BackgroundA large number of computational methods have been proposed for predicting protein functions. The underlying techniques adopted by most of these methods revolve around predicting the functions of an unannotated protein p from already annotated proteins that have similar characteristics as p. Recent Information Extraction methods take advantage of the huge growth of biomedical literature to predict protein functions. They extract biological molecule terms that directly describe protein functions from biomedical texts. However, they consider only explicitly mentioned terms that co-occur with proteins in texts. We observe that some important biological molecule terms pertaining functional categories may implicitly co-occur with proteins in texts. Therefore, the methods that rely solely on explicitly mentioned terms in texts may miss vital functional information implicitly mentioned in the texts.
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