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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: ctakes with icd10; 2015 versions available on sourceforge!
Date Fri, 11 Dec 2015 05:11:43 GMT
Hi Alaa,

Sorry for the late reply, I'll try to get you something a little more useful in the next few
days.

Sean

-----Original Message-----
From: Alaa al Barari [mailto:alaa.albarari@gmail.com] 
Sent: Thursday, December 10, 2015 12:27 PM
To: dev@ctakes.apache.org
Subject: Re: ctakes with icd10; 2015 versions available on sourceforge!

I am really thankful.

I believe the issue is in here    static public void writeCuiCodes( final
String termFilePath,
                                     final Map<String, Map<String, Collection<String>>>
cuiCodes ) {
      final List<String> codeSources = Arrays.asList( "ICD10PCS", "ICD9CM", "RXNORM",
"SNOMEDCT" );



On Thu, Dec 10, 2015 at 7:02 PM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:

> Hi Alaa,
>
> No worries, it can be pretty confusing.
>
> 1  The tool is a prototype hack.  So, it is in the svn sandbox 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_re
> pos_asf_ctakes_sandbox_dictionarytool&d=BQIBaQ&c=qS4goWBT7poplM69zy_3x
> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m
> =wBMbFil3i5cO-Hj7So0Rfeh7-Npz3u-btUXhUDQN1T0&s=146RtcAn3FCAHFfaBKzLD4r
> bCpXrMPtO-jh4jo6AfI8&e=
>
> 2  I think that you should be able to add "icd10cm" as a line in your 
> CtakesSources.txt data file.  But I should probably test it myself 
> before you waste any time on it.  If a change to the code is required 
> I can take care of it.  I will try to get to it ~10:pm eastern time.
>
> 3  The lines that you are seeing look perfect.
>
> 4  The tuis inside CtakesAnatTui.txt are the codes for the semantic 
> types that comprise the "Anatomical Site" semantic group in ctakes.  
> You should never need to change the file, but you do need to point to it.
>
> 5  Unfortunately there isn't any real documentation, just help emails 
> from myself and others on the devlist.  As I said, it is a prototype 
> and not an official tool or part of the ctakes release.
>
> Sean
>
>
>
> -----Original Message-----
> From: Alaa al Barari [mailto:alaa.albarari@gmail.com]
> Sent: Thursday, December 10, 2015 10:38 AM
> To: dev@ctakes.apache.org
> Subject: Re: ctakes with icd10; 2015 versions available on sourceforge!
>
> Hi Finan,
>
> I am sorry if I am asking too much but I am really stuck ...
>
> 1- could you please give me a link where I can download the latest 
> version of dictionarytool
> 2- The current version I have always produce for icd10pcs although I 
> have in the -src file icd10CM,  icd10pcs is statically added inside 
> dictionarytool ?  if I changed from within the code it should work ?
> 3- after running the tool lines like below are added to the .script 
> file am i on the right track ?
> INSERT INTO CUI_TERMS VALUES(20417,1,2,'hyoid bones','bones') INSERT 
> INTO CUI_TERMS VALUES(20417,0,2,'os hyoideum','os')
>
> 4- as naive as this sound but what is tui insides CtakesAnatTuis.txt?
>
> 5- any documentation you advice to read ?
>
>
> On Thu, Dec 10, 2015 at 10:37 AM, Alaa al Barari 
> <alaa.albarari@gmail.com>
> wrote:
>
> > Finan, from where to download the 2015. properties from sourceforg.
> > those all ICDs and snowmed ?
> >
> > I prefer to learn how to generate my own db because I will need to 
> > create my own later on, so your help is appreciated.
> >
> > On Thu, Dec 10, 2015 at 9:13 AM, Alaa al Barari 
> > <alaa.albarari@gmail.com>
> > wrote:
> >
> >> Thank, but what I endup with is
