The RNA Ontology Consortium: An open invitation to the RNA community

NEOCLES B. LEONTIS; RUSS B. ALTMAN; HELEN M. BERMAN; STEVEN E. BRENNER; JAMES W. BROWN; DAVID R. ENGELKE; STEPHEN C. HARVEY; STEPHEN R. HOLBROOK; FABRICE JOSSINET; SUZANNA E. LEWIS; FRANÇOIS MAJOR; DAVID H. MATHEWS; JANE S. RICHARDSON; JAMES R. WILLIAMSON; ERIC WESTHOF

doi:10.1261/rna.2343206

The RNA Ontology Consortium: An open invitation to the RNA community

¹Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43402, USA
²Stanford Medical Informatics, Stanford University Medical Center, Stanford, California 94305, USA
³Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, New Jersey 08854, USA
⁴Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, USA
⁵Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695, USA
⁶Department of Biological Chemistry, The University of Michigan, Ann Arbor, Michigan 48103, USA
⁷School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
⁸Department of Structural Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8118, USA
⁹Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200, USA
¹⁰Département d’Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, Québec H3C 3J7, Canada
¹¹Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
¹²Department of Biochemistry, Duke University, Durham, North Carolina 27710-3711, USA
¹³Department of Molecular Biology, Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, California 92037, USA
¹⁴Institut de Biologie Moléculaire et Cellulaire du CNRS, UPR ‘Architecture et réactivité de l’ARN,’ Université Louis Pasteur, 67084 Strasbourg, France

Abstract

The aim of the RNA Ontology Consortium (ROC) is to create an integrated conceptual framework—an RNA Ontology (RO)—with a common, dynamic, controlled, and structured vocabulary to describe and characterize RNA sequences, secondary structures, three-dimensional structures, and dynamics pertaining to RNA function. The RO should produce tools for clear communication about RNA structure and function for multiple uses, including the integration of RNA electronic resources into the Semantic Web. These tools should allow the accurate description in computer-interpretable form of the coupling between RNA architecture, function, and evolution. The purposes for creating the RO are, therefore, (1) to integrate sequence and structural databases; (2) to allow different computational tools to interoperate; (3) to create powerful software tools that bring advanced computational methods to the bench scientist; and (4) to facilitate precise searches for all relevant information pertaining to RNA. For example, one initial objective of the ROC is to define, identify, and classify RNA structural motifs described in the literature or appearing in databases and to agree on a computer-interpretable definition for each of these motifs. To achieve these aims, the ROC will foster communication and promote collaboration among RNA scientists by coordinating frequent face-to-face workshops to discuss, debate, and resolve difficult conceptual issues. These meeting opportunities will create new directions at various levels of RNA research. The ROC will work closely with the PDB/NDB structural databases and the Gene, Sequence, and Open Biomedical Ontology Consortia to integrate the RO with existing biological ontologies to extend existing content while maintaining interoperability.

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