AKANE System : Protein-Protein Interaction 1 AKANE System : Protein-Protein Interaction Pairs in the BioCreAtIvE 2 Challenge , PPI-IPS subtask

This report summarizes the participation of the Tsujii-lab group in the 2006 BioCreative2 text mining challenge. It describes the systems used, the results attained, and the lessons learned. The basic idea was to see how well the AKANE system could perform on a full-text ProteinProtein Interaction (PPI) Information Extraction (IE) task. AKANE system is a recently developed, sentence-level PPI system that achieved a 57.3 F-score on the AImed corpus. In order to use the AKANE system for the BioCreative task, the given training data had to be preprocessed. The BioCreative training data contained just a list of interacting protein pair identifiers for each given full-text article, while the expected input for the AKANE system is annotated sentences like in the AImed corpus. In order to transform the full-text articles into AImed sentence-level annotations, the text was first stripped of all HTML coding to get a plain text representation. Then, each mention of protein names were tagged by a Named Entity Recognizer (NER), and all interacting and co-occurring pairs in single sentences were used for training. A pipeline architecture was made to deal with each of these challenges. Some postprocessing was also necessary, in order to transform the results from the AKANE system into the expected format for the BioCreative2 challenge. The postprocessing included filtering and ranking the results, and balancing precision and recall to maximize the F-score.