Highlights of the BioTM 2010 workshop on advances in bio text mining

This meeting report gives an overview of the keynote lectures, the panel discussion and a selection of the contributed presentations. The workshop was held in Gent, Belgium on May 10-11. It featured a tutorial aimed towards a broad audience of (computational) biologists, (computational) linguists and researchers working purely on text mining

RetroMine, or how to provide in-depth retrospective studies from Medline in a glance: the hepcidin use-case

International audienceThe rapid expansion of biomedical literature has provoked an increased development of advanced text mining tools to rapidly extract relevant events from the continuously increasing amount of knowledge published periodically in PubMed. However, bioinvestigators are still reluctant to use these tools for two reasons: i) a large volume of events is often extracted upon a query, and this volume is hard to manage, and ii) background events dominate search results and overshadow more pertinent published information, especially for domain experts. In this paper, we propose an approach that incorporates the temporal dimension of published events to the process of information extraction to improve data selection and prioritize more pertinent periodically published knowledge for scientists. Indeed, instead of providing the total knowledge associated with a PubMed query, which is usually a mix of trivial background information and non-background information, we propose a method that incorporates time and selects non background and highly relevant biological entities and events published over time for bioinvestigators. Before excluding background events from the total knowledge extracted, a quantification of their amount is also provided. This work is illustrated by a case study regarding Hepcidin gene publications over a decade, a duration that is sufficiently long enough to generate alternative views on the overall data extracted