Abstract: Formidable complexity of systemic human physiology often give rises of unintended effects of therapeutic compounds during the drug development processes or even after the drug approvals. Though the beneficial unintended effects could lead opportunities of repositioning drugs, the harmful effects might put critical hurdles against successful drug development. We have been developing a virtual human system, CODA, which can explore functional effects of therapeutic compounds in the systemic level. CODA integrates three types of physiological knowledge from public structured databases, literature, and in-house experiments into a unified format of physiological interactions. More than ten public databases including KEGG, GO, and CTD have been transformed; around 25 million PUBMED abstracts have been text-mined; and more than 5,000 in-house novel findings have been incorporated. We have also developed two types of analysis on the CODA knowledge repository. Given therapeutic compounds of interest, CODA can identify possible phenotypic effects in the systemic level. When therapeutic compounds and their observed functional effects are given, CODA can enumerate possible effect paths encompassing molecular, functional, and disease level interactions. We have been testing CODA by applying it to various tasks including drug repositioning, drug-drug interactions, and side effect prediction with known benchmark datasets. Though we are enriching CODA with more knowledge sources and more sophisticated analysis techniques, the current version is already providing unique analysis capabilities and one of the most comprehensive information for drug discovery.
Prof. Doheon Lee is Professor in the Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology and Director of Bio-Synergy National Research Center, Korea. He also serves as the President of Korean Society for Bioinformatics. Doheon Lee received the B.S., M.S., and Ph.D. degrees in computer science from Korea Advanced Institute of Science and Technology (KAIST), Korea, in 1990, 1992, and 1995, respectively. He was a visiting professor of Stanford University, Indiana University, Translational Genomics Research Institute (TGEN) and Univ. of Texas at Austin, USA. Currently, he is a professor in Department of Bio and Brain Engineering, KAIST, and the director of Bio-Synergy Research Center (BSRC), a Korean national project where over 30 principal investigators are collaborating for natural product bioinformatics and systems biology. He was an Associate Editor for ACM Transactions on Internet Technology for nine years. He is also serving Scientific Reports, International Journal of Data Mining in Bioinformatics, and Healthcare Informatics Research as an Editorial Board Member. He is a co-founder of ACM International Workshop on Data and Text Mining for Biomedical Informatics. He has published over 200 academic papers in bioinformatics, medical informatics, neuroinformatics, and data mining.