From Protein-Protein Interaction to Molecular Event Extraction

This document describes the methods and results for our participation in the BioNLP’09 Shared Task #1 on Event Extraction. It also contains some error analysis and a brief discussion of the results. Previous shared tasks in the BioNLP community have focused on extracting gene and protein names, and on finding (direct) protein-protein interactions (PPI). This year’s task was slightly different, since the protein names were already manually annotated in the text. The new challenge was to extract biological events involving these given gene and gene products. We modified a publicly available system (AkanePPI) to apply it to this new, but similar, protein interaction task. AkanePPI has previously achieved state-of-the-art performance on all existing public PPI corpora, and only small changes were needed to achieve competitive results on this event extraction task. Our official result was an F-score of 36.9%, which was ranked as number six among submissions from 24 different groups. We later balanced the recall/precision by including more predictions than just the most confident one in ambiguous cases, and this raised the F-score on the test-set to 42.6%. The new Akane program can be used freely for academic purposes.