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Genome Res. 2014 Feb;24(2):356-64. doi: 10.1101/gr.157495.113. Epub 2013 Oct 25.

Variation Ontology for annotation of variation effects and mechanisms.

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Department of Experimental Medical Science, Lund University, SE-221 84 Lund, Sweden; Institute of Biomedical Technology, FI-33014 University of Tampere, Finland; BioMediTech, Tampere, Finland.


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, and pattern recognition and statistics, as well as development of analysis and prediction tools. The Variation Ontology (VariO) 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 nongenetic origin. VariO annotations are position-specific and can be used for variations in any organism.

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