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From "Geise, Brandon D." <bdge...@geisinger.edu>
Subject Re: ctakes with icd10; 2015 versions available on sourceforge!
Date Tue, 08 Dec 2015 22:17:03 GMT
Hi David,

For step 1 the file may have been updated. At the time I wrote the instructions only SNOMED
was listed in the file.

For step 2 yes, this is a new directory location where the new dictionary will be created.

Yes you need to build or use the one Sean built and has in the repo.

Sorry the instructions aren't clear. They seemed to make sense when I wrote them at the time.

Hope that helps,
Brandon


_____________________________
From: David Kincaid <kincaid.dave@gmail.com<mailto:kincaid.dave@gmail.com>>
Sent: Tuesday, December 8, 2015 4:57 PM
Subject: Re: ctakes with icd10; 2015 versions available on sourceforge!
To: <dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>>


Thanks, Sean! It's great that cTAKES may soon have an up to date database
out of the box. Hopefully it will cut down on the need for many to build
their own DB's. Thank you much for doing that.

Unfortunately, I still will need to build a custom one for us. I work in
veterinary medicine so I need to add in the veterinary extension for
SNOMED-CT into the database.

I looked over the steps below that Brandon included and have some questions:

step 1 says to "Change /data/default/CtakesSources.txt from "SNOMEDCT" to
"SNOMEDCT_US". The file that I have has two lines in it. First line is
SNOMED, second line is SNOMEDCT_US. So this step doesn't really make sense.

step 2 should reference the two scripts as being in resource/memdbtemplate
so others don't have to search for them. Not sure what it means to move
them to "location to put new UMLS DB". Does that mean move them into a new
directory where the newly created UMLS DB will get written?

steps 3 and 4 for running the tools reference dictionarytool.jar which
doesn't exist. Does one need to build that somehow from the source before
running it? The command line also adds "lib/*" to the classpath. Is that
the lib directory inside the dictionarytool source code or some other
location?

What else would I need to do to include the SNOMED-CT Veterinary Extension
along with the snomedct and rxnorm sources?

I'll probably not have time to try this out for a while yet, but when I do
I'd be happy to write up an easy to follow tutorial for building a custom
dictionary assuming I am able to get it to work.

Has anyone considered making this tool available outside of the source code
itself? Like including it in the main cTAKES release? It seems there is
demand for it.

- Dave

On Tue, Dec 8, 2015 at 3:22 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.harvard.edu>> wrote:

> Hi Brandon, thanks for finding and forwarding the instructions!
>
> I have checked in two new hsqldb dictionaries, both from the 2015AB
> version of the UMLS. They both have codes for snomedct_us, rxnorm, icd9cm
> and icd10pcs - as well as the usual cui, tui, preferred term mappings.
>
> One uses cuis filtered by snomed and rxnorm, the other adds cuis filtered
> by icd9 and icd10.
> What this means: Cuis that exist for a [filter source] are added to the
> dictionary, as are all text variations from all sources that contain that
> cui. Both dictionaries also use the standard ctakes semantic group tui
> filters.
>
> The names are ctakessnorx2015 and ctakesicd2015
>
> The snomed rxnorm :
>
> http://sourceforge.net/p/ctakesresources/code/HEAD/tree/trunk/ctakes-resources-snomed-rword-hsqldb-2011ab/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/ctakessnorx2015/
>
> The snomed rxnorm icd9 icd10:
>
> http://sourceforge.net/p/ctakesresources/code/HEAD/tree/trunk/ctakes-resources-snomed-rword-hsqldb-2011ab/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/ctakesicd2015/
>
> The svn root for the whole ugly thing is:
> svn checkout svn://svn.code.sf.net/p/ctakesresources/code/trunk
>
> Stats:
> ctakessnorx2015
> 545,913 Terms
> 229,251 Concepts (Cuis)
> 272,987 Snomed codes
> 32,419 Rxnorm codes
> 11,321 icd9 codes
> 61 icd10 codes
>
> Ctakesicd2015
> 611,230 Terms
> 282,211 Concepts
> 18,626 icd9 codes
> 45,818 icd10 codes
> Snomed and Rxnorm counts are the same
>
> So, adding the icd filters gave us an extra ~53,000 concepts and ~65,000
> terms.
>
> I would like to move this all to a better root (not
> ctakes-resources-snomed-rword-hsqldb-2011ab) but I wasn't able to write
> directly in trunk (??) and need to get moving on to other things.
>
> There is help on the ctakes wiki:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+-+Fast+Dictionary+Lookup
> Though I should probably add a few items ...
>
>
> Sean
>
>
> -----Original Message-----
> From: Geise, Brandon D. [mailto:bdgeise@geisinger.edu]
> Sent: Tuesday, December 08, 2015 12:51 PM
> To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>
> Subject: RE: ctakes with icd10
>
> 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<mailto: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<mailto: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<mailto: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<mailto: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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