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
-Or
Hi all,
For those that may be interested, I've just released a small web app, developed
in Python Flask and Javascript, to view Ctakes annotations from XMIs in a
batch. It can be found at https://github.com/GeisingerBTI/AnnotViewer. Feel
free to contribute if you'd like and I hope some find i
I've used the demos as a resource for building web applications with Ctakes and
would suggest taking a look at http://healthnlp.github.io/examples/
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, May 16, 2016 3:00 PM
To: dev@ctakes.apache.org
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
ected coding
schemes to the concept factory. Is it not doing what you need?
Sean
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, March 02, 2016 12:43 PM
To: 'dev@ctakes.apache.org'
Subject: JdbcConceptFactory Fast Dictionary
Hi
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
org.apache.ctakes
pernym) 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.juni
cestor (hypernym) 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)
> a
graph api
I was using 2015AB. Can you copy/paste the error trace that junit gives you?
Thanks
Tim
On 01/29/2016 01:04 PM, Geise, Brandon D. wrote:
> Very cool.
>
> I started going through your instructions. Everything seemed to be working
> except for the GraphFunction Junit test
Very cool.
I started going through your instructions. Everything seemed to be working
except for the GraphFunction Junit test fails on the first assertion. I'm
using 2015AA and it doesn't appear that the isa relationship holds true, unless
I messed something up. What UMLS version did you tes
; >
>> > I found couple of issues in the dictionary tool, it does not work
>> > well with relative paths.
>> >
>> >
>> > On Wed, Dec 9, 2015 at 7:11 AM, Pei Chen wrote:
>> >
>> >> Brandon,
>> >> That sounds great!
>
t; write directly in trunk (??) and need to get moving on to other things.
>
> There is help on the ctakes 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&d=BQIBaQ&c=q
te
> directly in trunk (??) and need to get moving on to other things.
>
> There is help on the ctakes wiki:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+-+Fast+Dictionary+Lookup
> Though I should probably add a few items ...
>
>
> Sean
>
>
> -Original Mess
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 memdbtempla
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: Ge
ar for lib/ - 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
resources\org\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,
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-
Fro
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 loadi
the steps you did so far
and post them here.
Regards,
Tomasz
____________
From: Geise, Brandon D. [bdge...@geisinger.edu]
Sent: Thursday, September 17, 2015 4:18 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
I'm getting output now with CUIs. I think
You can disregard my question about the relation extraction as I fixed this by
building the new dictionary with the default data files in the dictionarytool.
I am curious about the SNOMED change still though.
Thanks,
Brandon
-Original Message-
From: Geise, Brandon D.
Sent: Thursday
ps something
will click with me later ...
Did you also run 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
u also run 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@ct
oaded?
-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
up 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
Subject: RE: Fast Dictionary Update
Not specifically loaded. Here's what I see when loading the pipeline:
17 Sep 2015 12:58:54 INFO J
py 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:
of the sql tool 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
Su
he .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 Dictionary Update
When I run the tool it outp
-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
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.
Thank
me 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<mailto:bdge...@geisinger.edu>]
Sent: Wednesday, September 16, 2015 5:05 PM
SO.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 piec
as 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
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.
kup-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 fo
sday, 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: Wednes
rong 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&
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
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"
he AE. Check
ctakes-clinical-pipeline/desc/[ae]/AggregatePlaintextFastUMLSProcessor.xml for
an example. As for the CASPool, I don't think that it will make any difference
for cTakes.
Sean
____
From: Geise, Brandon D. [bdge...@geisinger.edu]
Sent: Friday, D
2014 at 1:29 PM, Geise, Brandon D.
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, 2
l, I don't 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 f
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. Howev
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