Sean,
Thanks for the detailed answer, I appreciate it, I'm looking into it.
Regards,
Tomasz
From: Finan, Sean [sean.fi...@childrens.harvard.edu]
Sent: Tuesday, November 10, 2015 11:55 AM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Updat
DeliveryUtil have some experimental code that is not used by
default, but one could always play around.
I know that -official- documentation outside of doc/howto.txt would be great.
However I would rather spend free time throwing a gui around the tool to make
things more intuitive.
Sean
--
nt: Monday, October 19, 2015 9:02 AM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Hi Brandon,
Good catch, and thanks for letting me know. Feel free to check in a fix,
otherwise it will probably be a while before I get to it.
Thanks,
Sean
-Original Message-
From: Geise,
@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Hi Sean,
I finally had a chance to look at the SNOMEDCT issue further regarding the
codingScheme populating using the default value. What I found was in the
dictionary tool when running the CodeMapCreator, when the CuiCodesDbWriter is
called, the
[mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, September 21, 2015 10:39 AM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Hi Brandon,
Sorry for the late reply - I've been out for an extended weekend.
The coding scheme change is fairly simply explained (imo). The plain ol
Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, September 21, 2015 10:39 AM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Hi Brandon,
Sorry for the late reply - I've been out for an extended weekend.
The coding scheme change is fairly simply explained (imo). The pla
y it will throw umls relations
into a format that ctakes can directly use. For the time being it should be
avoided.
Sean
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Thursday, September 17, 2015 10:23 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dic
ql.xml and update dictionary location
Thanks,
Brandon
-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Friday, September 18, 2015 11:39 AM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Brandon,
Yes, I think it would be great if you could document
Sent: Thursday, September 17, 2015 12:57 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Making an alternate copy of cTakesHsql.xml and pointing to the new dictionary
is all that is necessary. Do you see a message in the initialization output
indicating that the dictionary d
, September 17, 2015 9:40 PM
To: cTAKES Developer list
Subject: RE: Fast Dictionary Update
Thanks Dmitriy. I was referring to the RelationsExtractor class found in the
dictionarytool. On a similar note, the coding scheme for all SNOMEDCT codes
for the new dictionary is CTAKES compared to SNOMED
the dictionary
creation that I'm missing?
Thanks,
Brandon
-Original Message-
From: Dligach, Dmitriy [mailto:dmitriy.dlig...@childrens.harvard.edu]
Sent: Thursday, September 17, 2015 8:42 PM
To: cTAKES Developer list
Subject: Re: Fast Dictionary Update
Hi Brandon,
Relation extracti
sage-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Thursday, September 17, 2015 1:02 PM
To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>
Subject: RE: Fast Dictionary Update
Not specifically loaded. Here's what I see when loading the pipeline:
17 Se
hanks,
Brandon
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, September 17, 2015 1:18 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
It claims that the database is connected and the preceding line of are spat out
during lo
ember 17, 2015 12:57 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Making an alternate copy of cTakesHsql.xml and pointing to the new dictionary
is all that is necessary. Do you see a message in the initialization output
indicating that the dictionary db has been l
: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
It claims that the database is connected and the preceding line of are spat out
during loading, which took ~3-4 seconds (so something was there):
17 Sep 2015 12:58:58 INFO JdbcConnectionFactory - Database connected
Strange. I
Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Thursday, September 17, 2015 1:02 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Not specifically loaded. Here's what I see when loading the pipeline:
17 Sep 2015 12:58:54 INFO JdbcConnectionFactory - Connecting to
jdbc:hsql
x2015:
17 Sep 2015 12:58:58 INFO JdbcConnectionFactory - Database connected
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, September 17, 2015 12:57 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Making an alternate co
erent then what worked for me.
Brandon
-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Thursday, September 17, 2015 12:24 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
I am still having the problem of only writeRxNorm terms being writt
: Thursday, September 17, 2015 12:54 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Great, thanks both seemed to work for populating the script table.
Besides the path to the new dictionary needing to be changed in cTakesHsql.xml,
does anything else need to be modified to use the
to:sean.fi...@childrens.harvard.edu]
Sent: Thursday, September 17, 2015 10:40 AM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Correct, Hsql should automatically read the .log file upon first use, and then
perform the inserts into the .script file.
In case you want to play it safe, check the
Cuis and Texts to testout.bsv
Wrote 0 terms to testout.bsv
[..]
From: Finan, Sean [sean.fi...@childrens.harvard.edu]
Sent: Thursday, September 17, 2015 9:39 AM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Correct, Hsql should
. [mailto:bdge...@geisinger.edu]
Sent: Thursday, September 17, 2015 10:31 AM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
When I run the tool it outputs a file with a .log extension that has all the
insert statements. Do I copy this to the .script template from memcachedb in
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 9:59 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Excellent!
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday
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
, 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
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
mail
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>>
A
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 too
ache.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 y
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 MRCON
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 c
, 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
@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
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
don 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 pro
hanks,
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
nomed 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 S
om: 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-loo
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
@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
dge...@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 sa
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 w
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 Upd
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