Table 1.

Features of functional annotations described by AIGO metrics

Measure	Feature of a functional annotation
Coverage	Proportion of genes annotated by a FA
Richness	Proportion of GO terms used by a FA
Nb. of annotations	Number of annotations of a given gene
Coherence	Similarity of the terms in a set of annotations
Compactness	Similarity of the annotation sets in a FA
Specificity	Specificity of the annotations for a given gene
Information Content	Informativeness of the annotations for a given gene
Redundancy	Proportion of redundant terms in a set of annotations
Obsolescence	Proportion of obsolete terms in a FA
Semantic similarity	Degree of functional relatedness between two annotation sets
Hierarchical Precision	Proportion of the annotations in a given FA being also found in a gold-standard
Hierarchical Recall	Proportion of the annotations in the gold-standard being also found in a given FA

The different metrics computed by AIGO allow describing particular features of functional annotations.