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From "Mattmann, Chris A (3980)" <chris.a.mattm...@jpl.nasa.gov>
Subject Re: How to update cTAKES so that new top level categories come out based on local dictionary?
Date Tue, 06 Oct 2015 20:31:04 GMT
Hi Sean,

Thanks so much for your reply. For now I don’t care about the secondary
codes and I for sure have < 1000 terms. Can you tell me how to wire up
the BSV file by editing specific places in cTAKES? What specific commands
should I run or what format should the BSV file look like? I must admit
I have never heard of BSV files and the Internet varies on these between
Bluespec System Verilog and BASIC bsave files.

Then after I make the BSV file, what steps next? Recompile cTAKES? Can
I take the BSV file and simply point to it from a binary installation of
cTAKES? Thank you!

Cheers,
Chris

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Chris Mattmann, Ph.D.
Chief Architect
Instrument Software and Science Data Systems Section (398)
NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
Office: 168-519, Mailstop: 168-527
Email: chris.a.mattmann@nasa.gov
WWW:  http://sunset.usc.edu/~mattmann/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Adjunct Associate Professor, Computer Science Department
University of Southern California, Los Angeles, CA 90089 USA
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++





-----Original Message-----
From: "Finan, Sean" <Sean.Finan@childrens.harvard.edu>
Reply-To: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
Date: Tuesday, October 6, 2015 at 8:05 AM
To: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
Subject: RE: How to update cTAKES so that new top level categories come
out based on local dictionary?

>Hi Chris,
>
>There are a few ways to do this:
>1.  Create an additional dictionary with the terms of interest and add it
>as a source
>2.  Create a new dictionary hsqldb that contains everything, old and new
>3.  Add to the existing hsqldb dictionary
>
>The best approach for you would probably depend upon
>1.  How many new terms you have
>2.  Whether or not you desire additional codes, i.e. rxnorm, snomed
>
>If you don't have many new terms (<1000) and you don't care about
>secondary codes then the easiest thing would be to create a BSV file with
>the new terms and cuis.
>
>If you have a lot of new terms or do care about secondary codes, then a
>less facile solution would be to create a new hsqldb with only the new
>info or a complete replacement with new and old/existing terms.  Of the
>two hsql options creating a new all-inclusive database would probably be
>easier unless you want to learn the ins and outs of hsql.  If all of the
>terms are in the umls, then the new all-inclusive hsqldb would definitely
>be easiest (I think) as you could use the dictionary tool to create it.
>
>If you let me know your exact situation then I may be able to better
>expound.
>
>Sean
>
>-----Original Message-----
>From: Mattmann, Chris A (3980) [mailto:chris.a.mattmann@jpl.nasa.gov]
>Sent: Monday, October 05, 2015 7:36 PM
>To: dev@ctakes.apache.org
>Subject: How to update cTAKES so that new top level categories come out
>based on local dictionary?
>
>Hi cTAKES team,
>
>
>
>Hope you’re well! I had a quick question. I was wondering if someone
>
>could provide me a step-by-step guide to updating cTAKES to be based
>
>off a local dictionary, so that in addition to e.g.,
>
>
>
>ProceduralMention
>
>  Value1 position etc
>
>  Value2 position etc
>
>
>
>MedicationMention
>
>  Value1 position etc
>
>  Value2 position etc
>
>
>
>
>
>NewTopLevelCategoryFromMyDictionary
>
>  FoundValue1 position etc
>
>  FoundValue2 position etc
>
>
>
>
>
>I realize this has something to do with updating the annotation
>
>descriptions etc in XML, so if I someone just could tell me what
>
>to update I’d really appreciate it.
>
>
>
>Thank you!
>
>
>
>Cheers,
>
>Chris
>
>
>
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>Chris Mattmann, Ph.D.
>
>Chief Architect
>
>Instrument Software and Science Data Systems Section (398)
>
>NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
>
>Office: 168-519, Mailstop: 168-527
>
>Email: chris.a.mattmann@nasa.gov
>
>WWW:  
>https://urldefense.proofpoint.com/v2/url?u=http-3A__sunset.usc.edu_-7Ematt
>mann_&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZst
>TpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=MEZE0aOE5pBHul1QA3A9xWbiwS6LzZaIq2rMw9a
>jiB0&s=cvi79MY1__guvBRsQmsYfc39lqPvv-1Yx1Pg8g5B0QU&e=
>
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>Adjunct Associate Professor, Computer Science Department
>
>University of Southern California, Los Angeles, CA 90089 USA
>
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>
>
>
>

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