In this paper, we present BioEve a fully automated event extraction system for bio-medical text. It first semantically classifies each sentence to the class type of the event mentioned in the sentence, and then using high coverage hand-crafted rules, it extracts the participants of that event. We participated in Task 1 of BioNLP 2009 Shared task, and the final evaluation results are described here. Our experimentation with different approaches to classify a sentence to bio-interaction classes are also shared.
Background. Recent advances in computational and biological methods in last two decades have remarkably changed the scale of biomedical research and with it began the unprecedented growth in both the production of biomedical data and amount of published literature discussing it. An automated extraction system coupled with a cognitive search and navigation service over these document collections would not only save time and effort, but also pave the way to discover hitherto unknown information implicitly conveyed in the texts. Results. We developed a novel framework (named “BioEve”) that seamlessly integrates Faceted Search (Information Retrieval) with Information Extraction module to provide an interactive search experience for the researchers in life sciences. It enables guided step-by-step search query refinement, by suggesting concepts and entities (like genes, drugs, and diseases) to quickly filter and modify search direction, and thereby facilitating an enriched paradigm where user can discover related concepts and keywords to search while information seeking. Conclusions. The BioEve Search framework makes it easier to enable scalable interactive search over large collection of textual articles and to discover knowledge hidden in thousands of biomedical literature articles with ease.
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