Flagging Medical Record Number

[Sehr, Andrew J]

Hello,

Is there a way to flag the medical record number when running a ctakes job?

Thanks,
Andrew Sehr
Enterprise Architect
Indiana University Health
950 N Meridian St, Indianapolis, IN 46204
317-963-0249
as...@iuhealth.org

RE: Flagging Medical Record Number

[Finan, Sean]

Hi Andrew,

I'm not sure if this is what you are looking for, but you can look at the 
org.apache.ctakes.typesystem.type.structured.MetaData class, which has a 
setPatientID(long) method.
org.apache.ctakes.core.util. SourceMetadataUtil has a getPatientNum(JCas) 
method.

I don't know of any good examples that use setPatientID(long), but basically:
  final Metadata metadata = new Metadata( jCas );
  metadata.setPatientID( 1000 ) );
  jCas.addFsToIndexes( metadata );

If you want to add metadata for a specific note/visit, there is a little bit 
more:
  final SourceData sourcedata = new SourceData( jCas );
  sourcedata.setSourceEncounterId( "Visit For Hiccups" );
  metadata.setSourceData( sourcedata );

org.apache.ctakes.typesystem.type.structured.SourceData has some other useful 
methods.


Sean



-Original Message-
From: Sehr, Andrew J [mailto:as...@iuhealth.org] 
Sent: Wednesday, September 16, 2015 11:28 AM
To: dev@ctakes.apache.org
Subject: Flagging Medical Record Number

Hello,

Is there a way to flag the medical record number when running a ctakes job?

Thanks,
Andrew Sehr
Enterprise Architect
Indiana University Health
950 N Meridian St, Indianapolis, IN 46204
317-963-0249
as...@iuhealth.org

Fast Dictionary Update

[Geise, Brandon D.]

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 
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CTAKES-377 : Upgrade to Java 8

[Finan, Sean]

Can anybody out there think of a reason why we shouldn't upgrade to Java 8?  
Please comment on Jira.

https://issues.apache.org/jira/browse/CTAKES-377

Thanks,
Sean

RE: Fast Dictionary Update

[Finan, Sean]

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.

RE: Fast Dictionary Update

[Geise, Brandon D.]

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.

RE: Fast Dictionary Update

[Finan, Sean]

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.

RE: Fast Dictionary Update

[Geise, Brandon D.]

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.

Re: CTAKES-377 : Upgrade to Java 8

[Pei Chen]

+1 upgrading to Java 8; been using it unofficially locally.

On Wed, Sep 16, 2015 at 1:37 PM, Finan, Sean
 wrote:
> Can anybody out there think of a reason why we shouldn't upgrade to Java 8?  
> Please comment on Jira.
>
> https://issues.apache.org/jira/browse/CTAKES-377
>
> Thanks,
> Sean
>
>

RE: Fast Dictionary Update

[Finan, Sean]

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.

RE: Fast Dictionary Update

[Geise, Brandon D.]

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.

RE: Fast Dictionary Update

[Finan, Sean]

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.

RE: Fast Dictionary Update

[Geise, Brandon D.]

Sorry for not being clearer in my question.

All 3 run when the command is issued, but when anat and snomed run nothing is 
output to the bsv file whereas with RXNorm 74,421 CUIs are written.  So my 
dictionary only ends up being RXNorm CUIs and doesn't include snomed.

Does that clarify?

Thanks,
Brandon

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] 
Sent: Wednesday, September 16, 2015 3:34 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

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), dest

Re: Fast Dictionary Update

[Maite Meseure Hugues]

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 

RE: Fast Dictionary Update

[Finan, Sean]

I'm not sure.  What 3 are you talking about?  There should only be a single run.

-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu] 
Sent: Wednesday, September 16, 2015 3:38 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Sorry for not being clearer in my question.

All 3 run when the command is issued, but when anat and snomed run nothing is 
output to the bsv file whereas with RXNorm 74,421 CUIs are written.  So my 
dictionary only ends up being RXNorm CUIs and doesn't include snomed.

