Hi Dima,
I believe this is related to the path of LVG. You can try coping the LVG data
folder to the same directory (This is at least how I've gotten around it) when
running a compiled jar. You can also search the mailing list for additional
discussion on this issue.
Thanks,
Brandon
I haven't tried it and is a guess based on reading the code, but you might be
able to change the dictionary implementation name in the xml file from
UmlsJdbcRareWordDictionary to ConceptFactory, since Umls factory implements
from ConceptFactory.
-Original Message-
From: Miller, Timothy
Hi all,
I was curious if anyone has spent time to develop a more robust/dynamic method
for easily adding in new SAB sources from UMLS as coding schema's other than
manually editing or adding new code?
The process I used for the short term was adding the additional SABs to the
) is: C0006826
... (many more lines like this)
If so, it could be that it is indexing correctly but my test is 2015AB specific
somehow.
Tim
On 01/29/2016 01:12 PM, Geise, Brandon D. wrote:
> java.lang.AssertionError
> at org.junit.Assert.fail(Assert.java:92)
> at org.junit.Assert.a
) is: C0006826
... (many more lines like this)
If so, it could be that it is indexing correctly but my test is 2015AB specific
somehow.
Tim
On 01/29/2016 01:12 PM, Geise, Brandon D. wrote:
> java.lang.AssertionError
> at org.junit.Assert.fail(Assert.java:92)
> at org.junit.Assert.a
Not to perpetuate the instructions again but I sent these out not long ago when
I was going through the process and Sean was helping me.
1. Change /data/default/CtakesSources.txt from "SNOMEDCT" to
"SNOMEDCT_US"
2. Copy ctakesumls.properties and ctakesumls.script from
wiki:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_
> confluence_display_CTAKES_cTAKES-2B3.2-2B-2D-2BFast-2BDictionary-2BLoo
> kup=BQIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZ
> stTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=SRqwsl3FmuUXq77GmVlfXn0lE0pVRkL53
> DNhukcaW6c=98W_vAH
The " RelationsExtractor" in the dictionary creator tool is completely
experimental and unfinished - but perhaps some day 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,
\apache\ctakes\dictionary\lookup\fast\cakesHsql.xml.
I've double checked all my paths and tried changing from relative to absolute
but still no luck? Has anyone run into this before and have a suggestion on
where to look?
Thanks,
Brandon
From: Geise, Brandon D.
Sent: Monday, September 21, 2015 9
/ - or
follow the rest of your strategy accordingly.
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Tuesday, September 22, 2015 7:28 AM
To: 'dev@ctakes.apache.org'
Subject: RE: Packaging Ctakes Application
As a follow-up I've followed the distribution
Hi All,
I've created a test application using Ctakes and now would like to package into
jar. What I've tried is creating a single jar with all resources in the JAR
and it starts loading the models as expected for the TokenizerAnnotatorPTB
(default from cTakes) but close to the end of the
The " RelationsExtractor" in the dictionary creator tool is completely
experimental and unfinished - but perhaps some day 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,
-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
file. It is a strange setup/workflow, but
it seems to work.
Sean
-Original Message-
From: Geise, Brandon D. [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
everything should be
moved from the .log to the .script file. It is a strange setup/workflow, but
it seems to work.
Sean
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Thursday, September 17, 2015 10:31 AM
To: dev@ctakes.apache.org
Subject: RE: Fast
org.apache.ctakes.dictionarytool.CodeMapCreator ? It isn't
strictly necessary but it stores the tuis in the database so that cTakes can
identify the semantic group of a mention.
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Thursday, September 17, 2015 1:02 PM
To: dev@ctakes.apache.org
?
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: 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
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 loaded?
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Thursday, September 17, 2015 12:54 PM
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, 2
ctly
> 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.
>
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
RCONSO.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 p
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
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,
Good afternoon,
I'm working on trying to recreate the UMLS 2011AB files in 2015AA. I've
checked out the dictionaryTool from Sandbox. In order to recreate the same
files my understanding is I'd need to run the dictionarytool with the following
argument:
* -umls path to UMLS 2015AA
*
Hi,
I'm new to cTakes and the UIMA framework. I've read most of the UIMA
documentation and was able to take the BagofCUIGenerator example and modify to
read notes from a DB, process using the UMLS AE in the clinical-pipeline using
a local DB version of UMLS, and output the CUIs to a DB.
think that it will make any difference
for cTakes.
Sean
From: Geise, Brandon D. [bdge...@geisinger.edu]
Sent: Friday, December 05, 2014 12:40 PM
To: dev@ctakes.apache.org
Subject: Scaling cTakes
Hi,
I'm new to cTakes and the UIMA framework. I've read
:29 PM, Geise, Brandon D. bdge...@geisinger.edu
wrote:
Thanks Sean. I'll take a look and see if this speeds the pipeline up.
Thanks,
Brandon
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Friday, December 05, 2014 1:14 PM
To: dev
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