Shortest path dependency trees for the protein pair in the sentence from Example 2. Figure 2a represents the shortest path between the two proteins in the dependency tree for the sentence: "Sigma F
activity regulates the processing of sigma E
within the mother cell compartment." Figures 2b and 2c represent respectively the corresponding POS shortest path and the syntactic path. Note that 2a contains lexical and deep syntactic information, while 2b contains shallow and deep syntactic information, and 2c contains only deep syntactic information.