Re: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup
That would definitely make sense
On Thursday, August 21, 2014, Chen, Pei
wrote:
> VJ,
> Would it make sense to add in('SNOMEDCT_US') to the default
> ctakes-ytex/scripts/data/**/insert_view.sql?
> That way it'll support umls2011 as well as the newer 2014 naming
> conventions?
> Ex: inner join MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( 'SNOMEDCT',
> 'SNOMEDCT_US','RXNORM')
>
> --Pei
>
> > -Original Message-
> > From: clayclay...@gmail.com [mailto:clayclay...@gmail.com
> ] On Behalf Of
> > Clayton Turner
> > Sent: Thursday, August 21, 2014 4:25 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: Change from SNOMEDCT to SNOMEDCT_US affecting
> > v_snomed_fword_lookup
> >
> > Ah, I just switched to the ytex branch and all is good now. The SNOMED_US
> > issue has been plaguing me for weeks now so thanks a million for that.
> >
> >
> > On Thu, Aug 21, 2014 at 2:13 PM, Clayton Turner >
> > wrote:
> >
> > > Awesome. This is just what I needed for the longest time.
> > >
> > > I'm having a slight issue. When running either the ytex pipeline or
> > > ytex version of the AggregatePlaintextUMLSProcessor I get an error
> > > during initialization.
> > >
> > > My DictionaryLookupAnnotator.xml is raising a
> > > org.apache.uima.resource.ResourceInitializationException causedby:
> > > java.lang.ClassNotFoundException:
> > > edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
> > >
> > > I feel like I may have drifted away from what I need, though, because
> > > before this the CPE was complaining about a lack of
> > > LookupDesc_SNOMED.xml file. I found a ytex version of this on a google
> > > code site somewhere and pasted it where the CPE was looking for it. Now
> > this error is coming up.
> > >
> > > Could my problem be solved with just a re-run of the ant script (was
> > > just trying to avoid since it takes ages) or is it a different issue?
> > >
> > >
> > > On Tue, Aug 19, 2014 at 12:58 PM, Tim O'Connell
> > > >
> > > wrote:
> > >
> > >> Hi John,
> > >>
> > >> I'm not sure what was going on with the @db.schema@ error, although I
> > >> was getting it as well before with my prior build of 3.1.2 - I assume
> > >> that you've fixed something (thank you!) to make this go away. I
> > >> rebuilt everything from scratch and it's working now.
> > >>
> > >> I think one other thing I had to change was that after I had finished
> > >> the install/build, the cTakes version of LookupDesc_Db.xml doesn't
> > >> work (in
> > >> resources\org\apache\ctakes\dictionary\lookup) - I'm pretty sure I
> > >> had to copy in an older version of the file from 3.1.1 to get the
> > >> default cTakes AggregatePlaintextUMLSProcessor pipeline working,
> > >> although please double-check that as my memory is a little foggy.
> > >>
> > >> But yes, here's what I have working since re-building:
> > >> 1. ytex-pipeline.xml
> > >> 2. ytex version of AggregatePlaintextUMLSProcessor.xml
> > >> 3. cTakes version of AggregatePlaintextUMLSProcessor.xml (with
> > >> swapping the LookupDesc_Db.xml file as above)
> > >>
> > >> I've even made modifications to the ytex version of
> > >> LookupDesc_SNOMED.xml to get it tagging Disease Disorders, along with
> > database modifications to
> > >> have it store these entries as well, which is working great.
> Literally,
> > >> everything is working perfectly now.
> > >>
> > >> Still so much for me to learn! Let me know if you need any more
> details.
> > >>
> > >> All the best,
> > >> Tim
> > >>
> > >>
> > >>
> > >> On Tue, Aug 19, 2014 at 4:31 AM, John Green
> > >> >
> > >> wrote:
> > >>
> > >> > I have not had time to implement this - to clarify out of
> > >> > curiosity,
> > >> does
> > >> > this clear up the @db.schema@ error Tim? And did you successfully
> > >> > run ytex with the ctakes dictionary-lookup?
