The top-level terms in the Sequence Ontology used in variant annotation. There are 1,792 terms in SO, most of which (1,312) are sequence features. There are 100 terms in the ontology that are kinds of sequence variant, of which the two top level terms are shown, and three sub-types, shown with dashed lines, that demonstrate the detail of these terms. The parts of SO that are used to annotate sequence variation files are sequence alteration to categorize the change (five subtypes shown with dashed lines), sequence feature to annotate the genomic features that the alteration intersects, and sequence variant to annotate the kind of sequence variant with regards to the reference sequence.
Reese et al. Genome Biology 2010 11:R88 doi:10.1186/gb-2010-11-8-r88