Gene name extraction using FlyBase resources

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Abstract
Machine-learning based entity extraction requires a large corpus of annotated training to achieve acceptable results. However, the cost of expert annotation of relevant data, coupled with issues of inter-annotator variability, makes it expensive and time-consuming to create the necessary corpora. We report here on a simple method for the automatic creation of large quantities of imperfect training data for a biological entity (gene or protein) extraction system. We used resources available in the FlyBase model organism database; these resources include a curated lists of genes and the articles from which the entries were drawn, together a synonym lexicon. We applied simple pattern matching to identify gene names in the associated abstracts and filtered these entities using the list of curated entries for the article. This process created a data set that could be used to train a simple Hidden Markov Model (HMM) entity tagger. The results from the HMM tagger were comparable to those reported by other groups (F-measure of 0.75). This method has the advantage of being rapidly transferable to new domains that have similar existing resources.

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