Re: v_snomed_fword_lookup view
Hello Clayton,
I do not know about ytex, but I did switch from dictionary-lookup to
dictionary-lookup-fast.
I update my ctakes-dictionary-lookup-fast project using maven.
I think I used Team- Update and switched to the latest revision available
and then
I downloaded new 3.2 resources from the for umls. and then I added these
resources to my
ctakes-dictionary-lookup-fast resources folder and also the classpath in
ctakes-clinical-pipeline.
Then I changed the pom.xml file which belongs to the whole ctakes project
and
added
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-res/artifactId
version${ctakes.version}/version
/dependency
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-fast/artifactId
version${ctakes.version}/version
/dependency
these two dependencies to the file.
After this, I also added the dependency
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-fast/artifactId
/dependency
to the pom.xml of ctakes-clinical-pipeline.
And then add the resources folder in ctakes-clinical-pipeline using build
path configuration under add class option.
After this it should work.
Regards,
Harpreet
On Mon, Aug 11, 2014 at 12:44 PM, Clayton Turner caturn...@g.cofc.edu
wrote:
I still get the same error with the ctakes3.2 branch. Any suggestions?
On Mon, Aug 11, 2014 at 12:06 PM, Clayton Turner caturn...@g.cofc.edu
wrote:
I'm going to do a clean install through the repo rather than the binaries
and see if that fixes my issue because I think I just read a past post
saying the lookup2 folders exist there.
On Mon, Aug 11, 2014 at 11:52 AM, Clayton Turner caturn...@g.cofc.edu
wrote:
When navigating to ctakes-dictionary-lookup-fast\desc\analysis_engine
there are 2 files, assumedly analysis engines.
SnomedLookupAnnotator.xml and SnomedOvLookupAnnotator.xml
If I pick either, I put in my UMLS information but receive an error when
trying to run the CPE:
Initialization of CAS Processor with name SnomedOvLookupAnnotator
failed.
CausedBy: org.apache.uima.resource.ResourceConfigurationException:
Initialization of CAS processor with name SnomedOvLookupAnnotator
failed.
CausedBy: org.apache.uima.resource.ResourceInitializationException:
Error
initializing org.apache.uima.resource.impl.DataResource_impl from
descriptor
file:..SnomedLookupAnnotator.xml
CausedBy: org.apache.uima.resource.ResourceInitializationException:
Could
not
access the resource data at
file:org\apache\ctakes\dictionary\lookup2\Snomed2011ab_ctakesTui\cTakesSnomed.xml
Now, I don't even have a lookup2 folder and, subsequently the Tui
folder and cTakesSnomed.xml file. This seems to be the problem, but I'm
not
sure where these files are supposed to be grabbed from.
On Mon, Aug 11, 2014 at 11:47 AM, Clayton Turner caturn...@g.cofc.edu
wrote:
Hi again:
How exactly do you switch to using the cTakes dictionary-lookup-fast.
Do
I need to go in and alter xml files or is it as simple as adding a
certain
item to the list of analysis engines?
On Fri, Aug 8, 2014 at 3:48 PM, Finan, Sean
sean.fi...@childrens.harvard.edu wrote:
Hi Clayton,
I don't know how the ytex dictionary lookup works, so I'm afraid that
I
can't help you with an answer. Maybe Vijay is the best person to do
this.
If you aren't tied to ytex you could try the new cTakes
dictionary-lookup-fast. I tested Patient came in with a malar rash
and
it found malar and malar rash.
Vijay,
At some point the lookup-fast module will be the default for the
cTakes
clinical pipeline. In order to synchronize the ytex lookup with
cTakes,
would you like to eventually work together on reusing the same code
for
ytex? I have no idea what ytex does, but I know the ins and outs of
the
cdl-fast module.
Sean
-Original Message-
From: clayclay...@gmail.com [mailto:clayclay...@gmail.com] On
Behalf
Of
Clayton Turner
Sent: Friday, August 08, 2014 2:08 PM
To: dev@ctakes.apache.org
Subject: v_snomed_fword_lookup view
Hi Everyone:
I have a question about how the v_snomed_fword_lookup view works
when
running the CPE.
So my understanding of the view is that it is a view comprised of
the
ytex.umls_aui_fword table, the umls.mrconso table and bits/pieces
from
other umls tables.
I feel like this is not completely correct or my idea of how the
join
to
create the view works is off. For example, let's say I want the CPE
to find
malar (e.g. malar rash) as a concept in the annotations. It
never
happens after running my CPE descriptor and I cannot find it in my
v_snomed_fword_lookup view.
select count(*) from umls_aui_fword where fword='malar'; yields 34
results
select count(*) from umls.mrconso where str='malar'; yields 3
results.
