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. 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