Quality of Computationally Inferred Gene Ontology Annotations
Figure 2
Outline of the strategy to evaluate electronic Gene Ontology annotations.
(A) Reliability measures the proportion of electronic annotations confirmed by future experimental annotations: an electronic annotation in an older database release is either 1) confirmed by a new experimental annotation in the later release, 2) falsified by a new, contradictory experimental annotation (corresponding GO term, but with ‘NOT’ qualifier, which amounts to an explicit rejection), 3) removed from the new UniProt-GOA release (implicit rejection), or 4) unchanged, which is uninformative and does not affect the reliability measure. (B) Coverage measures the extent to which electronic annotations can predict future experimental annotations: an experimental annotation in the newer release is either 1) correctly predicted by an electronic annotation in the older release, or 2) not correctly predicted (“missed”). Note that the strategy is outlined for electronic annotations, but any subset of annotations can be analyzed this way, e.g. annotations assigned using a selection of evidence or reference codes.