Does that clarify?

Thanks,
Brandon

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] 
Sent: Wednesday, September 16, 2015 3:34 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

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 disclosu

RE: Fast Dictionary Update

[Finan, Sean]

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, distribu

RE: Fast Dictionary Update

[Geise, Brandon D.]

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 24list of Tuis 24
Compiling list of Cuis with wanted Tuis using 
/patto/UMLS_Current_Version/META/MRSTY.RRF
File Line 20 Cuis 60895
File Line 30 Cuis 85750
File Line 40 Cuis 135098
File Line 60 Cuis 183925
File Line 170Cuis 376338
File Line 180Cuis 471009
File Line 190Cuis 568375
File Line 210Cuis 674715
File Line 280Cuis 903583
File Line 330Cuis 973791
File Lines 3370173   Cuis 999451
..File Line 10   Valid 
Cuis 0
..File Line 20   Valid 
Cuis 0
..File Line 30   Valid 
Cuis 0
..File Line 40   Valid 
Cuis 0
..File Line 50   Valid 
Cuis 0
..File Line 60   Valid 
Cuis 0
..File Line 70   Valid 
Cuis 0
..File Line 80   Valid 
Cuis 0
..File Line 90   Valid 
Cuis 0
..File Line 100  Valid 
Cuis 0
..File Line 110  Valid 
Cuis 0
..File Line 120  Valid 
Cuis 0
..File Line 130  Valid 
Cuis 0
..File Line 140  Valid 
Cuis 0
..File Line 150  Valid 
Cuis 0
..File Line 160  Valid 
Cuis 0
..File Line 170  Valid 
Cuis 0
..File Line 180  Valid 
Cuis 0
..File Line 190  Valid 
Cuis 0
..File Line 200  Valid 
Cuis 0
..File Line 210  Valid 
Cuis 0
..File Line 220  Valid 
Cuis 0
..File Line 230  Valid 
Cuis 0
..File Line 240  Valid 
Cuis 0
..File Line 250  Valid 
Cuis 0
..File Line 260  Valid 
Cuis 0
..File Line 270  Valid 
Cuis 0
..File Line 280  Valid 
Cuis 0
..File Line 290  Valid 
Cuis 0
..File Line 300  Valid 
Cuis 0
..File Line 310  Valid 
Cuis 0
..File Line 320  Valid 
Cuis 0
..File Line 330  Valid 
Cuis 0
..File Line 340  Valid 
Cuis 0
..File Line 350  Valid 
Cuis 0
..File Line 360  Valid 
Cuis 0
..File Line 370  Valid 
Cuis 0
..File Line 380  Valid 
Cuis 0
..File Line 390  Valid 
Cuis 0
..File Line 400  Valid 
Cuis 0
..File Line 410  Valid 
Cuis 0
..File Line 420  Valid 
Cuis 0
..File Line 430  Valid 
Cuis 0
..File Line 440  Valid 
Cuis 0
..File Line 450  Valid 
Cuis 0
..File Line 460  Valid 
Cuis 0
..File Line 470  Valid 
Cuis 0
..File Line 480  Valid 
Cuis 0
..

Boston cTAKES Hackathon?

[Pei Chen]

Hi,
I hope everyone had a great summer.  I just wanted to resurrect the
Docker integration idea.
Anyone interested in joining a small hackathon with the single goal of
deploying cTAKES in a docker container.
One of the evenings 6pm?

--Pei

Re: Boston cTAKES Hackathon?

[britt fitch]

I am interested in participating!



Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
britt.fi...@wiredinformatics.com

> On Sep 16, 2015, at 4:23 PM, Pei Chen  wrote:
> 
> Hi,
> I hope everyone had a great summer.  I just wanted to resurrect the
> Docker integration idea.
> Anyone interested in joining a small hackathon with the single goal of
> deploying cTAKES in a docker container.
> One of the evenings 6pm?
> 
> --Pei



signature.asc
Description: Message signed with OpenPGP using GPGMail

RE: Fast Dictionary Update

[Finan, Sean]

Ah, now I see what you mean.  Can you do a grep on your MRCONSO.RRF for 
"SNOMEDCT" ?  

