Finding Gene Names

Successful use of text mining algorithms to facilitate genomics research hinges on the ability to recognize the names of genes in scientific text. In this chapter we address the critical issue of gene name recognition. Once gene names can be recognized in the scientific text, we can begin to understand what the text says about those genes. This is a much more challenging issue than one might appreciate at first glance. Gene names can be inconsistent and confusing; automated gene name recognition efforts have therfore turned out to be quite challenging to implement with high accuracy. Gene name recognition algorithms have a wide range of useful applications. Until this chapter we have been avoiding this issue and have been using only gene-article indices. In practice these indices are manually assembled. Gene name recognition algorithms offer the possibility of automating and expediting the laborious task of building reference indices. Article indices can be built that associate articles to genes based on whether or not the article mentions the gene by name. In addition, gene name recognition is the first step in doing more detailed sentence-by-sentence text analysis. For example, in Chapter 10 we will talk about identifying relationships between genes from text. Frequently, this requires identifying sentences refering to two gene names, and understanding what sort of relationship the sentence is describing between these genes. Sophisticated natural language processing techniques to parse sentences and understand gene function cannot be done in a meaningful way without recognizing where the gene names are in the first place. The major concepts of this chapter are presented in the frame box. We begin by describing the commonly used strategies that can be used alone or in concert to identify gene names. At the end of the chapter we introduce one successful name finding algorithm that combines many of the different strategies. There are several commonly used approaches that can be exploited to recognize gene names in text (Chang, Shutze, et al. 2004). Often times these approaches can be combined into even more effective multifaceted algorithms.