ANNOTATION PROPAGATION: WHEN TO CUT, COPY AND PASTE?
The quality and quantity of annotation data varies within and between genomes. To reduce these inconsistencies, we would like to replace poor annotations with better information. We have developed an ‘annotation propagation’ tool within ERIC–ASAP to facilitate the comparison, evaluation and replacement of annotations across related genome features. This tool compares the text of annotation data between source and destination features as well as the evidence supporting the annotations. If the source feature annotation is supported by better evidence, the existing annotations for the destination feature are replaced with the annotation from the source feature. The user of the annotation propagation tool chooses the source and destination features and assigns the relative values to different categories of supporting evidence. Using this tool, high-quality annotations from well-curated genomes or protein families can be rapidly applied to other genomes while at the same time preserving any well-supported manual annotations that may already exist. The database retains a record of all annotations, regardless of their approval status, so no information is lost and can be reapplied as necessary.
Propagation of inaccurate or erroneous annotations has potential to do great harm to the quality of genome annotations. Care must be taken to ensure that only high-quality annotations are propagated across appropriate genome features. For example, propagation of annotations to members of EnteroFam families across genomes required that the annotation of the EnteroFam family be ‘curated’, and that membership in the family was approved by a curator. If a genome already contained an annotation with better supporting evidence, such as a gene product description with an experimental evidence code linked to a publication, the existing annotation was preserved. New annotations added by the propagation procedure all contain an indication that they were added by an automated process and have a link to the SOP describing the procedure.
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