James W. Brown

Associate Professor & Undergraduate Coordinator
Department of Microbiology, NC State University

Abstract# 95, RNA 2009 (RNA Society), May 26-31, 2009, Madison, WI

The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data

Colin Batchelor1, Thomas Bittner2, James Brown3, Karen Eilbeck4, Rob Knight5, Chris Mungall6, Jane Richardson7, Jesse Stombaugh8, Craig Zirbel9, Eric Westhof10, Neocles Leontis8

1Royal Society of Chemistry, Thomas Graham House, Milton Road, Cambridge, UK CB4 0WF, 2Department of Philosophy, University at Buffalo, 135 Bark Hall, Buffalo, NY 14260, 3Department of Microbiology, NC State University, Raleigh, NC 27695, 4Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT 84112, 5Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309 USA, 6Division of Life Sciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, 7Department of Biochemistry, Duke University Medical Center, Durham NC 27710 USA, 8Department of Chemistry, Bowling Green State University, Bowling Green, OH 43402, 9Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43402, 10Architecture et ractivite de l'ARN, Universite de Strasbourg, Strasbourg, France

Biomedical Ontologies facilitate the integration of diverse biomedical data to enable intelligent data-mining and the translation of basic research into useful knowledge. We present the first version of the RNA Ontology (RNAO), an ontology for integrating databases pertaining to RNA structures, homologous sequences, and RNA functions.
RNA data is usually distributed as 3D atomic coordinate files that represent the structure of a specific molecule. Such data have broader significance beyond the representation of particular molecules by representing a whole class of homologous molecules that differ in sequence but share core structural features of functional importance. 3D structural RNA data thus gain value by being linked to homologous sequences in genomic data or to databases of sequence alignments. Similarly, genomic data gain value when shared structural features are annotated and linked to specific functions. The RNAO facilitates the integration of RNA data by providing precise definitions for nucleic acid stereochemistry, base pairing families, base stacking, base-backbone hydrogen bonding, and backbone connectivity and conformations, and enables their logical manipulation. The RNAO is intended to serve as an important component of the Open Biomedical Ontologies (OBO) Consortium, and is a companion to the Sequence Ontology (SO). It is available as an OWL or OBO file. The RNAO will provide logically rigorous ways of linking genomic and structural databases.

nullLast updated May 30, 2009 by James W Brown