Re: v_snomed_fword_lookup view
Okay, I believe I have ctakes dictionary fast working now. Something I'm
curious about, though, is how you extract the data in order to conduct
analysis.
I've, in the past, been using the SparseDataExporterImpl from ytex in order
to create a .arff file for use in weka, but the ctakes pipeline I'm using
doesn't seem to be compatible with this ytex exporting as I'm not getting
any cuis in my arff file.
I'm using the aggregate plain text umls processor analysis engine from
ctakes and then using the dbconsumer analysis engine from ytex (for storing
into the database with regard to analysis batch).
Any tips for exporting or some simple issue I'm missing?
Thanks,
Clayton
On Mon, Aug 11, 2014 at 2:09 PM, Harpreet Khanduja hsk5...@rit.edu wrote:
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
RE: v_snomed_fword_lookup view
is the purpose of a CasConsumer to essentially save your data
Correct, though it is a generic (and archaic) term indicating any end-user of
the cas.
-Original Message-
From: clayclay...@gmail.com [mailto:clayclay...@gmail.com] On Behalf Of
Clayton Turner
Sent: Wednesday, August 13, 2014 2:10 PM
To: dev@ctakes.apache.org
Subject: Re: v_snomed_fword_lookup view
Oh okay, so is the purpose of a CasConsumer to essentially save your data in a
representation that you can do some kind of data mining or classification on
it?
If so, then I think I need to look into making/using one of those.
On Wed, Aug 13, 2014 at 1:41 PM, Finan, Sean
sean.fi...@childrens.harvard.edu wrote:
Hi Clayton,
I'm glad that you got it working. Though I stated that I would, I
haven't yet checked the fidelity of trunk. Urgent data request one
day, must have writing the next ... and I still live with the
delusion that I left academia to have free time ...
I have never used ytex or weka, so I'm unfamiliar with all things .arff .
Could it be that the ytex .arff exporter needs to change consumed
cTakes annotation classes (3.1)?
I have a custom CasConsumer that saves text spans and Cuis to file in
a simple list, and that is what I used for the performance analysis of
the lookup module. For our other projects here in Beantown we have
other various outputs that fit the job at hand: text flat files, xml
files, sql database tables, knot-encoded lace doilies, etc.
I'm sure that none of the above helps you, but I felt obliged to
provide some kind of answer to your question.
Sean
-Original Message-
From: clayclay...@gmail.com [mailto:clayclay...@gmail.com] On Behalf
Of Clayton Turner
Sent: Wednesday, August 13, 2014 12:25 PM
To: dev@ctakes.apache.org
Subject: Re: v_snomed_fword_lookup view
Okay, I believe I have ctakes dictionary fast working now. Something
I'm
curious
about, though, is how you extract the data in order to conduct analysis.
I've, in the past, been using the SparseDataExporterImpl from ytex
in
order to
create a .arff file for use in weka, but the ctakes pipeline I'm
using
doesn't seem
to be compatible with this ytex exporting as I'm not getting any
cuis in
my arff
file.
I'm using the aggregate plain text umls processor analysis engine
from
ctakes
and then using the dbconsumer analysis engine from ytex (for storing
into the
database with regard to analysis batch).
Any tips for exporting or some simple issue I'm missing?
Thanks,
Clayton
On Mon, Aug 11, 2014 at 2:09 PM, Harpreet Khanduja hsk5...@rit.edu
wrote:
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
RE: v_snomed_fword_lookup view
You can find example Cas Consumers in cTakes-core ..[dirPath]../cc/
-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Wednesday, August 13, 2014 2:20 PM
To: dev@ctakes.apache.org
Subject: Re: v_snomed_fword_lookup view
There's nothing conceptually special about the consumer model vs.
regular annotators (Analysis Engines). You can write an output format from any
analysis engine as long as it is after the annotations you need in the
pipeline. If
you have global constraints (like in an ARFF file I think you need to know
all the
CUIs in your corpus to write the attribute list?), then it is important to
use the
process() method [called once per document] to store CUIs in a non-UIMA class
variable (for example, a map from file id to a list/set/multiset of CUIs),
and then
use the collectionProcessComplete() [called once after all documents have been
processed] method to do the actual writing of the file.
