[BioNLP] AMIA workshop

Bob Futrelle bob.futrelle at gmail.com
Sat Oct 24 08:23:52 EDT 2009


Maybe Anni could answer these questions for all of us on the list.

 - Bob Futrelle
   BioNLP.org
   Northeastern University

On Fri, Oct 23, 2009 at 5:03 PM, Scott DuVall <Scott.DuVall at hsc.utah.edu>wrote:

>  I would like to attend this workshop, but have not found it on the AMIA
> program.  Is sign up required?  Is there a cost?
>
> Scott DuVall
>
> ------ Forwarded Message
>
> *From: *Anni R Coden <*anni at us.ibm.com*>
> *Reply-To: *Natural language processing for biology <*
> bionlp at lists.ccs.neu.edu*>
> *Date: *Fri, 23 Oct 2009 12:37:53 -0600
> *To: *<*bionlp at lists.ccs.neu.edu*>
> *Subject: *[BioNLP] AMIA 2009 - NLP Workshop - Second Announcement
>
> *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* <*http://www.ohnlp.org*> ) and donated their systems to
> open source.
>
> 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* <*http://
> www.eclipse.org/*> ) and UIMA (*http://incubator.apache.org/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
> USA
> Tel: (914) 784 7073 t/l 863 7073
> *anni at us.ibm.com
> *
>
> ------ End of Forwarded Message
>
>
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>
>
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