Novel Methods for Extracting Knowledge (for Precision Medicine) from Text

Tuesday, May 3, 2016 - 18:00
TH 331
Professor Russ Altman

We have been building a personalized medicine resource, the Pharmacogenomics Knowledgeable (PharmGKB, since 2000. PharmGKB is a manually curated collection of information about how human genetic variation impacts drug response. The task of curating the literature is expensive and challenging, and so we have embarked on a series of research projects to test the ability of modern natural language processing (NLP) algorithms to assist our curators in identifying and extracting information about genes, drugs, diseases and genetic variation. In this talk, I will review progress in this area, including some of the work that we are pursuing with collaborators at SFSU.


Russ Biagio Altman is a professor of bioengineering, genetics, & medicine (and of computer science, by courtesy) and past chairman of the Bioengineering Department at Stanford University. His primary research interests are in the application of computing and informatics technologies to problems relevant to medicine. He is particularly interested in methods for understanding drug action at molecular, cellular, organism and population levels. His lab studies how human genetic variation impacts drug response (e.g. Other work focuses on the analysis of biological molecules to understand the action, interaction and adverse events of drugs ( Dr. Altman holds an A.B. from Harvard College, and M.D. from Stanford Medical School, and a Ph.D. in Medical Information Sciences from Stanford. He received the U.S. Presidential Early Career Award for Scientists and Engineers and a National Science Foundation CAREER Award. He is a fellow of the American College of Physicians (ACP), the American College of Medical Informatics (ACMI), the American Institute of Medical and Biological Engineering (AIMBE), and the American Association for the Advancement of Science (AAAS). He is a member of the Institute of Medicine of the National Academies. He is a past-President, founding board member, and a Fellow of the International Society for Computational Biology (ISCB), and a past-President of the American Society for Clinical Pharmacology & Therapeutics (ASCPT). He has chaired the Science Board advising the FDA Commissioner, and currently serves on the NIH Director’s Advisory Committee. He is an organizer of the annual Pacific Symposium on Biocomputing (, and a founder of Personalis, Inc. Dr. Altman is board certified in Internal Medicine and in Clinical Informatics. He received the Stanford Medical School graduate teaching award in 2000, and mentorship award in 2014.