Hope that is useful, sorry I couldn't tie it in to your previous YTEX
exporter but
I'm not familiar with that process.
Tim
On 08/13/2014 02:11 PM, Clayton Turner wrote:
Oh okay, so is the purpose of a CasConsumer to essentially save your
data in a representation that you can do some kind of data mining or
classification on it? If so, then I think I need to look into
making/using one of those.
On Wed, Aug 13, 2014 at 1:41 PM, Finan, Sean
sean.fi...@childrens.harvard.edu wrote:
Hi Clayton,
I'm glad that you got it working. Though I stated that I would, I
haven't yet checked the fidelity of trunk. Urgent data request one
day, must have writing the next ... and I still live with the
delusion that I left academia to have free time ...
I have never used ytex or weka, so I'm unfamiliar with all things .arff .
Could it be that the ytex .arff exporter needs to change consumed
cTakes annotation classes (3.1)?
I have a custom CasConsumer that saves text spans and Cuis to file in
a simple list, and that is what I used for the performance analysis
of the lookup module. For our other projects here in Beantown we
have other various outputs that fit the job at hand: text flat files,
xml files, sql database tables, knot-encoded lace doilies, etc.
I'm sure that none of the above helps you, but I felt obliged to
provide some kind of answer to your question.
Sean
-Original Message-
From: clayclay...@gmail.com [mailto:clayclay...@gmail.com] On Behalf
Of Clayton Turner
Sent: Wednesday, August 13, 2014 12:25 PM
To: dev@ctakes.apache.org
Subject: Re: v_snomed_fword_lookup view
Okay, I believe I have ctakes dictionary fast working now. Something
I'm
curious
about, though, is how you extract the data in order to conduct analysis.
I've, in the past, been using the SparseDataExporterImpl from ytex
in
order to
create a .arff file for use in weka, but the ctakes pipeline I'm
using
doesn't seem
to be compatible with this ytex exporting as I'm not getting any
cuis in
my arff
file.
I'm using the aggregate plain text umls processor analysis engine
from
ctakes
and then using the dbconsumer analysis engine from ytex (for storing
into the
database with regard to analysis batch).
Any tips for exporting or some simple issue I'm missing?
Thanks,
Clayton
On Mon, Aug 11, 2014 at 2:09 PM, Harpreet Khanduja hsk5...@rit.edu
wrote:
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${ctakes.version}/version
/dependency
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes
Re: v_snomed_fword_lookup view
Hello Clayton,
I do not know about ytex, but I did switch from dictionary-lookup to
dictionary-lookup-fast.
I update my ctakes-dictionary-lookup-fast project using maven.
I think I used Team- Update and switched to the latest revision available
and then
I downloaded new 3.2 resources from the for umls. and then I added these
resources to my
ctakes-dictionary-lookup-fast resources folder and also the classpath in
ctakes-clinical-pipeline.
Then I changed the pom.xml file which belongs to the whole ctakes project
and
added
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-res/artifactId
version${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 [mailto:clayclay
RE: v_snomed_fword_lookup view
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 what the cui and context(s) are for malar . Yet, whenever I run a gold standard set of notes through the CPE, malar is constantly flagged as just a word token and the concept is never grabbed. This is recurrent for lots of other concepts, as well, I just wanted to use an example to illustrate my issue. Some troubleshooting I already went through: 1) Reinstalled ytex and umls database objects 2) Reinstalled a second time after redownloading umls through metamorphosys, ensuring that snomed vocabularies were included (also checked file sizes and noticed a big difference so I know those vocabularies ARE included Anyone got any ideas as to what the issue could be? Thank you, Clayton Turner
