Thank you! I believe that was a change post 2011! You should actually be ok with both SNOMEDCT and SNOMEDCT_US in CtakesSources.txt
Cheers, Sean -----Original Message----- From: Maite Meseure Hugues [mailto:meseure.ma...@gmail.com] Sent: Wednesday, September 16, 2015 3:43 PM To: dev@ctakes.apache.org Subject: Re: Fast Dictionary Update If this can helps, I had to replace 'SNOMEDCT' with 'SNOMEDCT_US' in CtakesSources.txt. On Wed, Sep 16, 2015 at 2:33 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > I'm not sure that I understand your question. As I sent it, the anat, > snomed and rxnorm are not separate runs. The args line I sent earlier > is for a single run that will create a dictionary with snomed and > rxnorm terms. The anatomy tui list has a special use in correctly > processing snomed codes. > > -----Original Message----- > From: Geise, Brandon D. [mailto:bdge...@geisinger.edu] > Sent: Wednesday, September 16, 2015 3:27 PM > To: dev@ctakes.apache.org > Subject: RE: Fast Dictionary Update > > Ok, hopefully one last question. > > Based on your example everything runs, however the Anat and Snomed > runs don't produce any valid CUIs but RXNorm does. I'm not sure if > this has anything to do with it but every UMLS source read is against MRSTY. > > Here's my command > > java -cp dictionarytool.jar;lib/* > org.apache.ctakes.dictionarytool.DictionaryCreator2 -umls > /path/to/UMLS/META -fd ./data/tiny -atui > ./data/tiny/CtakesAnatTuis.txt -tui ./data/tiny/CtakesSnomedTuis.txt > -ol \path\to\file\Umls2015.bsv > > Any suggestions? > > Thanks again, > Brandon > > > -----Original Message----- > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > Sent: Wednesday, September 16, 2015 3:05 PM > To: dev@ctakes.apache.org > Subject: RE: Fast Dictionary Update > > Yes, that will make the rare word dictionary in a memory-based hsql > database - the same as the default for the dictionary-lookup-fast module. > > -----Original Message----- > From: Geise, Brandon D. [mailto:bdge...@geisinger.edu] > Sent: Wednesday, September 16, 2015 2:42 PM > To: dev@ctakes.apache.org > Subject: RE: Fast Dictionary Update > > Thanks Sean, much appreciated. To clarify the example below would > create the dictionary for use for the rare word approach? > > Thanks, > Brandon > > -----Original Message----- > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > Sent: Wednesday, September 16, 2015 2:16 PM > To: dev@ctakes.apache.org > Subject: RE: Fast Dictionary Update > > Hi Brandon, > > I just checked in a bin/dictionarytool.zip It should have everything > that you need (.jar, lib/, data/). > java -cp dictionarytool.jar;lib/* > org.apache.ctakes.dictionarytool.DictionaryCreator2 [args] Should do > the trick. > > To recreate a 2015 version of the current ctakes dictionary, the > arguments > are: > -umls my/path/to/2015AA/META -fd ./data/tiny -atui > ./data/tiny/CtakesAnatTuis.txt -tui ./data/tiny/CtakesSnomedTuis.txt > -db > jdbc:hsqldb:file:my/path/to/snorx2015 -tbl CUI_TERMS > > Create my/path/to/snorx2015 by copying > resources/memdbtemplate/ctakesumls.properties to > my/path/to/snorx2015.properties - there is a resources/README about this. > > Before populating a DB, I usually do a trial run first, writing to a > flat file. Replace "-db ... -tbl ..." with "-ol my/path/to/testout.bsv" > > > Sean > > -----Original Message----- > From: Geise, Brandon D. [mailto:bdge...@geisinger.edu] > Sent: Wednesday, September 16, 2015 1:49 PM > To: dev@ctakes.apache.org > Subject: RE: Fast Dictionary Update > > Hi Sean, > > That'd be great. > > I think I'm building it incorrectly because after I build the jar and > try to run specifying DictionaryCreator2 as the main class it says it > can't find it. I'm not too familiar with Java and building > projects/jars so it could be my ignorance causing the problem. > > Thanks, > Brandon > > -----Original Message----- > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > Sent: Wednesday, September 16, 2015 1:45 PM > To: dev@ctakes.apache.org > Subject: RE: Fast Dictionary Update > > Hi Brandon, > > I can send you a jar or commit one pre-built. What goes wrong when > you try to build the tool? > > Sean > > -----Original Message----- > From: Geise, Brandon D. [mailto:bdge...@geisinger.edu] > Sent: Wednesday, September 16, 2015 1:23 PM > To: 'dev@ctakes.apache.org' > Subject: Fast Dictionary Update > > Does someone have the DictionaryTool jar available? I'm having > trouble creating the jar file from the project and would like to be > able to create an updated UMLS fast dictionary for 2015. > > Thanks, > Brandon > > > 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. > > > >
