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:[email protected]]
Sent: Tuesday, December 08, 2015 12:47 PM
To: [email protected]
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 <
[email protected]> 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:[email protected]]
> Sent: Tuesday, December 08, 2015 12:17 PM
> To: [email protected]
> 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:[email protected]]
> Sent: Tuesday, December 8, 2015 10:01 AM
> To: [email protected]
> 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
>
IMPORTANT WARNING: The information in this message (and the documents attached
to it, if any) is confidential and may be legally privileged. It is intended
solely for the addressee. Access to this message by anyone else is
unauthorized. If you are not the intended recipient, any disclosure, copying,
distribution or any action taken, or omitted to be taken, in reliance on it is
prohibited and may be unlawful. If you have received this message in error,
please delete all electronic copies of this message (and the documents attached
to it, if any), destroy any hard copies you may have created and notify me
immediately by replying to this email. Thank you.
Geisinger Health System utilizes an encryption process to safeguard Protected
Health Information and other confidential data contained in external e-mail
messages. If email is encrypted, the recipient will receive an e-mail
instructing them to sign on to the Geisinger Health System Secure E-mail
Message Center to retrieve the encrypted e-mail.
