RKB: a Semantic Web knowledge base for RNA

Jose Cruz-Toledo, Michel Dumontier*, Marc Parisien, François Major

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


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.

Original languageEnglish
Pages (from-to)S2
JournalJournal of biomedical semantics
Volume1 Suppl 1
Publication statusPublished - 22 Jun 2010
Externally publishedYes


  • Journal Article

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