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Posted to dev@ctakes.apache.org by Alaa al Barari <al...@gmail.com> on 2016/01/03 14:31:52 UTC
Re: CTAKES DICTIONARY CREATOR GUI !!!
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
> > <al...@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
> > > <al...@gmail.com>
> > > wrote:
> > >
> > >> Thank, but what I endup with is
> > >> wrong ?
> > >> On Dec 10, 2015 4:26 AM, "Finan, Sean"
> > >> <Se...@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 <ch...@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.
> > >>> >> <bd...@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
>
--
Eng Alaa Al-Barari
phone 0599297470
RE: CTAKES DICTIONARY CREATOR GUI !!!
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Alaa,
That is a good question. The umls vocabularies have, in addition to general synonyms, other term types that are unwanted as searchable synonyms. For instance, you can look at https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/SNOMEDCT_US/stats.html
And see that OF is "Obsolete fully specified name". This would be something like "sorrel tenesmus [symptom]". While the validity of "sorrel tenesmus" as a searchable text could ignite great argument (please don't), the probability of having "sorrel tenesmus [symptom]" with "[symptom]" in the note is unlikely. Even if it is there, do you care about "[symptom]" ? Marking "Sorrel tenesmus" is most likely just fine.
Rxnorm is unique in that the SY synonym is generally undesirable. That is because it is (if memory serves) the full chemical formula for a drug - often spanning 20+ characters. If you really need that for your vocabulary then a toggle can be added to the gui to select it (and others) ...
Please keep in mind that the gui is still a prototype, but I think that it covers >90% of desired umls use cases. Also keep in mind that this is being developed by people in their free time, so quick upgrades are unlikely. Or, feel free to add it yourself - that would be fantastic.
Happy 2016,
Sean
-----Original Message-----
From: Alaa al Barari [mailto:alaa.albarari@gmail.com]
Sent: Sunday, January 03, 2016 8:32 AM
To: dev@ctakes.apache.org
Subject: Re: CTAKES DICTIONARY CREATOR GUI !!!
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=146RtcAn3FCAHFfaBKzLD
> > 4r
> > 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
> > <al...@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
> > > <al...@gmail.com>
> > > wrote:
> > >
> > >> Thank, but what I endup with is
> > >> wrong ?
> > >> On Dec 10, 2015 4:26 AM, "Finan, Sean"
> > >> <Se...@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=fs67GvlGZstTpy
> > >>> > Ii
> > >>> > sC
> > >>> > YNYm
> > >>> > QCP6r0bcpKGd4f7d4gTao&m=uJq_3OpLiUaBOz9vqxKBI-gUAtLhJMme9uKXqr
> > >>> > oH 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/c
> > >>> > ta
> > >>> > 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 <ch...@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.
> > >>> >> <bd...@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__source
> > >>> >> >> fo
> > >>> >> >> rg
> > >>> >> >> e.ne
> > >>> >> >> t_p_
> > >>> >> >> ctakesresources_code_HEAD_tree_trunk_ctakes-2Dresources-2D
> > >>> >> >> sn
> > >>> >> >> 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-hcqYWZXIPhsERg
> > >>> >> >> gD
> > >>> >> >> LC
> > >>> >> >> O-5g
> > >>> >> >> ppCR
> > >>> >> >> oS1Gav7r2A&e=
> > >>> >> >>
> > >>> >> >> The snomed rxnorm icd9 icd10:
> > >>> >> >>
> > >>> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__source
> > >>> >> >> fo
> > >>> >> >> rg
> > >>> >> >> e.ne
> > >>> >> >> t_p_
> > >>> >> >> ctakesresources_code_HEAD_tree_trunk_ctakes-2Dresources-2D
> > >>> >> >> sn
> > >>> >> >> 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_3x
> > >>> >> >> hK
> > >>> >> >> wE
> > >>> >> >> W14J
> > >>> >> >> ZMSd
> > >>> >> >> ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m
> > >>> >> >> =S
> > >>> >> >> Rq
> > >>> >> >> wsl3
> > >>> >> >> FmuU
> > >>> >> >> Xq77GmVlfXn0lE0pVRkL53DNhukcaW6c&s=RZ--ZQ2qvGnhm4h2Vvz1oU9
> > >>> >> >> 7q
> > >>> >> >> 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-2BDict
> > >>> >> >> io
> > >>> >> >> na
> > >>> >> >> ry-2
> > >>> >> >> BLoo
> > >>> >> >> kup&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
> > >>> >> >> &r
> > >>> >> >> =f
> > >>> >> >> s67G
> > >>> >> >> vlGZ
> > >>> >> >> stTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqwsl3FmuUXq77GmVlfX
> > >>> >> >> n0
> > >>> >> >> 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
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> > >>> >>
> > >>> >
> > >>> >
> > >>> >
> > >>> > --
> > >>> > Eng Alaa Al-Barari
> > >>> > phone 0599297470
> > >>> >
> > >>>
> > >>>
> > >>>
> > >>> --
> > >>> Eng Alaa Al-Barari
> > >>> phone 0599297470
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> > >>
> > >
> > >
> > > --
> > > Eng Alaa Al-Barari
> > > phone 0599297470
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> >
> >
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> > --
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> > phone 0599297470
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>
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Eng Alaa Al-Barari
phone 0599297470