> > >> >
> > >> >
> > >> > JG
> > >> > —
> > >> > Sent from Mailbox for iPhone
> > >> >
> > >> > On Sat, Aug 16, 2014 at 2:53 AM, Tim O'Connell
> > >> > >
> > >> > wrote:
> > >> >
> > >> > > Hi folks,
> > >> > > I was having an issue with the current build (from svn) of
> > >> > > ctakes/ytex
> > >> > not
> > >> > > identifying any annotations as some folks on this board. I
> > >> > > traced it
> > >> to
> > >> > > the fact that the UMLS database has at sometime in the relatively
> > >> recent
> > >> > > past changed the SAB tag in the MRCONSO table for SNOMED terms
> > >> > > from SNOMEDCT to SNOMEDCT_US. I just had a newer version of
> > UMLS
> > >> > > that uses SNOMEDCT_US. Thus when the install script tried to
> > >> > > create the v_snomed_fword_lookup table, it wasn't finding any of
> > >> > > the SNOMEDCT
> > >> terms,
> > >> > > thus nothing was getting annotated.
> > >> > > The ytex install script was just looking for things in MRCONSO
> > >> > > with
> > >> the
> > >> > > SNOMEDCT SAB tag when it created the ytex lookup table - so, by
> > >> changing
> > >> > > this to SNOMEDCT_US in the file
> > >> > >
> > >> >
> > >> CTAKES_HOME/bin/ctakes-
> > ytex/scripts/data/m
Re: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup
It didn't fix the @db.schema@ - I just went in and manually changed it whenever the CPE complained. I assume that's supposed to be reading from ytex.properties, but mine was set and it didn't resolve that @db.schema@ issue. On Thu, Aug 21, 2014 at 5:00 PM, John Green wrote: > Clayton - this indeed did fix the @db.schema@ for you? Im gonna try and > reproduce (havent had time yet) then ill close the Jira ticket out. > > > JG > — > Sent from Mailbox for iPhone > > On Thu, Aug 21, 2014 at 1:24 PM, Clayton Turner > wrote: > > > Ah, I just switched to the ytex branch and all is good now. The SNOMED_US > > issue has been plaguing me for weeks now so thanks a million for that. > > On Thu, Aug 21, 2014 at 2:13 PM, Clayton Turner > > wrote: > >> Awesome. This is just what I needed for the longest time. > >> > >> I'm having a slight issue. When running either the ytex pipeline or ytex > >> version of the AggregatePlaintextUMLSProcessor I get an error during > >> initialization. > >> > >> My DictionaryLookupAnnotator.xml is raising a > >> org.apache.uima.resource.ResourceInitializationException causedby: > >> java.lang.ClassNotFoundException: > >> edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl > >> > >> I feel like I may have drifted away from what I need, though, because > >> before this the CPE was complaining about a lack of > LookupDesc_SNOMED.xml > >> file. I found a ytex version of this on a google code site somewhere and > >> pasted it where the CPE was looking for it. Now this error is coming up. > >> > >> Could my problem be solved with just a re-run of the ant script (was > just > >> trying to avoid since it takes ages) or is it a different issue? > >> > >> > >> On Tue, Aug 19, 2014 at 12:58 PM, Tim O'Connell > > >> wrote: > >> > >>> Hi John, > >>> > >>> I'm not sure what was going on with the @db.schema@ error, although I > was > >>> getting it as well before with my prior build of 3.1.2 - I assume that > >>> you've fixed something (thank you!) to make this go away. I rebuilt > >>> everything from scratch and it's working now. > >>> > >>> I think one other thing I had to change was that after I had finished > the > >>> install/build, the cTakes version of LookupDesc_Db.xml doesn't work (in > >>> resources\org\apache\ctakes\dictionary\lookup) - I'm pretty sure I had > to > >>> copy in an older version of the file from 3.1.1 to get the default > cTakes > >>> AggregatePlaintextUMLSProcessor pipeline working, although please > >>> double-check that as my memory is a little foggy. > >>> > >>> But yes, here's what I have working since re-building: > >>> 1. ytex-pipeline.xml > >>> 2. ytex version of AggregatePlaintextUMLSProcessor.xml > >>> 3. cTakes version of AggregatePlaintextUMLSProcessor.xml (with swapping > >>> the > >>> LookupDesc_Db.xml file as above) > >>> > >>> I've even made modifications to the ytex version of > LookupDesc_SNOMED.xml > >>> to get it tagging Disease Disorders, along with database modifications > to > >>> have it store these entries as well, which is working great. > Literally, > >>> everything is working perfectly now. > >>> > >>> Still so much for me to learn! Let me know if you need any more > details. > >>> > >>> All the best, > >>> Tim > >>> > >>> > >>> > >>> On Tue, Aug 19, 2014 at 4:31 AM, John Green < > john.travis.gr...