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From Alaa al Barari <alaa.albar...@gmail.com>
Subject Re: ctakes with icd10; 2015 versions available on sourceforge!
Date Tue, 08 Dec 2015 23:48:34 GMT
Thank you very very much Finan,

I am still very nooob to ctakes so please bare with me.

1- Could you please post detailed instructions on how you built the
dictionaries ? or give as much as you can examples on the steps ?
2- what did you upload exactly, I only see a script and properties files
what are those ? and what I need to change in c takes to make it work with
them. like how to get icd10 codes ?

I am sorry for being noob, hope soon I will understand the whole thing and
be effective.

Thanks in advance

On Wed, Dec 9, 2015 at 1:12 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi Dave,
>
> I'm always happy to see interest in our stuff!
>
> >Step 1
> I built the tool to be able to build a dictionary using anything in the
> umls - snomed, icd9, hpo, etc. so using the veterinary extension shouldn't
> be a problem.  You just add it to the CtakesSources file (or create an
> alternate file and point to it with -src).  To answer another of your
> questions, there can be zero or more sources - you saw snomedct and
> snomedct_us (each valid in a different umls version).
> It also can include any semantic type, just add (or remove) the
> appropriate tuis in a different data file.
>
> >Step 2
> You have it right - you copy the templates to another location and output
> to that location.  Otherwise you 'lose' your templates.
>
> >Step 3 and 4
> The jar is built from source.  I need to (soon) check in updates to the
> source, and at the same time I can check in a default prebuilt .jar  The
> lib/ directory is in the source repository.
>
> Various people have toyed with the idea of putting the tool into a ctakes
> module, putting it into an "installation package", making a gui ...  The
> best option (imo) is probably to make an easy to use gui and keep a
> pre-built version in sandbox.  Someday, after the rainbow, maybe I'll get a
> chance to do that ...
>
> Sean
>
>
> -----Original Message-----
> From: David Kincaid [mailto:kincaid.dave@gmail.com]
> Sent: Tuesday, December 08, 2015 4:57 PM
> To: dev@ctakes.apache.org
> Subject: Re: ctakes with icd10; 2015 versions available on sourceforge!
>
> 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> 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 :
> >
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_p_
> > ctakesresources_code_HEAD_tree_trunk_ctakes-2Dresources-2Dsnomed-2Drwo
> > rd-2Dhsqldb-2D2011ab_src_main_resources_org_apache_ctakes_dictionary_l
> > ookup_fast_ctakessnorx2015_&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZM
> > SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqwsl3Fm
> > uUXq77GmVlfXn0lE0pVRkL53DNhukcaW6c&s=kWCcj3-hcqYWZXIPhsERggDLCO-5gppCR
> > oS1Gav7r2A&e=
> >
> > The snomed rxnorm icd9 icd10:
> >
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_p_
> > ctakesresources_code_HEAD_tree_trunk_ctakes-2Dresources-2Dsnomed-2Drwo
> > rd-2Dhsqldb-2D2011ab_src_main_resources_org_apache_ctakes_dictionary_l
> > ookup_fast_ctakesicd2015_&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSd
> > ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqwsl3FmuU
> > Xq77GmVlfXn0lE0pVRkL53DNhukcaW6c&s=RZ--ZQ2qvGnhm4h2Vvz1oU97qA8BG2G39Tw
> > w7EdYgKA&e=
> >
> > 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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_
> > confluence_display_CTAKES_cTAKES-2B3.2-2B-2D-2BFast-2BDictionary-2BLoo
> > kup&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZ
> > stTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqwsl3FmuUXq77GmVlfXn0lE0pVRkL53
> > DNhukcaW6c&s=98W_vAHGZ2FLEMPfrSgEHtZt-mQ3XJjF6yQYM26tqP4&e=
> > 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
> > 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
> > 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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-- 
Eng Alaa Al-Barari
phone 0599297470

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