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From Alaa al Barari <alaa.albar...@gmail.com>
Subject Re: CTAKES DICTIONARY CREATOR GUI !!!
Date Sun, 03 Jan 2016 13:31:52 GMT
Hi and happy new year.

why in the data base generator we have exclude list for example in the
rxnorm section we have EXCLUSION_RXNORM = "SY"; ? whats this is about ?

Regards.

On Sun, Dec 13, 2015 at 7:11 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Oh - and to start it ...
>
> These is only one psvm class:
> org.apache.ctakes.dictionary.creator.gui.CreatorGui
>
> No app parameters.
> You probably want to bump your vm -Xmx to accommodate large dictionaries.
> I use 3G.
>
> Make sure that lib/ is in your classpath
>
> Sean
>
>
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Sunday, December 13, 2015 12:05 AM
> To: dev@ctakes.apache.org
> Subject: CTAKES DICTIONARY CREATOR GUI !!!
>
> Well, a dictionary creator gui prototype.
>
> I have checked a functioning prototype into ctakes sandbox named
> dictionary-gui.
>
> Select your ctakes installation root.  This can be the dev source or app
> binary.
> Select your umls root.  That is one level above META/  - though if you use
> META/ it corrects for you.
> Selection can be done with the "Open" button or by dragging and dropping
> the dir from an OS window.
>
> When you select a umls root it will parse MRCONSO.RRF for all of the
> available vocabularies.  This is necessary since they change with every
> release.  Please Wait.  log4j will spit out progress info.
>
> Select your desired tuis in the left panel.  The tuis normally used by
> ctakes are preselected.
>
> Select your desired source and target vocabularies in the right panel.
> The vocabularies normally used by ctakes (snomed, rxnorm) are preselected.
> "Source" means that the vocabulary will be used to generate the list of
> stored concepts.
> "Target" means that the codes for that vocabulary will be available to
> ctakes.
> For instance, if I select "ICD10PCS" as a source but not target then I'll
> get all of the cuis unique to icd10 in my dictionary, but the icd10 codes
> will not be in there.
> "Target" cannot be selected for a vocabulary unless "Source" is selected.
> It is a little sticky right now: Prototype.
>
> Type a name for your custom dictionary.  Do NOT use the same name twice.
>
> Click "Build" and watch an episode of Vikings.  It will take a while.
> Info will be pumped through log4j.
>
> You should get a popup dialog when complete (or on error).
>
> What this gives you:
> 1.  A dictionary in
> [ctakes_root]/resources/org/apache/ctakes/dictionary/lookup/fast/
> The dictionary is in its own subdirectory [your_dictionary_name]/
> 2.  An .rc file in the same [your_dictionary_name]/ directory.  I'll get
> to that in a bit ...
> 3.  An .xml file usable by ctakes to set up the dictionary.
> The .xml is one directory up from [your_dictionary_name]/ and named
> [your_dictionary_name].xml
> It has all of the information required by ctakes-dictionary-lookup-fast to
> use your new dictionary.  Point to it in your descriptor file or uimafit
> parameter.
>
>
> The .rc file can be used with the hsqldb SqlTool.  If you are even
> slightly familiar with sql then you can play with the dictionary.  The
> easiest way is to copy the hsql***.jar from [ctakes_root]/lib/ or
> dictionary-gui/lib/ and type the following:
> java -cp hsqldb_1_8_0_10.jar org.hsqldb.util.SqlTool --rcfile
> [your_dictionary_name].rc [your_dictionary_name]
> Wait a little while and the SqlTool will open.
> \dt to get a list of the tables
> \q to quit
> Otherwise, plain old sql
>
> Enjoy,
> Sean
>
> p.s. please don't ask me any questions until Tuesday at the earliest.
>
> p.p.s. The gui still needs: unit tests, javadocs, wiki docs, code cleanup,
> optimization, splashscreen, gui niceties (tooltips, menubar, layout), and
> of course testing!
>
> p.p.p.s  Brandon, you are still on the hook wrt helping me with this ...
>
> p.p.p.p.s. I can't stand it when people pump out post-script trees ...
>
>
> -----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
> > >>> >> >> >
> > >>> >> >>
> > >>> >> >>
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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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> > --
> > Eng Alaa Al-Barari
> > phone 0599297470
> >
>
>
>
> --
> Eng Alaa Al-Barari
> phone 0599297470
>



-- 
Eng Alaa Al-Barari
phone 0599297470

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