[Corpora-List] Second Call for Participation

[Ozlem Uzuner]

           Announcement of Data Release and Second Call for Participation

                     Second i2b2 Shared-Task and Workshop
         Challenges in Natural Language Processing for Clinical Data
        Obesity Challenge (A Shared-Task on Obesity): Who's obese and what
 		co-morbidities do they (definitely/likely) have?

                         Data Release: 15 March, 2008
                         Evaluation: 23-25 June, 2008
                     Paper Submission: 1 September, 2008
                 Workshop: 7 November, 2008 in Washington, DC

 	Organizer: Informatics for Integrating Biology and the Bedside,
 		i2b2, a National Center for Biomedical Computing
 			Website: https://www.i2b2.org/NLP

The obesity challenge is a multi-class, multi-label classification task 
focused on obesity and its co-morbidities. The data for the challenge 
consist of discharge summaries from Partners Healthcare. All records have 
been fully de-identified. Obesity information and co-morbidities have been 
marked at a document level as present, absent, questionable, or 
unmentioned in the documents. For each patient, both textual judgments, 
i.e., what the text explicitly states about obesity and co-morbidities, 
and intuitive judgments, i.e., what the text implies about obesity and 
co-morbidities, are provided. The goal of the challenge is to evaluate 
systems on their ability to recognize whether a patient is obese and what 
co-morbidities they exhibit.

The obesity challenge opened to preregistration on February 1, 2008. 
Training data for the challenge will be released in installments; the 
first installment will be released on March 15, 2008. The rest of the 
installments will follow soon after. Test data are scheduled to be 
released for only three days and will be used only for evaluation 
purposes. The results of the challenge will be presented at the workshop 
organized by i2b2.

Evaluation Dates, File Formats, and Evaluation Metrics.

The obesity challenge evaluation will be on only the test data. Each team 
is allowed to upload up to three system runs. System output is expected in 
the form of standoff annotations, following the exact format of the ground 
truth annotations provided by i2b2. Precision, recall, and f-measure will 
be used as evaluation metrics.

Participants are asked to submit a short paper describing their system and 
analyzing their performance. Authors of top performing systems and of 
particularly novel approaches will be invited to present or demo their 
systems at the workshop.

Tentative Schedule
February 1, 2008    Preregistration Open
March 15, 2008    Training Data Release
April 15, 2008    Commitment to Participate in Challenge
June 23, 2008    Test Data Release at 9am EST
June 25, 2008    Output Due at Midnight EST
August 1, 2008    Notification of Results to Each Participant
September 1, 2008    Short Papers Due
October 1, 2008    Invitations to Present at the Workshop
November 7, 2008    Workshop

Organizing Committee:
Ozlem Uzuner, Chair, SUNY at Albany and Middle East Technical University North Cyprus Campus
Peter Szolovits, MIT CSAIL
Isaac Kohane, Partners Healthcare

Questions on the challenge can be addressed to Ozlem Uzuner, 
i2b2nlp at albany.edu.

 
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