-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu] 
Sent: Wednesday, September 16, 2015 4:04 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

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 24list of Tuis 24
Compiling list of Cuis with wanted Tuis using 
/patto/UMLS_Current_Version/META/MRSTY.RRF
File Line 20 Cuis 60895
File Line 30 Cuis 85750
File Line 40 Cuis 135098
File Line 60 Cuis 183925
File Line 170Cuis 376338
File Line 180Cuis 471009
File Line 190Cuis 568375
File Line 210Cuis 674715
File Line 280Cuis 903583
File Line 330Cuis 973791
File Lines 3370173   Cuis 999451
..File Line 10   Valid 
Cuis 0
..File Line 20   Valid 
Cuis 0
..File Line 30   Valid 
Cuis 0
..File Line 40   Valid 
Cuis 0
..File Line 50   Valid 
Cuis 0
..File Line 60   Valid 
Cuis 0
..File Line 70   Valid 
Cuis 0
..File Line 80   Valid 
Cuis 0
..File Line 90   Valid 
Cuis 0
..File Line 100  Valid 
Cuis 0
..File Line 110  Valid 
Cuis 0
..File Line 120  Valid 
Cuis 0
..File Line 130  Valid 
Cuis 0
..File Line 140  Valid 
Cuis 0
..File Line 150  Valid 
Cuis 0
..File Line 160  Valid 
Cuis 0
..File Line 170  Valid 
Cuis 0
..File Line 180  Valid 
Cuis 0
..File Line 190  Valid 
Cuis 0
..File Line 200  Valid 
Cuis 0
..File Line 210  Valid 
Cuis 0
..File Line 220  Valid 
Cuis 0
..File Line 230  Valid 
Cuis 0
..File Line 240  Valid 
Cuis 0
..File Line 250  Valid 
Cuis 0
..File Line 260  Valid 
Cuis 0
..File Line 270  Valid 
Cuis 0
..File Line 280  Valid 
Cuis 0
..File Line 290  Valid 
Cuis 0
..File Line 300  Valid 
Cuis 0
..File Line 310  Valid 
Cuis 0
..File Line 320  Valid 
Cuis 0
..File Line 330  Valid 
Cuis 0
..File Line 340  Valid 
Cuis 0
..File Line 350  Valid 
Cuis 0
..File Line 360  Valid 
Cuis 0
..File Line 370  Valid 
Cuis 0
..File Line 380  Valid 
Cuis 0
..File Line 390  Valid 
Cuis 0
..File Line 400  Valid 
Cuis 0
..File Line 410  Valid 
Cuis 0
..File Line 420  Valid 
Cuis 0
..File Line 430  Valid 
Cuis 0
..File Line 440  Valid 
Cuis 0
..File Line 450  Valid 

Re: Boston cTAKES Hackathon?

[Jay Vyas]

Yes I'd love to. How about some lightning talks also to start the night off?
I know Harvard is using ctakes for some stuff.


> On Sep 16, 2015, at 4:23 PM, Pei Chen  wrote:
> 
> Hi,
> I hope everyone had a great summer.  I just wanted to resurrect the
> Docker integration idea.
> Anyone interested in joining a small hackathon with the single goal of
> deploying cTAKES in a docker container.
> One of the evenings 6pm?
> 
> --Pei

RE: Fast Dictionary Update

[Geise, Brandon D.]

Yes, it finds "SNOMEDCT_US".

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] 
Sent: Wednesday, September 16, 2015 5:17 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Ah, now I see what you mean.  Can you do a grep on your MRCONSO.RRF for 
"SNOMEDCT" ?  

