En masse symbol-based assigment of Aberration Class with respect to wild type. - FlyBase (2007)
Prior to FlyBase release 2006_01, FlyBase classified an aberration only with respect to its progenitor. Previous releases of FlyBase used the Aberration Class field to support searches for categories of aberrations such as "deficiency" or "duplication". The results of these searches were sometimes misleading because Aberration Class did not necessarily describe a chromosome's deviation from wild-type. For example, a small duplication made by deleting part of a larger, progenitor duplication had an Aberration Class of "deficiency" although the chromosome was not deficient with respect to the wild-type genome. To begin to address this shortcoming, Aberration Class in FlyBase release 2006_01 uses controlled vocabulary terms from the Sequence Ontology (SO, www.sequenceontology.org) to classify 10,623 aberrations with respect to wild-type. FlyBase release 2007_01 extends this classification to all aberrations in the database. To allow this retrofit to be accomplished with the available manpower, most aberrations have been annotated with SO terms en mass, based on the class indicated in the aberration symbol. While the great majority of resulting classifications will be correct, some erroneous classifications will no doubt occur, and others will not reflect all of the information known about an aberration. For example, the parent SO term "chromosomal deletion" will usually be applied to an aberration instead of the more detailed child term "deficient inversion". FlyBase will revisit these classifications as time permits.