Courses/Tutorials/Workshps Using the i2b2 NLP Research DataSets

Clinical Information Extraction (IE) Course (2010-  )

Context:  “BMI 6115: Clinical Information Extraction” Graduate level Course at University of Utah School of Medicine; students learn about NLP in the clinical domain and develop a clinical information extraction application, as well as a reference standard of annotated clinical notes.

Developed by:  Stephane Meystre, MD, PhD, Assistant Professor of Biomedical Informatics, University of Utah with Wendy Chapman, PhD, UC San Diego, John Hurdle, MD, PhD and Oscar Ferrandez, PhD, U. Utah.

Link: stephane.meystre@hsc.utah.edu

Methods of Clinical NLP Course (2010-   )

Context: “BMI 6950: Methods of Clinical NLP” Graduate level Course at University of Utah School of Medicine; students adapt existing IE applications and compete for a simple clinical IE task.

Developed by:  John Hurdle, MD, PhD, Associate Professor of Biomedical Informatics, University of Utah with Stephane Meystre, MD, PhD and Qing Zeng, PhD, U. Utah.

Link: john.hurdle@utah.edu

Data Driven Medicine Course (2011-   )

Context:   Assignment for a new class in Stanford’s Biomedical Informatics Department: “BMI 215: Data Driven Medicine”.  Students are asked to participate in the “Obesity Challenge” by developing a completely new technique or by modifying a technique from one of the contest winners.

Developed by: Nigam Shah, PhD and Bethany Percha, Graduate Student and Teaching Assistant, Stanford University

Links: http://bmi215.stanford.edu;  blpercha@gmail.com

Text Annotation and NLP Application Development Workshop

Context:  2010 AMIA Now! Conference

Developed by: Stephane Meystre, PhD, Brett South, PhD, Scott Duvall, PhD and Shuying Shen, PhD, University of Utah.

Link: stephane.meystre@hs.utah.edu

NLP Tutorial (2011)

Context:  AMIA 2011 Annual Meeting; 75 reports from the 2009 Obesity Challenge were used and additionally annotated for new concepts of interest using Knowtator to generate the reference data

Developed by:  Brett South, PhD, University of Utah, Wendy Chapman, PhD, University of California San Diego and iDASH NCBC, Len D’Avolio, PhD,  

Link: Brett.South@hsc.utah.edu;

Next Generation Human Phenotyping (2010-   )

Context:  Graduate Course CPBS 7792 at University of Colorado School of Medicine

Developed by: Larry Hunter, PhD, Professor, U. Colorado School of Medicine

Link:  Larry.hunter@ucdenver.edu

Medical Informatics Text Mining (2010)

Context: Course

Developed by: Peter Wubbelt, PhD, Professor, University of Applied Sciences, Hannover, Germany.

Link:  Peter.Wuebbelt@fh-hannover.de

AMIA NLP Tutorial (2011)

Context: Tutorial at national meeting

Developed by:  Dina Demner-Fushman, Staff Scientist, NLM

Link:  ddemner@mail.nih.gov

Training graduate students and post docs in development of Information Extraction methods for PHI identification (2012).

Context:  General Training

Developed by: Marina Sokolova, PhD, Professor, University of Ottawa

Link: sokolova@uottawa.ca