So clearly these two tables know
RE: v_snomed_fword_lookup view
Thanks Harpreet,
That is definitely necessary to build!
Those lines should already be in the pom, but commented out. I think that some
version/branching issues may have arisen at some point wrt this module ...
If somebody beats me to it then cheers, otherwise I will try to check out
tonight and get all the bits in place.
Sean
-Original Message-
From: Harpreet Khanduja [mailto:hsk5...@rit.edu]
Sent: Monday, August 11, 2014 1:12 PM
To: dev@ctakes.apache.org
Subject: Re: v_snomed_fword_lookup view
Hello Clayton,
I do not know about ytex, but I did switch from dictionary-lookup to
dictionary-
lookup-fast.
I update my ctakes-dictionary-lookup-fast project using maven.
I think I used Team- Update and switched to the latest revision available
and
then
I downloaded new 3.2 resources from the for umls. and then I added these
resources to my
ctakes-dictionary-lookup-fast resources folder and also the classpath in
ctakes-
clinical-pipeline.
Then I changed the pom.xml file which belongs to the whole ctakes project and
added dependency groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-res/artifactId
version${ctakes.version}/version
/dependency
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-fast/artifactId
version${ctakes.version}/version
/dependency
these two dependencies to the file.
After this, I also added the dependency
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-fast/artifactId
/dependency
to the pom.xml of ctakes-clinical-pipeline.
And then add the resources folder in ctakes-clinical-pipeline using build path
configuration under add class option.
After this it should work.
Regards,
Harpreet
On Mon, Aug 11, 2014 at 12:44 PM, Clayton Turner caturn...@g.cofc.edu
wrote:
I still get the same error with the ctakes3.2 branch. Any suggestions?
On Mon, Aug 11, 2014 at 12:06 PM, Clayton Turner
caturn...@g.cofc.edu
wrote:
I'm going to do a clean install through the repo rather than the
binaries and see if that fixes my issue because I think I just read
a past post saying the lookup2 folders exist there.
On Mon, Aug 11, 2014 at 11:52 AM, Clayton Turner
caturn...@g.cofc.edu
wrote:
When navigating to
ctakes-dictionary-lookup-fast\desc\analysis_engine
there are 2 files, assumedly analysis engines.
SnomedLookupAnnotator.xml and SnomedOvLookupAnnotator.xml
If I pick either, I put in my UMLS information but receive an error
when trying to run the CPE:
Initialization of CAS Processor with name SnomedOvLookupAnnotator
failed.
CausedBy: org.apache.uima.resource.ResourceConfigurationException:
Initialization of CAS processor with name SnomedOvLookupAnnotator
failed.
CausedBy: org.apache.uima.resource.ResourceInitializationException:
Error
initializing org.apache.uima.resource.impl.DataResource_impl from
descriptor file:..SnomedLookupAnnotator.xml
CausedBy: org.apache.uima.resource.ResourceInitializationException:
Could
not
access the resource data at
file:org\apache\ctakes\dictionary\lookup2\Snomed2011ab_ctakesTui\cTake
sSnomed.xml
Now, I don't even have a lookup2 folder and, subsequently the Tui
folder and cTakesSnomed.xml file. This seems to be the problem, but
I'm
not
sure where these files are supposed to be grabbed from.
On Mon, Aug 11, 2014 at 11:47 AM, Clayton Turner
caturn...@g.cofc.edu
wrote:
Hi again:
How exactly do you switch to using the cTakes dictionary-lookup-fast.
Do
I need to go in and alter xml files or is it as simple as adding a
certain
item to the list of analysis engines?
On Fri, Aug 8, 2014 at 3:48 PM, Finan, Sean
sean.fi...@childrens.harvard.edu wrote:
Hi Clayton,
I don't know how the ytex dictionary lookup works, so I'm afraid
that
I
can't help you with an answer. Maybe Vijay is the best person to
do
this.
If you aren't tied to ytex you could try the new cTakes
dictionary-lookup-fast. I tested Patient came in with a malar rash
and
it found malar and malar rash.
Vijay,
At some point the lookup-fast module will be the default for the
cTakes
clinical pipeline. In order to synchronize the ytex lookup with
cTakes,
would you like to eventually work together on reusing the same
code
for
ytex? I have no idea what ytex does, but I know the ins and outs
of
the
cdl-fast module.
Sean
-Original Message-
From: clayclay...@gmail.com [mailto:clayclay...@gmail.com] On
Behalf
Of
Clayton Turner
Sent: Friday, August 08, 2014 2:08 PM
To: dev@ctakes.apache.org
Subject: v_snomed_fword_lookup view
Hi Everyone:
I have a question about how the v_snomed_fword_lookup view
works
when
running the CPE.
