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From Alaa al Barari <alaa.albar...@gmail.com>
Subject Re: ctakes with icd10; 2015 versions available on sourceforge!
Date Thu, 10 Dec 2015 08:37:26 GMT
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.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
>> >> >> >
>> >> >>
>> >> >>
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>> >
>> >
>> > --
>> > Eng Alaa Al-Barari
>> > phone 0599297470
>> >
>>
>>
>>
>> --
>> Eng Alaa Al-Barari
>> phone 0599297470
>>
>


-- 
Eng Alaa Al-Barari
phone 0599297470

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