-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 4:04 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

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 24list of Tuis 24
Compiling list of Cuis with wanted Tuis using 
/patto/UMLS_Current_Version/META/MRSTY.RRF
File Line 20 Cuis 60895
File Line 30 Cuis 85750
File Line 40 Cuis 135098
File Line 60 Cuis 183925
File Line 170Cuis 376338
File Line 180Cuis 471009
File Line 190Cuis 568375
File Line 210Cuis 674715
File Line 280Cuis 903583
File Line 330Cuis 973791
File Lines 3370173   Cuis 999451
..File Line 10   Valid 
Cuis 0
..File Line 20   Valid 
Cuis 0
..File Line 30   Valid 
Cuis 0
..File Line 40   Valid 
Cuis 0
..File Line 50   Valid 
Cuis 0
..File Line 60   Valid 
Cuis 0
..File Line 70   Valid 
Cuis 0
..File Line 80   Valid 
Cuis 0
..File Line 90   Valid 
Cuis 0
..File Line 100  Valid 
Cuis 0
..File Line 110  Valid 
Cuis 0
..File Line 120  Valid 
Cuis 0
..File Line 130  Valid 
Cuis 0
..File Line 140  Valid 
Cuis 0
..File Line 150  Valid 
Cuis 0
..File Line 160  Valid 
Cuis 0
..File Line 170  Valid 
Cuis 0
..File Line 180  Valid 
Cuis 0
..File Line 190  Valid 
Cuis 0
..File Line 200  Valid 
Cuis 0
..File Line 210  Valid 
Cuis 0
..File Line 220  Valid 
Cuis 0
..File Line 230  Valid 
Cuis 0
..File Line 240  Valid 
Cuis 0
..File Line 250  Valid 
Cuis 0
..File Line 260  Valid 
Cuis 0
..File Line 270  Valid 
Cuis 0
..File Line 280  Valid 
Cuis 0
..File Line 290  Valid 
Cuis 0
..File Line 300  Valid 
Cuis 0
..File Line 310  Valid 
Cuis 0
..File Line 320  Valid 
Cuis 0
..File Line 330  Valid 
Cuis 0
..File Line 340  Valid 
Cuis 0
..File Line 350  Valid 
Cuis 0
..File Line 360  Valid 
Cuis 0
..File Line 370  Valid 
Cuis 0
..File Line 380  Valid 
Cuis 0
..File Line 390  Valid 
Cuis 0
..File Line 400  Valid 
Cuis 0
..File Line 410  Valid 
Cuis 0
..File Line 420  Valid 
Cuis 0
.

RE: Fast Dictionary Update

[Tomasz Oliwa]

I have exactly the same problem with the tool.

A grep on MRCONSO.RRF for "SNOMEDCT" or for "SNOMEDCT_US" shows many lines.


From: Geise, Brandon D. [bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 5:05 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Yes, it finds "SNOMEDCT_US".

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 5:17 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Ah, now I see what you mean.  Can you do a grep on your MRCONSO.RRF for 
"SNOMEDCT" ?

-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 4:04 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

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 24list of Tuis 24
Compiling list of Cuis with wanted Tuis using 
/patto/UMLS_Current_Version/META/MRSTY.RRF
File Line 20 Cuis 60895
File Line 30 Cuis 85750
File Line 40 Cuis 135098
File Line 60 Cuis 183925
File Line 170Cuis 376338
File Line 180Cuis 471009
File Line 190Cuis 568375
File Line 210Cuis 674715
File Line 280Cuis 903583
File Line 330Cuis 973791
File Lines 3370173   Cuis 999451
..File Line 10   Valid 
Cuis 0
..File Line 20   Valid 
Cuis 0
..File Line 30   Valid 
Cuis 0
..File Line 40   Valid 
Cuis 0
..File Line 50   Valid 
Cuis 0
..File Line 60   Valid 
Cuis 0
..File Line 70   Valid 
Cuis 0
..File Line 80   Valid 
Cuis 0
..File Line 90   Valid 
Cuis 0
..File Line 100  Valid 
Cuis 0
..File Line 110  Valid 
Cuis 0
..File Line 120  Valid 
Cuis 0
..File Line 130  Valid 
Cuis 0
..File Line 140  Valid 
Cuis 0
..File Line 150  Valid 
Cuis 0
..File Line 160  Valid 
Cuis 0
..File Line 170  Valid 
Cuis 0
..File Line 180  Valid 
Cuis 0
..File Line 190  Valid 
Cuis 0
..File Line 200  Valid 
Cuis 0
..File Line 210  Valid 
Cuis 0
..File Line 220  Valid 
Cuis 0
..File Line 230  Valid 
Cuis 0
..File Line 240  Valid 
Cuis 0
..File Line 250  Valid 
Cuis 0
..File Line 260  Valid 
Cuis 0
..File Line 270  Valid 
Cuis 0
..File Line 280  Valid 
Cuis 0
..File Line 290  Valid 
Cuis 0
..File Line 300  Valid 
Cuis 0
..File Line 310  Valid 
Cuis 0
..File Line 320  Valid 
Cuis 0
..File Line 330  Valid 
Cuis 0
..File Line 340  Valid 
Cuis 0
..File Line 350  Valid 
Cuis 0
..File Line 360  Valid 
Cuis 0
..File Line 370  Valid 
Cuis 0
..File Line 380  Valid 
Cuis 0
..File Line

