RKB: a Semantic Web knowledge base for RNA.

Journal of Biomedical Semantics
Jose Cruz-ToledoFrançois Major

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.

References

Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
May 10, 2001·RNA·N B Leontis, E Westhof
Jun 29, 2002·RNA·Allison WaughFrançois Major
Oct 5, 2002·Nucleic Acids Research·Sébastien Lemieux, François Major
May 17, 2005·Genome Biology·Barry SmithCornelius Rosse
Feb 18, 2006·RNA·Neocles B LeontisEric Westhof
Oct 13, 2007·Nucleic Acids Research·Kirill DegtyarenkoMichael Ashburner
May 13, 2008·Journal of Biomedical Informatics·François BelleauJean Morissette
Jun 20, 2008·Journal of Biomedical Informatics·Natalia Villanueva-Rosales, Michel Dumontier
Oct 7, 2008·Nucleic Acids Research·UNKNOWN UniProt Consortium
Jul 16, 2010·Journal of Biomedical Semantics·Jose Cruz-ToledoFrançois Major

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Citations

Jul 16, 2010·Journal of Biomedical Semantics·Larisa N SoldatovaNigam H Shah
Jul 16, 2010·Journal of Biomedical Semantics·Jose Cruz-ToledoFrançois Major

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Methods Mentioned

BETA
SELEX
NMR

Software Mentioned

RKB
Pellet
RNAO
FaCT
MIREOT
Region Connection Calculus ( RCC 8
RNAML
Annotate
Protégé Ontology Editor
aATOM

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