Gene-function bigraph and DAG structure of ontology. This plot demonstrates how to build the structure of gene-function bigraph. The orange rectangles at the bottom level represent genes. The blue ellipses and arrows above form a subgraph of the DAG in the GO database. Solid edges represent the association between genes and functions. Dashed lines are added edges that reflect the semantic similarity of function annotations. The graph inside the red dashed box is the gene-function bipartite graph.