Demystifying protein annotations: toward increasing the compatibility of different corpora

While there are a number of corpora with protein annotations, the annotations in different corpora are not compatible with each other. It is, however, not yet well understood how they are different and how the incompatibilities can be overcome. The situation discourages utilization of the corpora in a united way. It also indicates that even within individual corpora, the actual annotations are not well understood. We first compare the protein annotations of two corpora, GENIA and GENETAG. Based on the result, we propose several strategies to increase the cross-corpus compatibility. Experimental results show that the proposed strategies are effective and the incompatibility of the protein annotations between the two corpora can be removed if we properly consider their differences.