Figure 3

Size distribution of depth 5 biological process GO terms ( S. cerevisiae ). Depth and size are commonly used metrics for assessing the biological specificity of GO terms, a necessary step in creating a functional gold standard from the ontology. Here, the number of direct and indirect annotations was counted for each depth 5 GO term and counts were binned to obtain a histogram of sizes for depth 5 GO terms. This reveals a wide range of sizes for terms at the same depth (from 0 annotations to 1381 annotations), suggesting size and depth are not capturing the same notion of specificity, and that likely neither is an appropriate measure for true biological specificity. A sampling of the largest and smallest depth 5 GO terms is shown in Table 1.