Variation Ontology for annotation of variation effects and mechanisms

Abstract

Ontology organizes and formally conceptualizes information in a knowledge domain with a controlled vocabulary having defined terms and relationships between them. Several ontologies have been used to annotate numerous databases in biology and medicine. Due to their unambiguous nature, ontological annotations facilitate systematic description and data organization, data integration and mining, pattern recognition and statistics, as well as development of analysis and prediction tools. The Variation Ontology was developed to allow the annotation of effects, consequences and mechanisms of DNA, RNA and protein variations. Variation types are systematically organized and a detailed description of effects and mechanisms is possible. VariO is for annotating the variant, not the normal state features or properties, and requires a reference (e.g. reference sequence, reference state property, activity etc) compared to which the changes are indicated. VariO is versatile and can be used for variations ranging from genomic multiplications to single nucleotide or amino acid changes whether of genetic or non-genetic origin. VariO annotations are position specific and can be used for variations in any organism.