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Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all(More)
MOTIVATION Protein-protein interactions (PPIs) play an important role in understanding biological processes. Although recent research in text mining has achieved a significant progress in automatic PPI extraction from literature, performance of existing systems still needs to be improved. RESULTS In this study, we propose a novel algorithm for extracting(More)
We introduce a new semantic annotation scheme for the Recognizing Textual Entailment (RTE) dataset as well as a manually annotated dataset that uses this scheme. The scheme addresses three types of modification that license entailment patterns: restrictive, appositive and conjunctive, with a formal semantic specification of these patterns' contribution for(More)
Hypothesis generation in molecular and cellular biology is an empirical process in which knowledge derived from prior experiments is distilled into a comprehensible model. The requirement of automated support is exemplified by the difficulty of considering all relevant facts that are contained in the millions of documents available from PubMed. Semantic Web(More)