I tried changing as suggested. Below is what I see for the snomed piece, but for RXNorm it writes terms at the end.
Reading list of Source Types from ./data/default/CtakesSources.txt File Lines 1 list of Source Types 1 Reading list of Tuis from ./data/tiny/CtakesSnomedTuis.txt File Lines 24 list of Tuis 24 Compiling list of Cuis with wanted Tuis using /patto/UMLS_Current_Version/META/MRSTY.RRF File Line 200000 Cuis 60895 File Line 300000 Cuis 85750 File Line 400000 Cuis 135098 File Line 600000 Cuis 183925 File Line 1700000 Cuis 376338 File Line 1800000 Cuis 471009 File Line 1900000 Cuis 568375 File Line 2100000 Cuis 674715 File Line 2800000 Cuis 903583 File Line 3300000 Cuis 973791 File Lines 3370173 Cuis 999451 ..................................................File Line 100000 Valid Cuis 0 ..................................................File Line 200000 Valid Cuis 0 ..................................................File Line 300000 Valid Cuis 0 ..................................................File Line 400000 Valid Cuis 0 ..................................................File Line 500000 Valid Cuis 0 ..................................................File Line 600000 Valid Cuis 0 ..................................................File Line 700000 Valid Cuis 0 ..................................................File Line 800000 Valid Cuis 0 ..................................................File Line 900000 Valid Cuis 0 ..................................................File Line 1000000 Valid Cuis 0 ..................................................File Line 1100000 Valid Cuis 0 ..................................................File Line 1200000 Valid Cuis 0 ..................................................File Line 1300000 Valid Cuis 0 ..................................................File Line 1400000 Valid Cuis 0 ..................................................File Line 1500000 Valid Cuis 0 ..................................................File Line 1600000 Valid Cuis 0 ..................................................File Line 1700000 Valid Cuis 0 ..................................................File Line 1800000 Valid Cuis 0 ..................................................File Line 1900000 Valid Cuis 0 ..................................................File Line 2000000 Valid Cuis 0 ..................................................File Line 2100000 Valid Cuis 0 ..................................................File Line 2200000 Valid Cuis 0 ..................................................File Line 2300000 Valid Cuis 0 ..................................................File Line 2400000 Valid Cuis 0 ..................................................File Line 2500000 Valid Cuis 0 ..................................................File Line 2600000 Valid Cuis 0 ..................................................File Line 2700000 Valid Cuis 0 ..................................................File Line 2800000 Valid Cuis 0 ..................................................File Line 2900000 Valid Cuis 0 ..................................................File Line 3000000 Valid Cuis 0 ..................................................File Line 3100000 Valid Cuis 0 ..................................................File Line 3200000 Valid Cuis 0 ..................................................File Line 3300000 Valid Cuis 0 ..................................................File Line 3400000 Valid Cuis 0 ..................................................File Line 3500000 Valid Cuis 0 ..................................................File Line 3600000 Valid Cuis 0 ..................................................File Line 3700000 Valid Cuis 0 ..................................................File Line 3800000 Valid Cuis 0 ..................................................File Line 3900000 Valid Cuis 0 ..................................................File Line 4000000 Valid Cuis 0 ..................................................File Line 4100000 Valid Cuis 0 ..................................................File Line 4200000 Valid Cuis 0 ..................................................File Line 4300000 Valid Cuis 0 ..................................................File Line 4400000 Valid Cuis 0 ..................................................File Line 4500000 Valid Cuis 0 ..................................................File Line 4600000 Valid Cuis 0 ..................................................File Line 4700000 Valid Cuis 0 ..................................................File Line 4800000 Valid Cuis 0 ..................................................File Line 4900000 Valid Cuis 0 ..................................................File Line 5000000 Valid Cuis 0 ..................................................File Line 5100000 Valid Cuis 0 ..................................................File Line 5200000 Valid Cuis 0 ..................................................File Line 5300000 Valid Cuis 0 ..................................................File Line 5400000 Valid Cuis 0 ..................................................File Line 5500000 Valid Cuis 0 ..................................................File Line 5600000 Valid Cuis 0 ..................................................File Line 5700000 Valid Cuis 0 ..................................................File Line 5800000 Valid Cuis 0 ..................................................File Line 5900000 Valid Cuis 0 ..................................................File Line 6000000 Valid Cuis 0 ..................................................File Line 6100000 Valid Cuis 0 ..................................................File Line 6200000 Valid Cuis 0 ..................................................File Line 6300000 Valid Cuis 0 ..................................................File Line 6400000 Valid Cuis 0 ..................................................File Line 6500000 Valid Cuis 0 ..................................................File Line 6600000 Valid Cuis 0 ..................................................File Line 6700000 Valid Cuis 0 ..................................................File Line 6800000 Valid Cuis 0 ..................................................File Line 6900000 Valid Cuis 0 ..................................................File Line 7000000 Valid Cuis 0 ..................................................File Line 7100000 Valid Cuis 0 ..................................................File Line 7200000 Valid Cuis 0 ..................................................File Line 7300000 Valid Cuis 0 ..................................................File Line 7400000 Valid Cuis 0 ..................................................File Line 7500000 Valid Cuis 0 ..................................................File Line 7600000 Valid Cuis 0 ..................................................File Line 7700000 Valid Cuis 0 ..................................................File Line 7800000 Valid Cuis 0 ..................................................File Line 7900000 Valid Cuis 0 ..................................................File Line 8000000 Valid Cuis 0 ..................................................File Line 8100000 Valid Cuis 0 ..................................................File Line 8200000 Valid Cuis 0 ..................................................File Line 8300000 Valid Cuis 0 ..................................................File Line 8400000 Valid Cuis 0 ..................................................File Line 8500000 Valid Cuis 0 ..................................................File Line 8600000 Valid Cuis 0 ..................................................File Line 8700000 Valid Cuis 0 ..................................................File Line 8800000 Valid Cuis 0 .............File Lines 8827152 Valid Cuis 0 Compiling map of Umls Cuis and Texts ..................................................File Line 100000 Terms 0 ..................................................File Line 200000 Terms 0 ..................................................File Line 300000 Terms 0 ..................................................File Line 400000 Terms 0 ..................................................File Line 500000 Terms 0 ..................................................File Line 600000 Terms 0 ..................................................File Line 700000 Terms 0 ..................................................File Line 800000 Terms 0 ..................................................File Line 900000 Terms 0 ..................................................File Line 1000000 Terms 0 ..................................................File Line 1100000 Terms 0 ..................................................File Line 1200000 Terms 0 ..................................................File Line 1300000 Terms 0 ..................................................File Line 1400000 Terms 0 ..................................................File Line 1500000 Terms 0 ..................................................File Line 1600000 Terms 0 ..................................................File Line 1700000 Terms 0 ..................................................File Line 1800000 Terms 0 ..................................................File Line 1900000 Terms 0 ..................................................File Line 2000000 Terms 0 ..................................................File Line 2100000 Terms 0 ..................................................File Line 2200000 Terms 0 ..................................................File Line 2300000 Terms 0 ..................................................File Line 2400000 Terms 0 ..................................................File Line 2500000 Terms 0 ..................................................File Line 2600000 Terms 0 ..................................................File Line 2700000 Terms 0 ..................................................File Line 2800000 Terms 0 ..................................................File Line 2900000 Terms 0 ..................................................File Line 3000000 Terms 0 ..................................................File Line 3100000 Terms 0 ..................................................File Line 3200000 Terms 0 ..................................................File Line 3300000 Terms 0 ..................................................File Line 3400000 Terms 0 ..................................................File Line 3500000 Terms 0 ..................................................File Line 3600000 Terms 0 ..................................................File Line 3700000 Terms 0 ..................................................File Line 3800000 Terms 0 ..................................................File Line 3900000 Terms 0 ..................................................File Line 4000000 Terms 0 ..................................................File Line 4100000 Terms 0 ..................................................File Line 4200000 Terms 0 ..................................................File Line 4300000 Terms 0 ..................................................File Line 4400000 Terms 0 ..................................................File Line 4500000 Terms 0 ..................................................File Line 4600000 Terms 0 ..................................................File Line 4700000 Terms 0 ..................................................File Line 4800000 Terms 0 ..................................................File Line 4900000 Terms 0 ..................................................File Line 5000000 Terms 0 ..................................................File Line 5100000 Terms 0 ..................................................File Line 5200000 Terms 0 ..................................................File Line 5300000 Terms 0 ..................................................File Line 5400000 Terms 0 ..................................................File Line 5500000 Terms 0 ..................................................File Line 5600000 Terms 0 ..................................................File Line 5700000 Terms 0 ..................................................File Line 5800000 Terms 0 ..................................................File Line 5900000 Terms 0 ..................................................File Line 6000000 Terms 0 ..................................................File Line 6100000 Terms 0 ..................................................File Line 6200000 Terms 0 ..................................................File Line 6300000 Terms 0 ..................................................File Line 6400000 Terms 0 ..................................................File Line 6500000 Terms 0 ..................................................File Line 6600000 Terms 0 ..................................................File Line 6700000 Terms 0 ..................................................File Line 6800000 Terms 0 ..................................................File Line 6900000 Terms 0 ..................................................File Line 7000000 Terms 0 ..................................................File Line 7100000 Terms 0 ..................................................File Line 7200000 Terms 0 ..................................................File Line 7300000 Terms 0 ..................................................File Line 7400000 Terms 0 ..................................................File Line 7500000 Terms 0 ..................................................File Line 7600000 Terms 0 ..................................................File Line 7700000 Terms 0 ..................................................File Line 7800000 Terms 0 ..................................................File Line 7900000 Terms 0 ..................................................File Line 8000000 Terms 0 ..................................................File Line 8100000 Terms 0 ..................................................File Line 8200000 Terms 0 ..................................................File Line 8300000 Terms 0 ..................................................File Line 8400000 Terms 0 ..................................................File Line 8500000 Terms 0 ..................................................File Line 8600000 Terms 0 ..................................................File Line 8700000 Terms 0 ..................................................File Line 8800000 Terms 0 .............File Line 8827152 Terms 0 Writing map of Cuis and Texts to \pathto\Umls2015.bsv -----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, September 16, 2015 4:00 PM To: dev@ctakes.apache.org Subject: RE: Fast Dictionary Update 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. > > > >