@gmail.com> > >>> wrote: > >>> > >>> > I have not had time to implement this - to clarify out of curiosity, > >>> does > >>> > this clear up the @db.schema@ error Tim? And did you successfully > run > >>> > ytex with the ctakes dictionary-lookup? > >>> > > >>> > > >>> > JG > >>> > — > >>> > Sent from Mailbox for iPhone > >>> > > >>> > On Sat, Aug 16, 2014 at 2:53 AM, Tim O'Connell < > tim.oconn...@gmail.com> > >>> > wrote: > >>> > > >>> > > Hi folks, > >>> > > I was having an issue with the current build (from svn) of > ctakes/ytex > >>> > not > >>> > > identifying any annotations as some folks on this board. I traced > it > >>> to > >>> > > the fact that the UMLS database has at sometime in the relatively > >>> recent > >>> > > past changed the SAB tag in the MRCONSO table for SNOMED terms from > >>> > > SNOMEDCT to SNOMEDCT_US. I just had a newer version of UMLS that > uses > >>> > > SNOMEDCT_US. Thus when the install script tried to create the > >>> > > v_snomed_fword_lookup table, it wasn't finding any of the SNOMEDCT > >>> terms, > >>> > > thus nothing was getting annotated. > >>> > > The ytex install script was just looking for things in MRCONSO with > >>> the > >>> > > SNOMEDCT SAB tag when it created the ytex lookup table - so, by > >>> changing > >>> > > this to SNOMEDCT_US in the file > >>> > > > >>> > > >>> > CTAKES_HOME/bin/ctakes-ytex/scripts/data/mysql/umls/insert_view_template.sql > >>> > > it now works (for mysql users) to find the annotations. You can > just > >>> > re-run > >>> > > the ytex setup script, but that takes hours - instead, I just > deleted > >>> all > >>> > > the data from the v_snomed_fword_lookup tabl
Re: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup
Clayton - this indeed did fix the @db.schema@ for you? Im gonna try and reproduce (havent had time yet) then ill close the Jira ticket out. JG — Sent from Mailbox for iPhone On Thu, Aug 21, 2014 at 1:24 PM, Clayton Turner wrote: > Ah, I just switched to the ytex branch and all is good now. The SNOMED_US > issue has been plaguing me for weeks now so thanks a million for that. > On Thu, Aug 21, 2014 at 2:13 PM, Clayton Turner > wrote: >> Awesome. This is just what I needed for the longest time. >> >> I'm having a slight issue. When running either the ytex pipeline or ytex >> version of the AggregatePlaintextUMLSProcessor I get an error during >> initialization. >> >> My DictionaryLookupAnnotator.xml is raising a >> org.apache.uima.resource.ResourceInitializationException causedby: >> java.lang.ClassNotFoundException: >> edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl >> >> I feel like I may have drifted away from what I need, though, because >> before this the CPE was complaining about a lack of LookupDesc_SNOMED.xml >> file. I found a ytex version of this on a google code site somewhere and >> pasted it where the CPE was looking for it. Now this error is coming up. >> >> Could my problem be solved with just a re-run of the ant script (was just >> trying to avoid since it takes ages) or is it a different issue? >> >> >> On Tue, Aug 19, 2014 at 12:58 PM, Tim O'Connell >> wrote: >> >>> Hi John, >>> >>> I'm not sure what was going on with the @db.schema@ error, although I was >>> getting it as well before with my prior build of 3.1.2 - I assume that >>> you've fixed something (thank you!) to make this go away. I rebuilt >>> everything from scratch and it's working now. >>> >>> I think one other thing I had to change was that after I had finished the >>> install/build, the cTakes version of LookupDesc_Db.xml doesn't work (in >>> resources\org\apache\ctakes\dictionary\lookup) - I'm pretty sure I had to >>> copy in an older version of the file from 3.1.1 to get the default cTakes >>> AggregatePlaintextUMLSProcessor pipeline working, although please >>> double-check that as my memory is a little foggy. >>> >>> But yes, here's what I have working since re-building: >>> 1. ytex-pipeline.xml >>> 2. ytex version of AggregatePlaintextUMLSProcessor.xml >>> 3. cTakes version of AggregatePlaintextUMLSProcessor.xml (with swapping >>> the >>> LookupDesc_Db.xml file as above) >>> >>> I've even made modifications to the ytex version of LookupDesc_SNOMED.xml >>> to get it tagging Disease Disorders, along with database modifications to >>> have it store these entries as well, which is working great. Literally, >>> everything