Biomedical Text Mining and Its Applications

This tutorial is intended for biologists and computational biologists interested in adding text mining tools to their bioinformatics toolbox. As an illustrative example, the tutorial examines the relationship between progressive multifocal leukoencephalopathy (PML) and antibodies. Recent cases of PML have been associated to the administration of some monoclonal antibodies such as efalizumab [1]. Those interested in a further introduction to text mining may also want to read other reviews [2–4]. Understanding large amounts of text with the aid of a computer is harder than simply equipping a computer with a grammar and a dictionary. A computer, like a human, needs certain specialized knowledge in order to understand text. The scientific field that is dedicated to train computers with the right knowledge for this task (among other tasks) is called natural language processing (NLP). Biomedical text mining (henceforth, text mining) is the subfield that deals with text that comes from biology, medicine, and chemistry (henceforth, biomedical text). Another popular name is BioNLP, which some practitioners use as synonymous with text mining. Biomedical text is not a homogeneous realm [5]. Medical records are written differently from scientific articles, sequence annotations, or public health guidelines. Moreover, local dialects are not uncommon [6]. For example, medical centers develop their own jargons and laboratories create their idiosyncratic protein nomenclatures. This variability means, in practice, that text mining applications are tailored to specific types of text. In particular, for reasons of availability and cost, many are designed for scientific abstracts in English from Medline. Main Concepts