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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: ctakes with icd10; 2015 versions available on sourceforge!
Date Thu, 10 Dec 2015 02:26:04 GMT
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.org_re
> pos_asf_ctakes_sandbox_dictionarytool_bin_dictionarytool.zip&d=BQIBaQ&
> c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYm
> QCP6r0bcpKGd4f7d4gTao&m=uJq_3OpLiUaBOz9vqxKBI-gUAtLhJMme9uKXqroHhMM&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/ctakesicd
> 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__sourceforge.ne
>> >> t_p_ 
>> >> ctakesresources_code_HEAD_tree_trunk_ctakes-2Dresources-2Dsnomed-2
>> >> Drwo 
>> >> rd-2Dhsqldb-2D2011ab_src_main_resources_org_apache_ctakes_dictiona
>> >> ry_l 
>> >> ookup_fast_ctakessnorx2015_&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW1
>> >> 4JZM 
>> >> SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqws
>> >> l3Fm 
>> >> uUXq77GmVlfXn0lE0pVRkL53DNhukcaW6c&s=kWCcj3-hcqYWZXIPhsERggDLCO-5g
>> >> ppCR
>> >> oS1Gav7r2A&e=
>> >>
>> >> The snomed rxnorm icd9 icd10:
>> >>
>> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.ne
>> >> t_p_ 
>> >> ctakesresources_code_HEAD_tree_trunk_ctakes-2Dresources-2Dsnomed-2
>> >> Drwo 
>> >> rd-2Dhsqldb-2D2011ab_src_main_resources_org_apache_ctakes_dictiona
>> >> ry_l 
>> >> ookup_fast_ctakesicd2015_&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J
>> >> ZMSd 
>> >> ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqwsl3
>> >> FmuU 
>> >> Xq77GmVlfXn0lE0pVRkL53DNhukcaW6c&s=RZ--ZQ2qvGnhm4h2Vvz1oU97qA8BG2G
>> >> 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-2BDictionary-2
>> >> BLoo 
>> >> kup&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67G
>> >> vlGZ
>> >> stTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqwsl3FmuUXq77GmVlfXn0lE0pVR
>> >> 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 
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>
>
>
> --
> Eng Alaa Al-Barari
> phone 0599297470
>



--
Eng Alaa Al-Barari
phone 0599297470
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