Biomedical Ontologies integrate diverse biomedical data to enable intelligent data-mining and to translate basic research into useful knowledge. I will discuss the first version of the RNA Ontology (RNAO), an ontology for integrating databases pertaining to RNA structures, homologous sequences, and RNA functions. Each RNA 3D atomic coordinate file represents the structure of a specific molecule, but such data have broader significance by representing a class of homologous molecules that differ in sequence but share core structural features of functional importance. 3D structural 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 contains the definitions and the concepts of nucleic acid stereochemistry, base pairing families, base stacking, base-backbone hydrogen bonding, and backbone connectivity and conformations, and enables their logical manipulation. The RNA is intended to serve as a core, orthogonal ontology 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.