Toward a Richer Representation of Sequence Variation in the Sequence Ontology

The Sequence Ontology (SO) is a member ontology of the Open Biomedical Ontologies (OBO) library that is charged with formally representing types of biomacromolecular sequences and their associated attributes as well as the interrelationships among these. By providing a common vocabulary and set of definitions, it is widely used to facilitate accurate storage, processing, and exchange of sequence data. While some parts of the SO are quite mature, particularly the independently defined sequence features, the current representation of sequence variation is more problematic in that the representation of corresponding variations, sequences containing these variations, and processes resulting in these variations and their interrelationships is incomplete. Additionally, corresponding variations in DNAs, RNAs, and polypeptides and their interrelationships are not represented. We report here on our progress in more completely and precisely representing these concepts, which will allow for more consistent annotation of variant sequence data. Furthermore, formally linking and defining these sequence-variation classes within the OBO framework will enable powerful, logically sound reasoning with various types of variant data as well as with other types of annotated biological data.