Famili, “Hierarchical Text Categorization as a Tool of Associating Genes with Gene Ontolog.pdf

Hierarchical Text Categorization as a Tool of Associating Genes with Gene Ontology Codes Svetlana Kiritchenko University of Ottawa P.O. Box 450 Stn A, Ottawa, Ontario K1N 6N5 Canada svkir@site.uottawa.ca Stan Matwin University of Ottawa P.O. Box 450 Stn A, Ottawa, Ontario K1N 6N5 Canada stan@site.uottawa.ca A. Fazel Famili IIT NRC 1200 Montreal Rd., Ottawa, Ontario K1A 0R6 Canada Fazel.Famili@nrc- cnrc.gc.ca ABSTRACT A great deal of genomics information accumulated through years is available nowadays in on-line text repositories such as Medline. These resources are essential for biomedical researchers in their everyday activities on planning and per- forming experiments and verifying the results. However, these resources do not still provide adequate mechanisms for retrieving the requisite information. We propose a new tool for assisting biologists with literature search for the task of associating genes with Gene Ontology codes. Unlike pre- vious research, we design the hierarchical text categoriza- tion framework to address this problem. The hierarchical approach helps visualize the results, address the scalability issue, improve classification accuracy and trade off between precision and recall. 1. INTRODUCTION In many genomics studies one of the major steps is the gene expression analysis using high-throughput DNA mi- croarrays. Measuring the expression profiles of genes from normal and disease tissues or from the same tissue exposed to different conditions can help discover genes responsible for the disease. It can also shed light on the functional- ity of previously unknown genes. Traditionally, most com- putational research on analyzing gene expression data has focused on working with microarray data alone, using sta- tistical or data mining tools. However, raw gene expression data are very hard to analyze even for an experienced sci- entist. On the other hand, there exists a wealth of infor- mation pertaining to the function and behavior of genes, described