is working perfectly now. >>> >>> Still so much for me to learn! Let me know if you need any more details. >>> >>> All the best, >>> Tim >>> >>> >>> >>> On Tue, Aug 19, 2014 at 4:31 AM, John Green >>> wrote: >>> >>> > I have not had time to implement this - to clarify out of curiosity, >>> does >>> > this clear up the @db.schema@ error Tim? And did you successfully run >>> > ytex with the ctakes dictionary-lookup? >>> > >>> > >>> > JG >>> > — >>> > Sent from Mailbox for iPhone >>> > >>> > On Sat, Aug 16, 2014 at 2:53 AM, Tim O'Connell >>> > wrote: >>> > >>> > > Hi folks, >>> > > I was having an issue with the current build (from svn) of ctakes/ytex >>> > not >>> > > identifying any annotations as some folks on this board. I traced it >>> to >>> > > the fact that the UMLS database has at sometime in the relatively >>> recent >>> > > past changed the SAB tag in the MRCONSO table for SNOMED terms from >>> > > SNOMEDCT to SNOMEDCT_US. I just had a newer version of UMLS that uses >>> > > SNOMEDCT_US. Thus when the install script tried to create the >>> > > v_snomed_fword_lookup table, it wasn't finding any of the SNOMEDCT >>> terms, >>> > > thus nothing was getting annotated. >>> > > The ytex install script was just looking for things in MRCONSO with >>> the >>> > > SNOMEDCT SAB tag when it created the ytex lookup table - so, by >>> changing >>> > > this to SNOMEDCT_US in the file >>> > > >>> > >>> CTAKES_HOME/bin/ctakes-ytex/scripts/data/mysql/umls/insert_view_template.sql >>> > > it now works (for mysql users) to find the annotations. You can just >>> > re-run >>> > > the ytex setup script, but that takes hours - instead, I just deleted >>> all >>> > > the data from the v_snomed_fword_lookup table and basically ran the >>> sql >>> > > command to repopulate the table and it worked fine. Here's the code, >>> n.b. >>> > > my schema name for my umls database is 'umls' - change the code below >>> if >>> > > yours is different. >>> > > delete from v_snomed_fword_lookup; >>> > > insert into v_snomed_fword_lookup (cui, tui, fword, fstem, tok_str, >>> > > stem_str) >>> > > select mrc.cui, t.tui, c.fword, c.fstem, c.tok_str, c.stem_str >>> > > from umls_aui_fword c >>> > > inner join umls.MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( >>> > > 'SNOMEDCT_US', 'RXNORM') >>> > > inner join >
RE: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup
VJ,
Would it make sense to add in('SNOMEDCT_US') to the default
ctakes-ytex/scripts/data/**/insert_view.sql?
That way it'll support umls2011 as well as the newer 2014 naming conventions?
Ex: inner join MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( 'SNOMEDCT',
'SNOMEDCT_US','RXNORM')
--Pei
> -Original Message-
> From: clayclay...@gmail.com [mailto:clayclay...@gmail.com] On Behalf Of
> Clayton Turner
> Sent: Thursday, August 21, 2014 4:25 PM
> To: dev@ctakes.apache.org
> Subject: Re: Change from SNOMEDCT to SNOMEDCT_US affecting
> v_snomed_fword_lookup
>
> Ah, I just switched to the ytex branch and all is good now. The SNOMED_US
> issue has been plaguing me for weeks now so thanks a million for that.
>
>
> On Thu, Aug 21, 2014 at 2:13 PM, Clayton Turner
> wrote:
>
> > Awesome. This is just what I needed for the longest time.
> >
> > I'm having a slight issue. When running either the ytex pipeline or
> > ytex version of the AggregatePlaintextUMLSProcessor I get an error
> > during initialization.
> >
> > My DictionaryLookupAnnotator.xml is raising a
> > org.apache.uima.resource.ResourceInitializationException causedby:
> > java.lang.ClassNotFoundException:
> > edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
> >
> > I feel like I may have drifted away from what I need, though, because
> > before this the CPE was complaining about a lack of
> > LookupDesc_SNOMED.xml file. I found a ytex version of this on a google
> > code site somewhere and pasted it where the CPE was looking for it. Now
> this error is coming up.
> >
> > Could my problem be solved with just a re-run of the ant script (was
> > just trying to avoid since it takes ages) or is it a different issue?
> >
> >
> > On Tue, Aug 19, 2014 at 12:58 PM, Tim O'Connell
> >
> > wrote:
> >
> >> Hi John,
> >>
> >> I'm not sure what was going on with the @db.schema@ error, although I
> >> was getting it as well before with my prior build of 3.1.2 - I assume
> >> that you've fixed something (thank you!) to make this go away. I
> >> rebuilt everything from scratch and it's working now.
