Chapter 5 AN APPLICATION OF ONTOLOGY-BASED DATA INTEGRATION FOR BIOMEDICAL RESEARCH Vipul Kashyap 1 , Kei-Hoi Cheung 2 , Donald Doherty 3 , Matthias Samwald 4 , M. Scott Marshall 5 , Joanne Luciano 6 , Susie Stephens 7 , Ivan Herman 8 and Raymond Hookway 9 1 Partners Healthcare System, Clinical Informatics R&D, 93 Worcester St, Suite 201, Welleley, MA, USA – vkashyap1@partners.org 2 Yale Center for Medical Informatics, Yale University School of Medicine, 300 George Street, Suite 501, New Haven, CT, USA – kei.cheung@yale.edu 3 Brainstage Research, 5001 Baum Blvd, Suite 725, Pittsburgh, PA,USA – donald.doherty@brainstage.com 4 Medical Expert and Knowledge Based Systems, Medical University of Vienna,Spitalgasse 23 A-1090, Vienna, Austria – matthias.samwald@meduniwien.ac.at 5 University of Amsterdam, Gersthove 41, 1112 HN Diemen, The Netherlands – marshall@science.uva.nl 6 Department of Genetics, Harvard Medical School, NRB Room 238, 77 Louis Pasteur Ave, Boston, MA 02115, USA – jluciano@gmail.com 7 Oracle Corporation, 10 Van de Graaf Drive, Burlington, MA, USA – susie.stephens@oracle.com 8 World Wide Web Consortium (W3C),c/o Centrum voor Wiskunde en Informatica, Kruislaan 413, 1098 SJ, Amsterdam, The Netherlands – ivan@w3.org 9 Hewlett Packard, Marlborough, USA. 1. INTRODUCTION The healthcare and life sciences sector is playing host to a battery of innovations triggered by the sequencing of the human genome as well as genomes of other organisms. A significant area of innovative activity is that of translational medicine which aims to improve the communication between basic and clinical science so that more diagnostic and therapeutic