For example, the syntaxbased grammar correctly finds two ubiquitination events and two negative regulations in the sentence "CYLD inhibits the ubiquitination of both TRAF2 and TRAF6" because the dependency graph correctly connects "ubiquitination" to "TRAF2" and "TRAF6", as seen in Figure 2.
the surface-based grammar misses the ubiquitination event involving "TRAF6" (and the negative regulation of this ubiquitination), because the last two tokens of the sentence are not explicitly handled by the rules.