> >>
> >> I think one other thing I had to change was that after I had finished
> >> the install/build, the cTakes version of LookupDesc_Db.xml doesn't
> >> work (in
> >> resources\org\apache\ctakes\dictionary\lookup) - I'm pretty sure I
> >> had to copy in an older version of the file from 3.1.1 to get the
> >> default cTakes AggregatePlaintextUMLSProcessor pipeline working,
> >> although please double-check that as my memory is a little foggy.
> >>
> >> But yes, here's what I have working since re-building:
> >> 1. ytex-pipeline.xml
> >> 2. ytex version of AggregatePlaintextUMLSProcessor.xml
> >> 3. cTakes version of AggregatePlaintextUMLSProcessor.xml (with
> >> swapping the LookupDesc_Db.xml file as above)
> >>
> >> I've even made modifications to the ytex version of
> >> LookupDesc_SNOMED.xml to get it tagging Disease Disorders, along with
> database modifications to
> >> have it store these entries as well, which is working great. Literally,
> >> everything is working perfectly now.
> >>
> >> Still so much for me to learn! Let me know if you need any more details.
> >>
> >> All the best,
> >> Tim
> >>
> >>
> >>
> >> On Tue, Aug 19, 2014 at 4:31 AM, John Green
> >>
> >> wrote:
> >>
> >> > I have not had time to implement this - to clarify out of
> >> > curiosity,
> >> does
> >> > this clear up the @db.schema@ error Tim? And did you successfully
> >> > run ytex with the ctakes dictionary-lookup?
> >> >
> >> >
> >> > JG
> >> > —
> >> > Sent from Mailbox for iPhone
> >> >
> >> > On Sat, Aug 16, 2014 at 2:53 AM, Tim O'Connell
> >> >
> >> > wrote:
> >> >
> >> > > Hi folks,
> >> > > I was having an issue with the current build (from svn) of
> >> > > ctakes/ytex
> >> > not
> >> > > identifying any annotations as some folks on this board. I
> >> > > traced it
> >> to
> >> > > the fact that the UMLS database has at sometime in the relatively
> >> recent
> >> > > past changed the SAB tag in the MRCONSO table for SNOMED terms
> >> > > from SNOMEDCT to SNOMEDCT_US. I just had a newer version of
> UMLS
> >> > > that uses SNOMEDCT_US. Thus when the install script tried to
> >> > > create the v_snomed_fword_lookup table, it wasn't finding any of
> >> > > the SNOMEDCT
> >> terms,
> >> > > thus nothing was getting annotated.
> >> > > The ytex install script was just looking for things in MRCONSO
> >> > > with
> >> the
> >> > > SNOMEDCT SAB tag when it created the ytex lookup table - so, by
> >> changing
> >> > > this to SNOMEDCT_US in the file
> >> > >
> >> >
> >> CTAKES_HOME/bin/ctakes-
> ytex/scripts/data/mysql/umls/insert_view_templ
> >> ate.sql
> >> > > it now works (for mysql users) to find the annotations. You can
> >> > > just
> >> > re-run
> >> > > the ytex setup script, but that takes hours - instead, I just
> >> > > deleted
> >> all
> >> > > the data from the v_snomed_fword_lookup table and basically ran
> >> > > the
> >> sql
> >> > > comma
Re: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup
Ah, I just switched to the ytex branch and all is good now. The SNOMED_US issue has been plaguing me for weeks now so thanks a million for that. On Thu, Aug 21, 2014 at 2:13 PM, Clayton Turner wrote: > Awesome. This is just what I needed for the longest time. > > I'm having a slight issue. When running either the ytex pipeline or ytex > version of the AggregatePlaintextUMLSProcessor I get an error during > initialization. > > My DictionaryLookupAnnotator.xml is raising a > org.apache.uima.resource.ResourceInitializationException causedby: > java.lang.ClassNotFoundException: > edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl > > I feel like I may have drifted away from what I need, though, because > before this the CPE was complaining about a lack of LookupDesc_SNOMED.xml > file. I found a ytex version of this on a google code site somewhere and > pasted it where the CPE was looking for it. Now this error is coming up. > > Could my problem be solved with just a re-run of the ant script (was just > trying to avoid since it takes ages) or is it a different issue? > > > On Tue, Aug 19, 2014 at 12:58 PM, Tim O'Connell > wrote: > >> Hi John, >> >> I'm not sure what was going on with