RE: Fast Dictionary Update

[Finan, Sean]

And you added "SNOMEDCT_US" to data/tiny/CtakesSources.txt ?

-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu] 
Sent: Wednesday, September 16, 2015 7:13 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

I have exactly the same problem with the tool.

A grep on MRCONSO.RRF for "SNOMEDCT" or for "SNOMEDCT_US" shows many lines.


From: Geise, Brandon D. [bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 5:05 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Yes, it finds "SNOMEDCT_US".

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 5:17 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Ah, now I see what you mean.  Can you do a grep on your MRCONSO.RRF for 
"SNOMEDCT" ?

-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 4:04 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

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 24list of Tuis 24
Compiling list of Cuis with wanted Tuis using 
/patto/UMLS_Current_Version/META/MRSTY.RRF
File Line 20 Cuis 60895
File Line 30 Cuis 85750
File Line 40 Cuis 135098
File Line 60 Cuis 183925
File Line 170Cuis 376338
File Line 180Cuis 471009
File Line 190Cuis 568375
File Line 210Cuis 674715
File Line 280Cuis 903583
File Line 330Cuis 973791
File Lines 3370173   Cuis 999451
..File Line 10   Valid 
Cuis 0
..File Line 20   Valid 
Cuis 0
..File Line 30   Valid 
Cuis 0
..File Line 40   Valid 
Cuis 0
..File Line 50   Valid 
Cuis 0
..File Line 60   Valid 
Cuis 0
..File Line 70   Valid 
Cuis 0
..File Line 80   Valid 
Cuis 0
..File Line 90   Valid 
Cuis 0
..File Line 100  Valid 
Cuis 0
..File Line 110  Valid 
Cuis 0
..File Line 120  Valid 
Cuis 0
..File Line 130  Valid 
Cuis 0
..File Line 140  Valid 
Cuis 0
..File Line 150  Valid 
Cuis 0
..File Line 160  Valid 
Cuis 0
..File Line 170  Valid 
Cuis 0
..File Line 180  Valid 
Cuis 0
..File Line 190  Valid 
Cuis 0
..File Line 200  Valid 
Cuis 0
..File Line 210  Valid 
Cuis 0
..File Line 220  Valid 
Cuis 0
..File Line 230  Valid 
Cuis 0
..File Line 240  Valid 
Cuis 0
..File Line 250  Valid 
Cuis 0
..File Line 260  Valid 
Cuis 0
..File Line 270  Valid 
Cuis 0
..File Line 280  Valid 
Cuis 0
..File Line 290  Valid 
Cuis 0
..File Line 300  Valid 
Cuis 0
..File Line 310  Valid 
Cuis 0
..File Line 320  Valid 
Cuis 0
..File Line 330  Valid 
Cuis 0
..File Line 340  Valid 
Cuis 0
..File Line 350  Valid 
Cuis 0
..File Line 360  Val

RE: Fast Dictionary Update

[Geise, Brandon D.]

