Re: v_snomed_fword_lookup view
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 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 > -- -- Clayton Turner email: caturn...@g.cofc.edu phone: (843)-424-3784 web: claytonturner.blogspot.com - “When scientifically investigating the natural world, the only thing worse than a blind believer is a seeing denier.” - Neil deGrasse Tyson
Re: v_snomed_fword_lookup view
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 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 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 >> > > > > -- > -- > Clayton Turner > email: caturn...@g.cofc.edu > phone: (843)-424-3784 > web: claytonturner.blogspot.com > > - > “When scientifically investigating the natural world, the only thing worse > than a blind believer is a seeing denier.” > - Neil deGrasse Tyson > -- -- Clayton Turner email: caturn...@g.cofc.edu phone: (843)-424-3784 web: claytonturner.blogspot.com - “When scientifically investigating the natural world, the only thing worse than a blind believer is a seeing denier.” - Neil deGrasse Tyson
Re: v_snomed_fword_lookup view
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 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 > 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 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 >>> >> >> >> >> -- >> -- >> Clayton Turner >> email: caturn...@g.cofc.edu >> phone: (843)-424-3784 >> web: claytonturner.blogspot.com >> >> - >> “When scientifically investigating the natural world, the only thing >> worse than a blind believer is a seeing denier.” >> - Neil deGrasse Tyson >> > > > > -- > -- > Clayton Turner > email: caturn...@g.cofc.edu > phone: (843)-424-3784 > web: claytonturner.blogspot.com > > -
Re: v_snomed_fword_lookup view
I still get the same error with the ctakes3.2 branch. Any suggestions? On Mon, Aug 11, 2014 at 12:06 PM, Clayton Turner 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 > 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 >> 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 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 >>> >>> >>> >>> -- >>> -- >>> Clayton Turner >>> email: caturn...@g.cofc.edu >>> phone: (843)-424-3784 >>> web: claytonturner.blogspot.com >>> >>> - >>> “When scientifically investigating the natural world, the only t
RE: v_snomed_fword_lookup view
Hi Clay, It has been a hectic day and I apologize for the late reply. > 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. I think that all directories "lookup2" were renamed "lookup-fast", but it looks like the links in the xml descriptors were not updated to match. In the SnomedLookupAnnotator.xml (or Ov equivalent), find DictionaryDescriptorFile file:org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml And adjust the file url accordingly. I haven't checked out trunk since the code was moved (I've been busy with other things), but the equivalent file should not be difficult to find. Unless you are on Windows the entire path to the dictionary database must be lowercase for hsql to work. I think that was checked in, but if it hasn't been then you'll need to rename the directory (and hsql files) to be all lower-case. Also, edit the line to match the rename in the cTakesSnomed.xml If you get this working could you please check in the changes? At some point I can do a full checkout and do it myself, but I won't get to it for a while. Sean > -Original Message- > From: clayclay...@gmail.com [mailto:clayclay...@gmail.com] On Behalf Of > Clayton Turner > Sent: Monday, August 11, 2014 11:53 AM > To: dev@ctakes.apache.org > Subject: Re: v_snomed_fword_lookup view > > 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\cTakesSn > omed.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 > 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 what the cui
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
org.apache.ctakes
ctakes-dictionary-lookup-res
${ctakes.version}
org.apache.ctakes
ctakes-dictionary-lookup-fast
${ctakes.version}
these two dependencies to the file.
After this, I also added the dependency
org.apache.ctakes
ctakes-dictionary-lookup-fast
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
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
> 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
> > 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
> >> 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
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 org.apache.ctakes
> ctakes-dictionary-lookup-res
> ${ctakes.version}
>
>
> org.apache.ctakes
> ctakes-dictionary-lookup-fast
> ${ctakes.version}
>
>
>
> these two dependencies to the file.
>
>
> After this, I also added the dependency
>
> org.apache.ctakes
> ctakes-dictionary-lookup-fast
>
>
> 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
> 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
> >
> > 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
> > >
> > > 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
> > >>
> > >> 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,
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 org.apache.ctakes
> > ctakes-dictionary-lookup-res
> > ${ctakes.version}
> >
> >
> > org.apache.ctakes
> > ctakes-dictionary-lookup-fast
> > ${ctakes.version}
> >
> >
> >
> > these two dependencies to the file.
> >
> >
> > After this, I also added the dependency
> >
> > org.apache.ctakes
> > ctakes-dictionary-lookup-fast
> >
> >
> > 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
> > 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
> > >
> > > 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
> > > >
> > > > 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
> > > >>
> > > >> 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,
>
