . jctoledo@connect.carleton.ca.
authors.forename: Jose
authors.initials: J
authors.lastname: Cruz-Toledo
authors.forename: Michel
authors.initials: M
authors.lastname: Dumontier
authors.forename: Marc
authors.initials: M
authors.lastname: Parisien
authors.forename: François
authors.initials: F
authors.lastname: Major