Sean,

I added that and still had the same issue.

Thanks,
Brandon
_
From: Finan, Sean 
mailto:sean.fi...@childrens.harvard.edu>>
Sent: Wednesday, September 16, 2015 7:56 PM
Subject: RE: Fast Dictionary Update
To: mailto:dev@ctakes.apache.org>>


And you added "SNOMEDCT_US" to data/tiny/CtakesSources.txt ?

-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Wednesday, September 16, 2015 7:13 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

I have exactly the same problem with the tool.

A grep on MRCONSO.RRF for "SNOMEDCT" or for "SNOMEDCT_US" shows many lines.


From: Geise, Brandon D. [bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 5:05 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Yes, it finds "SNOMEDCT_US".

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 5:17 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Ah, now I see what you mean. Can you do a grep on your MRCONSO.RRF for 
"SNOMEDCT" ?

-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 4:04 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

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 20 Cuis 60895
File Line 30 Cuis 85750
File Line 40 Cuis 135098
File Line 60 Cuis 183925
File Line 170 Cuis 376338
File Line 180 Cuis 471009
File Line 190 Cuis 568375
File Line 210 Cuis 674715
File Line 280 Cuis 903583
File Line 330 Cuis 973791
File Lines 3370173 Cuis 999451
..File Line 10 Valid Cuis 0
..File Line 20 Valid Cuis 0
..File Line 30 Valid Cuis 0
..File Line 40 Valid Cuis 0
..File Line 50 Valid Cuis 0
..File Line 60 Valid Cuis 0
..File Line 70 Valid Cuis 0
..File Line 80 Valid Cuis 0
..File Line 90 Valid Cuis 0
..File Line 
100 Valid Cuis 0
..File Line 
110 Valid Cuis 0
..File Line 
120 Valid Cuis 0
..File Line 
130 Valid Cuis 0
..File Line 
140 Valid Cuis 0
..File Line 
150 Valid Cuis 0
..File Line 
160 Valid Cuis 0
..File Line 
170 Valid Cuis 0
..File Line 
180 Valid Cuis 0
..File Line 
190 Valid Cuis 0
..File Line 
200 Valid Cuis 0
..File Line 
210 Valid Cuis 0
..File Line 
220 Valid Cuis 0
..File Line 
230 Valid Cuis 0
..File Line 
240 Valid Cuis 0
..File Line 
250 Valid Cuis 0
..File Line 
260 Valid Cuis 0
..File Line 
270 Valid Cuis 0
..File Line 
280 Valid Cuis 0
..File Line 
290 Valid Cuis 0
..File Line 
300 Valid Cuis 0
..File Line 
310 Valid Cuis 0
..File Line 
320 Valid Cuis 0
..File Line 
330 Valid Cuis 0
..File Line 
340 Valid Cuis 0
...

RE: Fast Dictionary Update

[Finan, Sean]

Did you add it to data/default/ CtakesSources.txt ?

If not then you need to specify -src ./data/tiny/CtakesSources.txt

Sorry for any confusion.

As soon as my inet isn't overloaded I'll download 2015AA and see if I can build 
a dictionary.

-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu] 
Sent: Wednesday, September 16, 2015 8:14 PM
To: dev@ctakes.apache.org; dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Sean,

I added that and still had the same issue.

Thanks,
Brandon
_
From: Finan, Sean 
mailto:sean.fi...@childrens.harvard.edu>>
Sent: Wednesday, September 16, 2015 7:56 PM
Subject: RE: Fast Dictionary Update
To: mailto:dev@ctakes.apache.org>>


And you added "SNOMEDCT_US" to data/tiny/CtakesSources.txt ?

-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Wednesday, September 16, 2015 7:13 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

I have exactly the same problem with the tool.

A grep on MRCONSO.RRF for "SNOMEDCT" or for "SNOMEDCT_US" shows many lines.


