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From "Geise, Brandon D." <bdge...@geisinger.edu>
Subject RE: ctakes with icd10
Date Tue, 08 Dec 2015 17:50:49 GMT
Not to perpetuate the instructions again but I sent these out not long ago when I was going
through the process and Sean was helping me.

	1. Change /data/default/CtakesSources.txt from "SNOMEDCT" to "SNOMEDCT_US"
	2. Copy ctakesumls.properties and ctakesumls.script from memdbtemplate to location to put
new UMLS DB
	3. Run DictionaryCreator2
	java -cp dictionarytool.jar;lib/* org.apache.ctakes.dictionarytool.DictionaryCreator2 -umls
"\pathToUmls\META" -atui ./data/tiny/CtakesAnatTuis.txt -db jdbc:hsqldb:file:pathTonewDB\snorx2015
-tbl CUI_TERMS
	4. Run CodeMapCreator
	java -cp dictionarytool.jar;lib/* org.apache.ctakes.dictionarytool.CodeMapCreator -umls "\pathToUmls\META"
-atui ./data/tiny/CtakesAnatTuis.txt -db jdbc:hsqldb:file:pathTonewDB\snorx2015 -tbl CUI_TERMS
	5. Copy new DB files to new location and create a copy of cTakesHsql.xml and update dictionary
location

Thanks,
Brandon

-----Original Message-----
From: David Kincaid [mailto:kincaid.dave@gmail.com] 
Sent: Tuesday, December 08, 2015 12:47 PM
To: dev@ctakes.apache.org
Subject: Re: ctakes with icd10

This seems like a pretty common request and with such an old version of UMLS database shipped
with cTAKES it's only going to get worse. I've been wanting to build a dictionary using the
latest UMLS release (as well as a custom database), so would be happy to write up the steps
as I go through it. That assumes that I can dig up the instructions in the dev list.

- Dave

On Tue, Dec 8, 2015 at 11:36 AM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:

> Hi Alaa,
>
> The -shortest- answer is that you'll need to run the dictionary 
> creation tool.  There are instructions in older devlist threads.  By 
> default the dictionary creation tool does add icd9 and icd10 tables to the dictionary.
> The problem is that in Umls 2011AB those codes weren't very well 
> populated.  The 2015AB icd# set is much more rich so those tables 
> should be pretty good.  Then in ctakes you would look up annotations 
> by icd9 or icd10 codes instead of by cui:
> OntologyConceptUtil.getAnnotationsByCode( jcas, lookupWindow, icd#Code 
> ); OntologyConceptUtil.getAnnotationsByCode( jcas, icd#Code );
>
> Sean
>
> -----Original Message-----
> From: Savova, Guergana [mailto:Guergana.Savova@childrens.harvard.edu]
> Sent: Tuesday, December 08, 2015 12:17 PM
> To: dev@ctakes.apache.org
> Subject: RE: ctakes with icd10
>
> Hi Alaa,
> You need to create a resource off the terminology/ontology you want to 
> use (in this case ICD9 or ICD10). Then run that resource with cTAKES 
> for the fast dictionary lookup. There is cTAKES code and some 
> documentation on how to create that resource. By default, cTAKES runs 
> with a resource created from the English version of SNOMED CT and RxNORM.
> Hope this helps.
> --Guergana
>
> -----Original Message-----
> From: Alaa al Barari [mailto:alaa.albarari@gmail.com]
> Sent: Tuesday, December 8, 2015 10:01 AM
> To: dev@ctakes.apache.org
> Subject: ctakes with icd10
>
> Hi,
>
> I downloaded Latest umls version, and I want to know how to make 
> ctakes work with icd10 and icd9.
>
>
> Thanks
>


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