The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data

Robert Hoehndorf, Colin Batchelor, Thomas Bittner, Michel Dumontier, Karen Eilbeck, Rob Knight, Chris J. Mungall, Jane S. Richardson, Jesse Stombaugh, Eric Westhof, Craig L. Zirbel, Neocles B. Leontis*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


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
Original languageEnglish
Pages (from-to)53-89
JournalApplied Ontology
Issue number1
Publication statusPublished - 2011
Externally publishedYes


  • Ontology of molecules
  • RNA ontology
  • covalent bonding relation
  • non-covalent bonding relation
  • base pairing relation
  • base stacking relation
  • RNA motif
  • RNA sequence alignment

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