Re: v_snomed_fword_lookup view
Yes, absolutely and
no problem at all.
Regards,
Harpreet
On Mon, Aug 11, 2014 at 1:16 PM, Finan, Sean
sean.fi...@childrens.harvard.edu wrote:
Thanks Harpreet,
That is definitely necessary to build!
Those lines should already be in the pom, but commented out. I think that
some version/branching issues may have arisen at some point wrt this module
...
If somebody beats me to it then cheers, otherwise I will try to check out
tonight and get all the bits in place.
Sean
-Original Message-
From: Harpreet Khanduja [mailto:hsk5...@rit.edu]
Sent: Monday, August 11, 2014 1:12 PM
To: dev@ctakes.apache.org
Subject: Re: v_snomed_fword_lookup view
Hello Clayton,
I do not know about ytex, but I did switch from dictionary-lookup to
dictionary-
lookup-fast.
I update my ctakes-dictionary-lookup-fast project using maven.
I think I used Team- Update and switched to the latest revision
available and
then
I downloaded new 3.2 resources from the for umls. and then I added
these
resources to my
ctakes-dictionary-lookup-fast resources folder and also the classpath
in ctakes-
clinical-pipeline.
Then I changed the pom.xml file which belongs to the whole ctakes
project and
added dependency groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-res/artifactId
version${ctakes.version}/version
/dependency
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-fast/artifactId
version${ctakes.version}/version
/dependency
these two dependencies to the file.
After this, I also added the dependency
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-fast/artifactId
/dependency
to the pom.xml of ctakes-clinical-pipeline.
And then add the resources folder in ctakes-clinical-pipeline using
build path
configuration under add class option.
After this it should work.
Regards,
Harpreet
On Mon, Aug 11, 2014 at 12:44 PM, Clayton Turner caturn...@g.cofc.edu
wrote:
I still get the same error with the ctakes3.2 branch. Any suggestions?
On Mon, Aug 11, 2014 at 12:06 PM, Clayton Turner
caturn...@g.cofc.edu
wrote:
I'm going to do a clean install through the repo rather than the
binaries and see if that fixes my issue because I think I just read
a past post saying the lookup2 folders exist there.
On Mon, Aug 11, 2014 at 11:52 AM, Clayton Turner
caturn...@g.cofc.edu
wrote:
When navigating to
ctakes-dictionary-lookup-fast\desc\analysis_engine
there are 2 files, assumedly analysis engines.
SnomedLookupAnnotator.xml and SnomedOvLookupAnnotator.xml
If I pick either, I put in my UMLS information but receive an error
when trying to run the CPE:
Initialization of CAS Processor with name SnomedOvLookupAnnotator
failed.
CausedBy: org.apache.uima.resource.ResourceConfigurationException:
Initialization of CAS processor with name SnomedOvLookupAnnotator
failed.
CausedBy: org.apache.uima.resource.ResourceInitializationException:
Error
initializing org.apache.uima.resource.impl.DataResource_impl from
descriptor file:..SnomedLookupAnnotator.xml
CausedBy: org.apache.uima.resource.ResourceInitializationException:
Could
not
access the resource data at
file:org\apache\ctakes\dictionary\lookup2\Snomed2011ab_ctakesTui\cTake
sSnomed.xml
Now, I don't even have a lookup2 folder and, subsequently the Tui
folder and cTakesSnomed.xml file. This seems to be the problem, but
I'm
not
sure where these files are supposed to be grabbed from.
On Mon, Aug 11, 2014 at 11:47 AM, Clayton Turner
caturn...@g.cofc.edu
wrote:
Hi again:
How exactly do you switch to using the cTakes
dictionary-lookup-fast.
Do
I need to go in and alter xml files or is it as simple as adding a
certain
item to the list of analysis engines?
On Fri, Aug 8, 2014 at 3:48 PM, Finan, Sean
sean.fi...@childrens.harvard.edu wrote:
Hi Clayton,
I don't know how the ytex dictionary lookup works, so I'm afraid
that
I
can't help you with an answer. Maybe Vijay is the best person to
do
this.
If you aren't tied to ytex you could try the new cTakes
dictionary-lookup-fast. I tested Patient came in with a malar
rash
and
it found malar and malar rash.
Vijay,
At some point the lookup-fast module will be the default for the
cTakes
clinical pipeline. In order to synchronize the ytex lookup with
cTakes,
would you like to eventually work together on reusing the same
code
for
ytex? I have no idea what ytex does, but I know the ins and outs
of
the
cdl-fast module.
Sean
-Original Message-
From: clayclay...@gmail.com
