Tutorials

Tutorials are scheduled for Wednesday, March 10, 8:30 a.m. to 12:00 p.m.  Please click on the titles for detailed descriptions.

(T01) Introduction to Translational Bioinformatics
Atul Butte, Stanford University

AMIA recently added Translational Bioinformatics as one of its three major domains of informatics. This tutorial is designed around the successful curriculum used in Stanford's course in Translational Bioinformatics, one of the first courses to be offered in this field. This tutorial is designed to teach the basics of the various types of molecular data and methodologies currently used in bioinformatics and genomics research, and how these can interface with clinical data. This tutorial will address the hypotheses one can start with by integrating molecular biological data with clinical data, and will show how to implement systems to address these hypotheses. The tutorial will cover real-world case-studies of how genetic, genomics, and proteomic data has been integrated with clinical data.

(T02) Introduction to Natural Language Translational Bioinformatics
Leonard D'Avolio, VA Boston Healthcare System; Wendy Chapman, University of Pittsburgh; Dina Demner-Fushman, National Library of Medicine; John Pestian, Cincinnati Children’s Hospital

This half-day tutorial is designed to introduced clinicians and informaticians to the practice, tools, techniques, and science of clinical natural language processing. The tutorial will focus primary on clinical NLP, although related uses and methods such as literature-based NLP and text mining will be discussed to lend context. Topics covered include: an overview of clinical NLP and its uses in medicine; a brief history of clinical NLP and the evolution of NLP methods; the challenges to NLP; the number of approaches used to process natural language and the strengths and weaknesses of each; implementation considerations, creating annotated corpora as training / test sets, evaluation of NLP, and a review of open source tools for natural language processing. Demonstrations and in-class exercises will be used to help tie the theory of NLP to everyday research problems addressed by these technologies.

(T03) Ontologies in Biomedicine - CANCELLED

(T04) How to i2b2
Shawn Murphy, Massachusetts General Hospital, Griffin Weber, Harvard University, Isaac Kohane, Harvard Medical School, Guergana Savova, Mayo Clinic, Susanne Churchill, i2b2 National Center for Biomedical Computing

i2b2 is deployed across over 30 academic health centers. We summarize typical applications and use cases. We then describe a step by step approach to implementing i2b2 at your institution, writing new analytic "plugins" and leveraging advanced services such as natural language processing. We conclude with a roadmap for the near term and longer term i2b2 developments.