> >> wrong ?
> >> On Dec 10, 2015 4:26 AM, "Finan, Sean"
> >> <Sean.Finan@childrens.harvard.edu>
> >> wrote:
> >>
> >>> Hi Alaa,
> >>>
> >>> If you downloaded the 2015 .property and .script files then you do 
> >>> not need to run the dictionary creation tool.  Those databases are 
> >>> already populated and ready to use.
> >>>
> >>> Sean
> >>>
> >>>
> >>> -----Original Message-----
> >>> From: Alaa al Barari [mailto:alaa.albarari@gmail.com]
> >>> Sent: Wednesday, December 09, 2015 6:33 PM
> >>> To: dev@ctakes.apache.org
> >>> Subject: Re: ctakes with icd10; 2015 versions available on sourceforge!
> >>>
> >>> so basically looks like the path had Desktop as capital thats why 
> >>> it did not work.
> >>>
> >>> I ended up having rows like this inside ctakesicd2015.scripts :
> >>>
> >>> INSERT INTO CUI_TERMS VALUES(2723481,8,15,'magnesium sulfate 1000 
> >>> mg /
> >>> 50 ml - nacl 0 . 9 % intravenous solution','nacl') INSERT INTO 
> >>> CUI_TERMS VALUES(2723481,9,16,'magnesium sulfate , 2 g / 100 ml
> >>> - nacl 0 . 9 % intravenous solution','nacl') INSERT INTO CUI_TERMS 
> >>> VALUES(2723481,0,7,'magnesium sulfate 20 mg / ml
> >>> injection','magnesium')
> >>>
> >>>
> >>> does this mean it worked ?
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Thu, Dec 10, 2015 at 1:07 AM, Alaa al Barari 
> >>> <alaa.albarari@gmail.com
> >>> >
> >>> wrote:
> >>>
> >>> > Thanks Finan and Brandon, your help is appreciated a lot.
> >>> >
> >>> > I downloaded the dictionary tool from 
> >>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.
> >>> > or
> >>> > g_re
> >>> > pos_asf_ctakes_sandbox_dictionarytool_bin_dictionarytool.zip&d=B
> >>> > QI
> >>> > BaQ&
> >>> > c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIi
> >>> > sC
> >>> > YNYm
> >>> > QCP6r0bcpKGd4f7d4gTao&m=uJq_3OpLiUaBOz9vqxKBI-gUAtLhJMme9uKXqroH
> >>> > hM M&s= JVOlLM08gTn5rV2T3R_bqeZT8XbMDgLhfKg8Fo5mAQw&e=
> >>> > I hope its the latest and bug free.
> >>> >
> >>> >
> >>> > my running command is : java -cp ./dictionarytool.jar:lib/*
> >>> > org.apache.ctakes.dictionarytool.DictionaryCreator2 -umls 
> >>> > /home/abarari/Desktop/umls/2015AB/META/ -atui 
> >>> > ./data/optional/CtakesAnatTuis.txt -db 
> >>> > jdbc:hsqldb:file:/home/abarari/Desktop/dictionarytool/output/cta
> >>> > ke
> >>> > sicd
> >>> > 2015 -tbl CUI_TERMS -df ./data/optional/ -src 
> >>> > ./data/small/ConversionSources.txt
> >>> > -tui ./data/optional/CtakesAllTuis.txt
> >>> >
> >>> >
> >>> >
> >>> > I am running on ubuntu by the way ... anyway under 
> >>> > /home/abarari/Desktop/dictionarytool/output/
> >>> >
> >>> > there is only
> >>> >
> >>> >  abarari@ubuntu:~/Desktop/dictionarytool/output$ ls 
> >>> > ctakesicd2015.log ctakesicd2015.properties  ctakesicd2015.script
> >>> >
> >>> >
> >>> > where is the database ? am I doing something wrong ? do I need 
> >>> > to create the database before executing the dictionarytool or what
?
> >>> >
> >>> >
> >>> > I found couple of issues in the dictionary tool, it does not 
> >>> > work well with relative paths.
> >>> >
> >>> >
> >>> > On Wed, Dec 9, 2015 at 7:11 AM, Pei Chen <chenpei@apache.org>
wrote:
> >>> >
> >>> >> Brandon,
> >>> >> That sounds great!
> >>> >> Please open a Jira ticket for any contributions (anyone should

> >>> >> be able to create a Jira account).  There are some legal items

> >>> >> built into the ASF Jira attachments for accepting contributions/donations.
> >>> >> It will also credit the contributors with the merit appropriately.
> >>> >> Anyone who is interested can follow the Jira item. (Even better

