Bio-medical entity extraction using support vector machines

Objective: Support vector machines (SVMs) have achieved state-of-the-art performance in several classification tasks. In this article we apply them to the identification and semantic annotation of scientific and technical terminology in the domain of molecular biology. This illustrates the extensibility of the traditional named entity task to special domains with large-scale terminologies such as those in medicine and related disciplines. Methods and materials: The foundation for the model is a sample of text annotated by a domain expert according to an ontology of concepts, properties and relations. The model then learns to annotate unseen terms in new texts and contexts. The results can be used for a variety of intelligent language processing applications. We illustrate SVMs capabilities using a sample of 100 journal abstracts texts taken from the {human, blood cell, transcription factor} domain of MEDLINE. Results: Approximately 3400 terms are annotated and the model performs at about 74% F-score on cross-validation tests. A detailed analysis based on empirical evidence shows the contribution of various feature sets to performance. Conclusion: Our experiments indicate a relationship between feature window size and the amount of training data and that a combination of surface words, orthographic features and head noun features achieve the best performance among the feature sets tested.