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.albar...@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.albar...@gmail.com> wrote: > Thanks Finan and Brandon, your help is appreciated a lot. > > I downloaded the dictionary tool from > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_re > pos_asf_ctakes_sandbox_dictionarytool_bin_dictionarytool.zip&d=BQIBaQ& > c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYm > QCP6r0bcpKGd4f7d4gTao&m=uJq_3OpLiUaBOz9vqxKBI-gUAtLhJMme9uKXqroHhMM&s= > JVOlLM08gTn5rV2T3R_bqeZT8XbMDgLhfKg8Fo5mAQw&e= > I hope its the latest and bug free. > > > my running command is : java -cp ./dictionarytool.jar:lib/* > org.apache.ctakes.dictionarytool.DictionaryCreator2 -umls > /home/abarari/Desktop/umls/2015AB/META/ -atui > ./data/optional/CtakesAnatTuis.txt -db > jdbc:hsqldb:file:/home/abarari/Desktop/dictionarytool/output/ctakesicd > 2015 -tbl CUI_TERMS -df ./data/optional/ -src > ./data/small/ConversionSources.txt > -tui ./data/optional/CtakesAllTuis.txt > > > > I am running on ubuntu by the way ... anyway under > /home/abarari/Desktop/dictionarytool/output/ > > there is only > > abarari@ubuntu:~/Desktop/dictionarytool/output$ ls ctakesicd2015.log > ctakesicd2015.properties ctakesicd2015.script > > > where is the database ? am I doing something wrong ? do I need to > create the database before executing the dictionarytool or what ? > > > I found couple of issues in the dictionary tool, it does not work well > with relative paths. > > > On Wed, Dec 9, 2015 at 7:11 AM, Pei Chen <chen...@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. >> <bdge...@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.fi...@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.d...@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.fi...@childrens.harvard.edu> wrote: >> > >> >> Hi Brandon, thanks for finding and forwarding the instructions! >> >> >> >> I have checked in two new hsqldb dictionaries, both from the >> >> 2015AB version of the UMLS. They both have codes for snomedct_us, >> >> rxnorm, icd9cm and icd10pcs - as well as the usual cui, tui, >> >> preferred term >> mappings. >> >> >> >> One uses cuis filtered by snomed and rxnorm, the other adds cuis >> >> filtered by icd9 and icd10. >> >> What this means: Cuis that exist for a [filter source] are added >> >> to the dictionary, as are all text variations from all sources >> >> that contain that cui. Both dictionaries also use the standard >> >> ctakes semantic group tui filters. >> >> >> >> The names are ctakessnorx2015 and ctakesicd2015 >> >> >> >> The snomed rxnorm : >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.ne >> >> t_p_ >> >> ctakesresources_code_HEAD_tree_trunk_ctakes-2Dresources-2Dsnomed-2 >> >> Drwo >> >> rd-2Dhsqldb-2D2011ab_src_main_resources_org_apache_ctakes_dictiona >> >> ry_l >> >> ookup_fast_ctakessnorx2015_&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW1 >> >> 4JZM >> >> SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqws >> >> l3Fm >> >> uUXq77GmVlfXn0lE0pVRkL53DNhukcaW6c&s=kWCcj3-hcqYWZXIPhsERggDLCO-5g >> >> ppCR >> >> oS1Gav7r2A&e= >> >> >> >> The snomed rxnorm icd9 icd10: >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.ne >> >> t_p_ >> >> ctakesresources_code_HEAD_tree_trunk_ctakes-2Dresources-2Dsnomed-2 >> >> Drwo >> >> rd-2Dhsqldb-2D2011ab_src_main_resources_org_apache_ctakes_dictiona >> >> ry_l >> >> ookup_fast_ctakesicd2015_&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J >> >> ZMSd >> >> ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqwsl3 >> >> FmuU >> >> Xq77GmVlfXn0lE0pVRkL53DNhukcaW6c&s=RZ--ZQ2qvGnhm4h2Vvz1oU97qA8BG2G >> >> 39Tw >> >> w7EdYgKA&e= >> >> >> >> The svn root for the whole ugly thing is: >> >> svn checkout svn://svn.code.sf.net/p/ctakesresources/code/trunk >> >> >> >> Stats: >> >> ctakessnorx2015 >> >> 545,913 Terms >> >> 229,251 Concepts (Cuis) >> >> 272,987 Snomed codes >> >> 32,419 Rxnorm codes >> >> 11,321 icd9 codes >> >> 61 icd10 codes >> >> >> >> Ctakesicd2015 >> >> 611,230 Terms >> >> 282,211 Concepts >> >> 18,626 icd9 codes >> >> 45,818 icd10 codes >> >> Snomed and Rxnorm counts are the same >> >> >> >> So, adding the icd filters gave us an extra ~53,000 concepts and >> >> ~65,000 terms. >> >> >> >> I would like to move this all to a better root (not >> >> ctakes-resources-snomed-rword-hsqldb-2011ab) but I wasn't able to >> >> write directly in trunk (??) and need to get moving on to other things. >> >> >> >> There is help on the ctakes wiki: >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache. >> >> org_ >> >> confluence_display_CTAKES_cTAKES-2B3.2-2B-2D-2BFast-2BDictionary-2 >> >> BLoo >> >> kup&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67G >> >> vlGZ >> >> stTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqwsl3FmuUXq77GmVlfXn0lE0pVR >> >> kL53 DNhukcaW6c&s=98W_vAHGZ2FLEMPfrSgEHtZt-mQ3XJjF6yQYM26tqP4&e= >> >> Though I should probably add a few items ... >> >> >> >> >> >> Sean >> >> >> >> >> >> -----Original Message----- >> >> From: Geise, Brandon D. [mailto:bdge...@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.d...@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.fi...@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.sav...@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.albar...@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
