[BioNLP] AMIA 2009 - NLP Workshop - Second Announcement

Anni R Coden anni at us.ibm.com
Fri Oct 23 14:37:53 EDT 2009

Unleash the Knowledge from your Unstructured Clinical Text
IBM and Mayo Clinic jointly present the Open Health NLP Consortium
Anni Coden (IBM, T.J. Watson Research), James Masanz and Guergana Savova 
(Mayo Clinic) medNLP at us.ibm .com and clinicalnlp at mayo.edu
AMIA Annual Symposium - Sunday 11/15/2009 at 5:30pm in room Yosemite C
As an increasing percentage of health care and academic medical centers 
adopt electronic medical records, searching and extracting information 
from them in an automated fashion becomes essential. IBM and Mayo Clinic 
jointly developed a system for extracting information from more than 25 
million free-text clinical notes and pathology reports based on IBM's 
open-source Unstructured Information Management Architecture (UIMA), an 
OASIS standard. As part of the system, developers put together series of 
"annotators" creating a pipeline, allowing physicians to mine the text for 
references of specific conditions, drugs, diseases, signs and symptoms, 
anatomical areas or organs, cancer disease characteristics, cancer staging 
or treatment procedures. With the goal of promoting past and current 
development efforts and to encourage participation in advancing future 
efforts in this area, IBM and Mayo Clinic founded the Open Health Natural 
Language Consortium (www.ohnlp.org) and donated their systems to open 
The focus of this workshop is to describe the various open source 
components in more detail with an emphasis on how to deploy them in your 
institution and how to adapt them to different types of clinical reports 
(e.g. clinical notes, pathology notes, radiology notes, discharge 
summaries). The open source components address lexical, syntactic and 
semantic analysis and their adaptation both to the clinical domain and to 
the type of report. Several dictionary lookup methodologies will be 
discussed, as well as dictionary development and negation detection. An 
implementation of relationship extraction will be shared. The formal 
presentation will conclude with a discussion on how to execute an NLP 
system within an institutional system and how to become an active member 
of the consortium.
The second part will be “hands-on” – so, if you are interested, bring your 
laptop and install Eclipse (http://www.eclipse.org) and UIMA (
http://incubator.apache.org/uima/) on it. We will walk through examples of 
code and complete “pipelines” and address any particular development 
questions you may encounter. 
Please e-mail us with any questions and suggestions. It would be helpful 
if you could indicate whether you are planning to attend, however, an RSVP 
is not required!

Hope to see you there!

Dr. Anni R. Coden
Manager, Medical Text and Image Analysis
IBM T.J. Watson Research Center
19 Skyline Drive
P.O. Box 704
Hawthorne, NY 10532
Tel: (914) 784 7073 t/l 863 7073
anni at us.ibm.com
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