Complex-to-Pairwise Mapping of Biological Relationships using a Semantic Network Representation

This study examines representations of protein–protein interactions focusing on the mapping between simple, pairwise annotation and complex, structured annotation. A simple semantic network representation equivalent to the BioInfer predicate formalism is introduced and used to transform the complex annotation of BioInfer into pairwise annotation through hand-written rules. Evaluation shows that this binarisation can be largely validly performed with limited loss of information, but also reveals specific challenges. The binarised BioInfer is the first corpus of this type where the inclusion rules are formalised to the level of a computational implementation and is freely available at http://www.it.utu.fi/BioInfer .