From: Geise, Brandon D. [bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 5:05 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Yes, it finds "SNOMEDCT_US".

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 5:17 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Ah, now I see what you mean. Can you do a grep on your MRCONSO.RRF for 
"SNOMEDCT" ?

-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 4:04 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

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 20 Cuis 60895
File Line 30 Cuis 85750
File Line 40 Cuis 135098
File Line 60 Cuis 183925
File Line 170 Cuis 376338 File Line 180 Cuis 
471009 File Line 190 Cuis 568375 File Line 
210 Cuis 674715 File Line 280 Cuis 903583 
File Line 330 Cuis 973791 File Lines 3370173 Cuis 
999451 ..File Line 10 Valid 
Cuis 0 ..File Line 20 Valid 
Cuis 0 ..File Line 30 Valid 
Cuis 0 ..File Line 40 Valid 
Cuis 0 ..File Line 50 Valid 
Cuis 0 ..File Line 60 Valid 
Cuis 0 ..File Line 70 Valid 
Cuis 0 ..File Line 80 Valid 
Cuis 0 ..File Line 90 Valid 
Cuis 0 ..File Line 
100 Valid Cuis 0 
..File Line 
110 Valid Cuis 0 
..File Line 
120 Valid Cuis 0 
..File Line 
130 Valid Cuis 0 
..File Line 
140 Valid Cuis 0 
..File Line 
150 Valid Cuis 0 
..File Line 
160 Valid Cuis 0 
..File Line 
170 Valid Cuis 0 
..File Line 
180 Valid Cuis 0 
..File Line 
190 Valid Cuis 0 
..File Line 
200 Valid Cuis 0 
..File Line 
210 Valid Cuis 0 
..File Line 
220 Valid Cuis 0 
..File Line 
230 Valid Cuis 0 
..File Line 
240 Valid Cuis 0 
..File Line 
250 Valid Cuis 0 
..File Line 
260 Valid Cuis 0 
..File Line 
270 Valid Cuis 0 
..File Line 
280 Valid Cuis 0 
.

RE: Fast Dictionary Update

[Geise, Brandon D.]

No, I had changed it on the Tiny source file.  I just changed the default file 
and it looks to be running as expected now.

Thank you for all your help and patience,
Brandon

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] 
Sent: Wednesday, September 16, 2015 9:35 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Did you add it to data/default/ CtakesSources.txt ?

If not then you need to specify -src ./data/tiny/CtakesSources.txt

Sorry for any confusion.

As soon as my inet isn't overloaded I'll download 2015AA and see if I can build 
a dictionary.

-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 8:14 PM
To: dev@ctakes.apache.org; dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Sean,

I added that and still had the same issue.

Thanks,
Brandon
_
From: Finan, Sean 
mailto:sean.fi...@childrens.harvard.edu>>
Sent: Wednesday, September 16, 2015 7:56 PM
Subject: RE: Fast Dictionary Update
To: mailto:dev@ctakes.apache.org>>


And you added "SNOMEDCT_US" to data/tiny/CtakesSources.txt ?

-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Wednesday, September 16, 2015 7:13 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

I have exactly the same problem with the tool.

A grep on MRCONSO.RRF for "SNOMEDCT" or for "SNOMEDCT_US" shows many lines.


From: Geise, Brandon D. [bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 5:05 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Yes, it finds "SNOMEDCT_US".

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 5:17 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Ah, now I see what you mean. Can you do a grep on your MRCONSO.RRF for 
"SNOMEDCT" ?

