Issue title: Biomedical Ontologies
Article type: Research Article
Authors: Hoehndorf, Robert | Batchelor, Colin | Bittner, Thomas | Dumontier, Michel | Eilbeck, Karen | Knight, Rob; | Mungall, Chris J. | Richardson, Jane S. | Stombaugh, Jesse | Westhof, Eric | Zirbel, Craig L. | Leontis, Neocles B.;
Affiliations: Department of Genetics, University of Cambridge, Cambridge, UK | Royal Society of Chemistry, Cambridge, UK | Department of Philosophy, University at Buffalo, Buffalo, NY, USA | Department of Biology School of Computer Science, Carleton University, Ottawa, ON, Canada | Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, USA | Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA | Life Sciences Division, Lawrence Berkeley National Lab, CA, USA | Department of Biochemistry, Duke University Medical School, Durham, NC, USA | Architecture et réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France | Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH, USA | Department of Chemistry, Bowling Green State University, Bowling Green, OH, USA | Howard Hughes Medical Institute, Boulder, CO, USA
Note: [] Corresponding author: Neocles B. Leontis, Department of Chemistry, Bowling Green State University, Bowling Green, OH 43402, USA. E-mail: [email protected].
Abstract: Biomedical Ontologies integrate diverse biomedical data and enable intelligent data-mining and help translate basic research into useful clinical knowledge. We present the RNA Ontology (RNAO), an ontology for integrating diverse RNA data, including RNA sequences and sequence alignments, three-dimensional structures, and biochemical and functional data. For example, individual atomic resolution RNA structures have broader significance as representatives of classes of homologous molecules, which can differ significantly in sequence while sharing core structural features and common roles or functions. Thus, structural data gain value by being linked to homologous sequences in genomic data and databases of sequence alignments. Likewise, the value of genomic data is enhanced by annotation of shared structural features, especially when these can be linked to specific functions. Moreover, the significance of biochemical, functional and mutational analyses of RNA molecules are most fully understood when linked to molecular structures and phylogenies. To achieve these goals, RNAO provides logically rigorous definitions of the components of RNA primary, secondary and tertiary structure and the relations between these entities. RNAO is being developed to comply with the developing standards of the Open Biomedical Ontologies (OBO) Consortium. The RNAO can be accessed at http://code.google.com/p/rnao/.
Keywords: Ontology of molecules, RNA ontology, covalent bonding relation, non-covalent bonding relation, base pairing relation, base stacking relation, RNA motif, RNA sequence alignment
DOI: 10.3233/AO-2011-0082
Journal: Applied Ontology, vol. 6, no. 1, pp. 53-89, 2011
