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 < [email protected]> 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:[email protected]] > Sent: Sunday, December 13, 2015 12:05 AM > To: [email protected] > 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:[email protected]] > Sent: Thursday, December 10, 2015 12:27 PM > To: [email protected] > 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 < > [email protected]> 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:[email protected]] > > Sent: Thursday, December 10, 2015 10:38 AM > > To: [email protected] > > 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 > > <[email protected]> > > 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 > > > <[email protected]> > > > wrote: > > > > > >> Thank, but what I endup with is > > >> wrong ? > > >> On Dec 10, 2015 4:26 AM, "Finan, Sean" > > >> <[email protected]> > > >> 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:[email protected]] > > >>> Sent: Wednesday, December 09, 2015 6:33 PM > > >>> To: [email protected] > > >>> 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 > > >>> <[email protected] > > >>> > > > >>> 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 <[email protected]> > 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. > > >>> >> <[email protected]> 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:[email protected]] > > >>> >> > Sent: Tuesday, December 08, 2015 6:12 PM > > >>> >> > To: [email protected] > > >>> >> > 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:[email protected]] > > >>> >> > Sent: Tuesday, December 08, 2015 4:57 PM > > >>> >> > To: [email protected] > > >>> >> > 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 < > > >>> >> [email protected]> 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:[email protected]] > > >>> >> >> Sent: Tuesday, December 08, 2015 12:51 PM > > >>> >> >> To: [email protected] > > >>> >> >> 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:[email protected]] > > >>> >> >> Sent: Tuesday, December 08, 2015 12:47 PM > > >>> >> >> To: [email protected] > > >>> >> >> 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 < > > >>> >> >> [email protected]> 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:[email protected]] > > >>> >> >> > Sent: Tuesday, December 08, 2015 12:17 PM > > >>> >> >> > To: [email protected] > > >>> >> >> > 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:[email protected]] > > >>> >> >> > Sent: Tuesday, December 8, 2015 10:01 AM > > >>> >> >> > To: [email protected] > > >>> >> >> > 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
