Thank you very very much Finan, I am still very nooob to ctakes so please bare with me.
1- Could you please post detailed instructions on how you built the dictionaries ? or give as much as you can examples on the steps ? 2- what did you upload exactly, I only see a script and properties files what are those ? and what I need to change in c takes to make it work with them. like how to get icd10 codes ? I am sorry for being noob, hope soon I will understand the whole thing and be effective. Thanks in advance On Wed, Dec 9, 2015 at 1:12 AM, Finan, Sean < [email protected]> wrote: > 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__sourceforge.net_p_ > > ctakesresources_code_HEAD_tree_trunk_ctakes-2Dresources-2Dsnomed-2Drwo > > rd-2Dhsqldb-2D2011ab_src_main_resources_org_apache_ctakes_dictionary_l > > ookup_fast_ctakessnorx2015_&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZM > > SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqwsl3Fm > > uUXq77GmVlfXn0lE0pVRkL53DNhukcaW6c&s=kWCcj3-hcqYWZXIPhsERggDLCO-5gppCR > > oS1Gav7r2A&e= > > > > The snomed rxnorm icd9 icd10: > > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_p_ > > ctakesresources_code_HEAD_tree_trunk_ctakes-2Dresources-2Dsnomed-2Drwo > > rd-2Dhsqldb-2D2011ab_src_main_resources_org_apache_ctakes_dictionary_l > > ookup_fast_ctakesicd2015_&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSd > > ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqwsl3FmuU > > Xq77GmVlfXn0lE0pVRkL53DNhukcaW6c&s=RZ--ZQ2qvGnhm4h2Vvz1oU97qA8BG2G39Tw > > 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-2BLoo > > kup&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZ > > stTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SRqwsl3FmuUXq77GmVlfXn0lE0pVRkL53 > > 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
