Figure 4

Depth and size properties of GO terms selected or excluded from the evaluation gold standard based on expert curation. The functional gold standard based on voting from an expert panel cannot be approximated by either a size or a depth measure of specificity. (a) Distribution of GO term depths for expert-selected terms (4–6 votes) and expert-excluded terms (1–3 votes). The selected set of terms cannot be separated from the "too general" excluded terms on the basis of depth. For instance, 53 of the 107 general GO terms appear at depth 4 or lower and 51 of 1692 specific GO terms appear at depth 3 or higher. (b) Distribution of GO term sizes (direct and indirect annotations) for the selected and excluded terms based on the expert voting analysis. As with term depth, size cannot effectively distinguish specific terms from those deemed too general by experts. For example, 28 of 107 GO terms deemed too general for inclusion in the standard have fewer than 100 annotations.