-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 4:04 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

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 20 Cuis 60895
File Line 30 Cuis 85750
File Line 40 Cuis 135098
File Line 60 Cuis 183925
File Line 170 Cuis 376338 File Line 180 Cuis 
471009 File Line 190 Cuis 568375 File Line 
210 Cuis 674715 File Line 280 Cuis 903583 
File Line 330 Cuis 973791 File Lines 3370173 Cuis 
999451 ..File Line 10 Valid 
Cuis 0 ..File Line 20 Valid 
Cuis 0 ..File Line 30 Valid 
Cuis 0 ..File Line 40 Valid 
Cuis 0 ..File Line 50 Valid 
Cuis 0 ..File Line 60 Valid 
Cuis 0 ..File Line 70 Valid 
Cuis 0 ..File Line 80 Valid 
Cuis 0 ..File Line 90 Valid 
Cuis 0 ..File Line 
100 Valid Cuis 0 
..File Line 
110 Valid Cuis 0 
..File Line 
120 Valid Cuis 0 
..File Line 
130 Valid Cuis 0 
..File Line 
140 Valid Cuis 0 
..File Line 
150 Valid Cuis 0 
..File Line 
160 Valid Cuis 0 
..File Line 
170 Valid Cuis 0 
..File Line 
180 Valid Cuis 0 
..File Line 
190 Valid Cuis 0 
..File Line 
200 Valid Cuis 0 
..File Line 
210 Valid Cuis 0 
..File Line 
220 Valid Cuis 0 
..File Line 
230 Valid Cuis 0 
..File Line 
2

RE: Fast Dictionary Update

[Finan, Sean]

Excellent! 

-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu] 
Sent: Wednesday, September 16, 2015 9:55 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

No, I had changed it on the Tiny source file.  I just changed the default file 
and it looks to be running as expected now.

Thank you for all your help and patience, Brandon

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 9:35 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Did you add it to data/default/ CtakesSources.txt ?

If not then you need to specify -src ./data/tiny/CtakesSources.txt

Sorry for any confusion.

As soon as my inet isn't overloaded I'll download 2015AA and see if I can build 
a dictionary.

-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 8:14 PM
To: dev@ctakes.apache.org; dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Sean,

I added that and still had the same issue.

Thanks,
Brandon
_
From: Finan, Sean 
mailto:sean.fi...@childrens.harvard.edu>>
Sent: Wednesday, September 16, 2015 7:56 PM
Subject: RE: Fast Dictionary Update
To: mailto:dev@ctakes.apache.org>>


And you added "SNOMEDCT_US" to data/tiny/CtakesSources.txt ?

-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Wednesday, September 16, 2015 7:13 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

I have exactly the same problem with the tool.

A grep on MRCONSO.RRF for "SNOMEDCT" or for "SNOMEDCT_US" shows many lines.


From: Geise, Brandon D. [bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 5:05 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Yes, it finds "SNOMEDCT_US".

-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 5:17 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

Ah, now I see what you mean. Can you do a grep on your MRCONSO.RRF for 
"SNOMEDCT" ?

-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 4:04 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update

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 20 Cuis 60895
File Line 30 Cuis 85750
File Line 40 Cuis 135098
File Line 60 Cuis 183925
File Line 170 Cuis 376338 File Line 180 Cuis 
471009 File Line 190 Cuis 568375 File Line 
210 Cuis 674715 File Line 280 Cuis 903583 
File Line 330 Cuis 973791 File Lines 3370173 Cuis 
999451 ..File Line 10 Valid 
Cuis 0 ..File Line 20 Valid 
Cuis 0 ..File Line 30 Valid 
Cuis 0 ..File Line 40 Valid 
Cuis 0 ..File Line 50 Valid 
Cuis 0 ..File Line 60 Valid 
Cuis 0 ..File Line 70 Valid 
Cuis 0 ..File Line 80 Valid 
Cuis 0 ..File Line 90 Valid 
Cuis 0 ..File Line 
100 Valid Cuis 0 
..File Line 
110 Valid Cuis 0 
..File Line 
120 Valid Cuis 0 
..File Line 
130 Valid Cuis 0 
..File Line 
140 Valid Cuis 0 
..File Line 
150 Valid Cuis 0 
..File Line 
160 Valid Cuis 0 
..File Line 
170 Valid Cuis 0 
..File Line 
180 Valid Cuis 0 
..File Line 
190 Valid Cuis 0 
..File Line 
200 Valid Cuis 0 
..File Line 
210 Valid Cuis 0 
..