Exploiting Big Data Semantics for Translational Medicine


March 25-26, 2013

Meeting Place

Indiana University Bloomington, Indiana Memorial Union


David Wild David Wild
Assistant Professor, IU School of Informatics and Computing
Director, IU Cheminformatics Program
Editor-in-Chief, Journal of Cheminformatics
CoPI, CICC / ChemBioGrid
PR^2 | Slides
Ying Ding Ying Ding
Associate Professor, Information Science, SLIS, Indiana University, Bloomington, IN
PR^2 | Slides
Katy Borner Katy Börner
Victor H. Yngve Professor of Information Science, SLIS, Indiana University
Director, Cyberinfrastructure for Network Science Center & Curator of Mapping Science exhibit, Bloomington, IN
PR^2 | Slides
Eric Gifford Eric Gifford

Workshop Goals & Agenda

There has recently been an explosion of public and proprietary healthcare and drug discovery data, and the development of powerful semantic, network and visualization technologies for integrating and mining these data, including the major E.U. sponsored OpenPHACTS project. These novel datasets and technologies open up many possibilities for drug discovery and translational medicine, including drug repurposing, target identification, gene-disease association and patient population mapping. In parallel, major efforts are underway such as the U.S. NCATS at NIH that support translational medicine and streamlined discovery of new medical therapies in the public sphere.

This small, focused workshop will bring together invited leading practitioners in semantic technologies, network science and visualization, and computational translational medicine to identify the most critical areas for collaboration between these fields to maximize impact on the next generation of disease treatments.

Monday, March 25, 2013
10:00am Student Meet Time - Indiana Memorial Union Persimmon Room
12:00pm Welcome by Organizers - Indiana Memorial Union Persimmon Room
12:15pm Introduction by Participants (5 min per person/organization)
2:30pm Break
3:00pm Overview Talks (Open for public)
Indiana Memorial Union, Dogwood Room

New opportunities for biomedical science and drug discovery using semantic technologies
Erik Schultes, Leiden University

New opportunities for biomedical science and drug discovery using semantic technologies
David Wild, Indiana University

Driving translational medicine through big data and ontologies
Nigam Shah, Stanford University

Open Code and Open Education: The Information Visualization MOOC
Katy Börner, Indiana University

5:00pm Break
5:30pm Discussion of Opportunities and Challenges
6:30pm Adjourn
7:00pm Joint dinner
The Irish Lion Restaurant & Pub
212 W Kirkwood Ave Bloomington, IN 47404

Tuesday, March 26, 2013


9:00am Light Breakfast - Indiana Memorial Union Persimmon Room
9:30am Breakout Session - Indiana Memorial Union Persimmon Room and Sassafras Room

Breakout Session Reports
[Session 1 | Session 2 | Session 3]

11:30am Second Best Ideas
12:30pm Joint Lunch
1:30pm Breakout Session

Breakout Session Reports
[Session 1 | Session 2]

3:00pm Break
3:15pm Financials for Horizontal and Vertical R&D Panel Discussion
4:00pm Collaboration and Funding Opportunities
5:00pm Adjourn

Invited Participants

Gary Berg-Cross Gary Berg-Cross
Executive Secretariat of the Spatial Ontology Community of Practice (SOCoP)
PR^2 | Slides
Christopher Chute Christopher Chute
Professor of Medical Informatics; Associate Professor of Epidemiology, Mayo Clinic
PR^2 | Slides
Michel Dumontier Michel Dumontier
Stanford University
PR^2 | Slides
Craig Eckert Craig Eckert
CEO of ChalkLabs
PR^2 | Slides
Rajarshi Guha Rajarshi Guha
Informatics Scientist, NIH Chemical Genomics Center
PR^2 | Slides
Peter Li Peter Li
Assistant Professor of Medical Informatics, Mayo Clinic
PR^2 | Slides
Erik Schultes

Erik Schultes
Leiden University

Nigam Shah

Nigam Shah
Assistant Professor of Medicine, Biomedical Informatics, Stanford Center for Biomedical Informatics Research
PR^2 | Slides

Amit Sheth

Amit Sheth
Professor: Computer Science & Engineering, Wright State University

Jeff Sutherland Jeff Sutherland
Eli Lilly
PR^2 | Slides

Valery Tkachenko Valery Tkachenko
CTO for RSC eScience

Tony Williams Antony Williams
VP Strategic Development, Head of Cheminformatics, Royal Society of Chemistry

Jeremy Yang

Jeremy Yang
Manager, Systems & Programming, University of New Mexico
PR^2 | Slides

Philip Yu Philip Yu
Professor and Wexler Chair in Information Technology, University of Illinois at Chicago
PR^2 | Slides

Interested but cannot attend

Vijay Bulusu Vijay Bulusu
Kay Connelly Kay Connelly
Associate Professor, Computer Science Department, Indiana University Bloomington, Co-director of CLEAR Health Information and Pervasive Health Information Technology (PHIT) Lab
Jon Duke Jon Duke
Research Scientist, Regenstrief Institute, Inc.; Assistant Professor Medicine, Indiana University School of Medicine
Paul Groth Paul Groth
Assistant Professor, VU University Amsterdam
Vasant Honavar Vasant Honavar
Professor of Computer Science, Iowa State University
Mic Lajiness Mic Lajiness
Eli Lilly
Barend Mons Barend Mons
Associate Professor, Bio-Semantics, Department of Medical Informatics, Erasmus Medical Centre, University of Rotterdam; Department of Human Genetics, Leiden University Medical Centre
Mark Musen Mark Musen
Professor of Medicine (Biomedical Informatics); Division Head (BMIR); Co-Director, Biomedical Informatics Training Program; Stanford Center for Biomedical Informatics Research
Tudor Oprea Tudor Oprea
Professor and Chief, Translational Informatics Division, Department of Internal Medicine at University of New Mexico
Dan Robertson Dan Robertson
Sr Director - LRL Research IT at Eli Lilly and Company
Mark Schreiber

Mark Schreiber
Associate Director of Knowledge Engineering at Novartis

Adam West Adam West
Eli Lilly

Maria Zemankova

Maria Zemankova
Program Director, National Science Foundation


Please contact Samantha Hale (sjhale@indiana.edu) with questions about travel.


See the contact page for the Cyberinfrastructure for Network Science Center, http://cns.slis.indiana.edu/contact.html or contact Samantha Hale (sjhale@indiana.edu)


This effort is supported by the James S. McDonnell Foundation and the Cyberinfrastructure for Network Science Center at Indiana University.