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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Fast Dictionary Update
Date Wed, 16 Sep 2015 20:00:13 GMT
Thank you!  I believe that was a change post 2011!  You should actually be ok with both SNOMEDCT
and SNOMEDCT_US in CtakesSources.txt

Cheers,
Sean

-----Original Message-----
From: Maite Meseure Hugues [mailto:meseure.maite@gmail.com] 
Sent: Wednesday, September 16, 2015 3:43 PM
To: dev@ctakes.apache.org
Subject: Re: Fast Dictionary Update

If this can helps, I had to replace 'SNOMEDCT' with 'SNOMEDCT_US' in CtakesSources.txt.

On Wed, Sep 16, 2015 at 2:33 PM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:

> I'm not sure that I understand your question.  As I sent it, the anat, 
> snomed and rxnorm are not separate runs.  The args line I sent earlier 
> is for a single run that will create a dictionary with snomed and 
> rxnorm terms.  The anatomy tui list has a special use in correctly 
> processing snomed codes.
>
> -----Original Message-----
> From: Geise, Brandon D. [mailto:bdgeise@geisinger.edu]
> Sent: Wednesday, September 16, 2015 3:27 PM
> To: dev@ctakes.apache.org
> Subject: RE: Fast Dictionary Update
>
> Ok, hopefully one last question.
>
> Based on your example everything runs, however the Anat and Snomed 
> runs don't produce any valid CUIs but RXNorm does.  I'm not sure if 
> this has anything to do with it but every UMLS source read is against MRSTY.
>
> Here's my command
>
> java -cp dictionarytool.jar;lib/*
> org.apache.ctakes.dictionarytool.DictionaryCreator2 -umls 
> /path/to/UMLS/META -fd ./data/tiny -atui 
> ./data/tiny/CtakesAnatTuis.txt -tui ./data/tiny/CtakesSnomedTuis.txt 
> -ol \path\to\file\Umls2015.bsv
>
> Any suggestions?
>
> Thanks again,
> Brandon
>
>
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Wednesday, September 16, 2015 3:05 PM
> To: dev@ctakes.apache.org
> Subject: RE: Fast Dictionary Update
>
> Yes, that will make the rare word dictionary in a memory-based hsql 
> database - the same as the default for the dictionary-lookup-fast module.
>
> -----Original Message-----
> From: Geise, Brandon D. [mailto:bdgeise@geisinger.edu]
> Sent: Wednesday, September 16, 2015 2:42 PM
> To: dev@ctakes.apache.org
> Subject: RE: Fast Dictionary Update
>
> Thanks Sean, much appreciated.  To clarify the example below would 
> create the dictionary for use for the rare word approach?
>
> Thanks,
> Brandon
>
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Wednesday, September 16, 2015 2:16 PM
> To: dev@ctakes.apache.org
> Subject: RE: Fast Dictionary Update
>
> Hi Brandon,
>
> I just checked in a bin/dictionarytool.zip It should have everything 
> that you need (.jar, lib/, data/).
> java -cp dictionarytool.jar;lib/*
> org.apache.ctakes.dictionarytool.DictionaryCreator2 [args] Should do 
> the trick.
>
> To recreate a 2015 version of the current ctakes dictionary, the 
> arguments
> are:
> -umls my/path/to/2015AA/META -fd ./data/tiny -atui 
> ./data/tiny/CtakesAnatTuis.txt -tui ./data/tiny/CtakesSnomedTuis.txt 
> -db
> jdbc:hsqldb:file:my/path/to/snorx2015 -tbl CUI_TERMS
>
> Create my/path/to/snorx2015 by copying 
> resources/memdbtemplate/ctakesumls.properties to
> my/path/to/snorx2015.properties   - there is a resources/README about this.
>
> Before populating a DB, I usually do a trial run first, writing to a 
> flat file.  Replace "-db ... -tbl ..." with "-ol my/path/to/testout.bsv"
>
>
> Sean
>
> -----Original Message-----
> From: Geise, Brandon D. [mailto:bdgeise@geisinger.edu]
> Sent: Wednesday, September 16, 2015 1:49 PM
> To: dev@ctakes.apache.org
> Subject: RE: Fast Dictionary Update
>
> Hi Sean,
>
> That'd be great.
>
> I think I'm building it incorrectly because after I build the jar and 
> try to run specifying DictionaryCreator2 as the main class it says it 
> can't find it.  I'm not too familiar with Java and building 
> projects/jars so it could be my ignorance causing the problem.
>
> Thanks,
> Brandon
>
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Wednesday, September 16, 2015 1:45 PM
> To: dev@ctakes.apache.org
> Subject: RE: Fast Dictionary Update
>
> Hi Brandon,
>
> I can send you a jar or commit one pre-built.  What goes wrong when 
> you try to build the tool?
>
> Sean
>
> -----Original Message-----
> From: Geise, Brandon D. [mailto:bdgeise@geisinger.edu]
> Sent: Wednesday, September 16, 2015 1:23 PM
> To: 'dev@ctakes.apache.org'
> Subject: Fast Dictionary Update
>
> Does someone have the DictionaryTool jar available?  I'm having 
> trouble creating the jar file from the project and would like to be 
> able to create an updated UMLS fast dictionary for 2015.
>
> Thanks,
> Brandon
>
>
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