> >>> >> if contributions were open discussion/open development.) --Pei
> >>> >>
> >>> >> On Tue, Dec 8, 2015 at 10:36 PM, Geise, Brandon D.
> >>> >> <bdgeise@geisinger.edu> wrote:
> >>> >> > I'd be interested in contributing to making the dictionary

> >>> >> > tool more
> >>> >> user friendly with a GUI.
> >>> >> >
> >>> >> > Thanks,
> >>> >> > Brandon
> >>> >> >
> >>> >> > -----Original Message-----
> >>> >> > From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> >>> >> > Sent: Tuesday, December 08, 2015 6:12 PM
> >>> >> > To: dev@ctakes.apache.org
> >>> >> > Subject: RE: ctakes with icd10; 2015 versions available on
> >>> sourceforge!
> >>> >> >
> >>> >> > 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__sourcefo
> >>> >> >> rg
> >>> >> >> e.ne
> >>> >> >> t_p_
> >>> >> >> ctakesresources_code_HEAD_tree_trunk_ctakes-2Dresources-2Dsn
> >>> >> >> om
> >>> >> >> ed-2
> >>> >> >> Drwo
> >>> >> >> rd-2Dhsqldb-2D2011ab_src_main_resources_org_apache_ctakes_di
> >>> >> >> ct
> >>> >> >> iona
> >>> >> >> ry_l
> >>> >> >> ookup_fast_ctakessnorx2015_&d=BQIBaQ&c=qS4goWBT7poplM69zy_3x
> >>> >> >> hK
> >>> >> >> wEW1
> >>> >> >> 4JZM
> >>> >> >> SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m
> >>> >> >> =S
> >>> >> >> Rqws
> >>> >> >> l3Fm
> >>> >> >> uUXq77GmVlfXn0lE0pVRkL53DNhukcaW6c&s=kWCcj3-hcqYWZXIPhsERggD
> >>> >> >> LC
> >>> >> >> O-5g
> >>> >> >> ppCR
> >>> >> >> oS1Gav7r2A&e=
> >>> >> >>
> >>> >> >> The snomed rxnorm icd9 icd10:
> >>> >> >>
> >>> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__sourcefo
> >>> >> >> rg
> >>> >> >> e.ne
> >>> >> >> t_p_
> >>> >> >> ctakesresources_code_HEAD_tree_trunk_ctakes-2Dresources-2Dsn
> >>> >> >> om
> >>> >> >> ed-2
> >>> >> >> Drwo
> >>> >> >> rd-2Dhsqldb-2D2011ab_src_main_resources_org_apache_ctakes_di
> >>> >> >> ct
> >>> >> >> iona
> >>> >> >> ry_l
> >>> >> >> ookup_fast_ctakesicd2015_&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhK
> >>> >> >> wE
> >>> >> >> W14J
> >>> >> >> ZMSd
> >>> >> >> ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=S
> >>> >> >> Rq
> >>> >> >> wsl3
> >>> >> >> FmuU
> >>> >> >> Xq77GmVlfXn0lE0pVRkL53DNhukcaW6c&s=RZ--ZQ2qvGnhm4h2Vvz1oU97q
> >>> >> >> A8
> >>> >> >> BG2G
> >>> >> >> 39Tw
> >>> >> >> 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-2BDictio
> >>> >> >> na
> >>> >> >> ry-2
> >>> >> >> BLoo
> >>> >> >> kup&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r
> >>> >> >> =f
> >>> >> >> s67G
> >>> >> >> vlGZ
> >>> >> >> stTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqwsl3FmuUXq77GmVlfXn0
> >>> >> >> lE
> >>> >> >> 0pVR
> >>> >> >> kL53
> >>> >> >> 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
> >>> >> >> >
> >>> >> >>
> >>> >> >>
> >>> >> >> 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.
> >>> >> >>
> >>> >>
> >>> >
> >>> >
> >>> >
> >>> > --
> >>> > Eng Alaa Al-Barari
> >>> > phone 0599297470
> >>> >
> >>>
> >>>
> >>>
> >>> --
> >>> Eng Alaa Al-Barari
> >>> phone 0599297470
> >>>
> >>
> >
> >
> > --
> > Eng Alaa Al-Barari
> > phone 0599297470
> >
>
>
>
> --
> Eng Alaa Al-Barari
> phone 0599297470
>



--
Eng Alaa Al-Barari
phone 0599297470
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