BACKGROUND: Bio-molecular event extraction from literature is recognized as an important task of bio text mining and, as such, many relevant systems have been developed and made available during the last decade. While such systems provide useful services individually, there is a need for a meta-service to enable comparison and ensemble of such services, offering optimal solutions for various purposes. RESULTS: We have integrated nine event extraction systems in the U-Compare framework, making them intercompatible and interoperable with other U-Compare components. The U-Compare event meta-service provides various meta-level features for comparison and ensemble of multiple event extraction systems. Experimental results show that the performance improvements achieved by the ensemble are significant. CONCLUSIONS: While individual event extraction systems themselves provide useful features for bio text mining, the U-Compare meta-service is expected to improve the accessibility to the individual systems, and to enable meta-level uses over multiple event extraction systems such as comparison and ensemble.

In our approach to event extraction, dependency graphs constitute the fundamental data structure for knowledge capture. Two types of trimming operations pave the way to more effective relation extraction. First, we simplify the syntactic representation structures resulting from parsing by pruning informationally irrelevant lexical material from dependency graphs. Second, we enrich informationally relevant lexical material in the simplified dependency graphs with additional semantic meta data at several layers of conceptual granularity. These two aggregation operations on linguistic representation structures are intended to avoid overfitting of machine learning-based classifiers which we use for event extraction (besides manually curated dictionaries). Given this methodological framework, the corresponding JReX system developed by the JulieLab Team from Friedrich-Schiller-Universität Jena (Germany) scored on 2nd rank among 24 competing teams for Task 1 in the “BioNLP’09 Shared Task on Event Extraction,” with 45.8% recall, 47.5% precision and 46.7% F1-score on all 3,182 events. In more recent experiments, based on slight modifications of JReX and using the same data sets, we were able to achieve 45.9% recall, 57.7% precision, and 51.1% F1-score.