the @db.schema@ error, although I was >> getting it as well before with my prior build of 3.1.2 - I assume that >> you've fixed something (thank you!) to make this go away. I rebuilt >> everything from scratch and it's working now. >> >> I think one other thing I had to change was that after I had finished the >> install/build, the cTakes version of LookupDesc_Db.xml doesn't work (in >> resources\org\apache\ctakes\dictionary\lookup) - I'm pretty sure I had to >> copy in an older version of the file from 3.1.1 to get the default cTakes >> AggregatePlaintextUMLSProcessor pipeline working, although please >> double-check that as my memory is a little foggy. >> >> But yes, here's what I have working since re-building: >> 1. ytex-pipeline.xml >> 2. ytex version of AggregatePlaintextUMLSProcessor.xml >> 3. cTakes version of AggregatePlaintextUMLSProcessor.xml (with swapping >> the >> LookupDesc_Db.xml file as above) >> >> I've even made modifications to the ytex version of LookupDesc_SNOMED.xml >> to get it tagging Disease Disorders, along with database modifications to >> have it store these entries as well, which is working great. Literally, >> everything is working perfectly now. >> >> Still so much for me to learn! Let me know if you need any more details. >> >> All the best, >> Tim >> >> >> >> On Tue, Aug 19, 2014 at 4:31 AM, John Green >> wrote: >> >> > I have not had time to implement this - to clarify out of curiosity, >> does >> > this clear up the @db.schema@ error Tim? And did you successfully run >> > ytex with the ctakes dictionary-lookup? >> > >> > >> > JG >> > — >> > Sent from Mailbox for iPhone >> > >> > On Sat, Aug 16, 2014 at 2:53 AM, Tim O'Connell >> > wrote: >> > >> > > Hi folks, >> > > I was having an issue with the current build (from svn) of ctakes/ytex >> > not >> > > identifying any annotations as some folks on this board. I traced it >> to >> > > the fact that the UMLS database has at sometime in the relatively >> recent >> > > past changed the SAB tag in the MRCONSO table for SNOMED terms from >> > > SNOMEDCT to SNOMEDCT_US. I just had a newer version of UMLS that uses >> > > SNOMEDCT_US. Thus when the install script tried to create the >> > > v_snomed_fword_lookup table, it wasn't finding any of the SNOMEDCT >> terms, >> > > thus nothing was getting annotated. >> > > The ytex install script was just looking for things in MRCONSO with >> the >> > > SNOMEDCT SAB tag when it created the ytex lookup table - so, by >> changing >> > > this to SNOMEDCT_US in the file >> > > >> > >> CTAKES_HOME/bin/ctakes-ytex/scripts/data/mysql/umls/insert_view_template.sql >> > > it now works (for mysql users) to find the annotations. You can just >> > re-run >> > > the ytex setup script, but that takes hours - instead, I just deleted >> all >> > > the data from the v_snomed_fword_lookup table and basically ran the >> sql >> > > command to repopulate the table and it worked fine. Here's the code, >> n.b. >> > > my schema name for my umls database is 'umls' - change the code below >> if >> > > yours is different. >> > > delete from v_snomed_fword_lookup; >> > > insert into v_snomed_fword_lookup (cui, tui, fword, fstem, tok_str, >> > > stem_str) >> > > select mrc.cui, t.tui, c.fword, c.fstem, c.tok_str, c.stem_str >> > > from umls_aui_fword c >> > > inner join umls.MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( >> > > 'SNOMEDCT_US', 'RXNORM') >> > > inner join >> > > ( >> > > select cui, min(tui) tui >> > > from umls.MRSTY sty >> > > where sty.tui in >> > > ( >> > >'T019', 'T020', 'T037', 'T046', 'T047', 'T048', 'T049', 'T050', >> > > 'T190', 'T191', 'T033', >> > >'T184', >> > >'T017', 'T029', 'T023', 'T030', 'T031', 'T022', 'T025', 'T026', >> > >'T018', 'T021', 'T024', >> > > '
Re: Web server
Disregard the couldnt deploy question, got it. Ill try and update the docs (e.g. Create a doc for the web server as it matures) but for folks like me linking web-inf/lib to the maven dependencies was not immediately clear. Figured it out. Other questions still stand :-) JG — Sent from Mailbox for iPhone On Thu, Aug 21, 2014 at 12:05 PM, John Green wrote: > Im trying to deploy the cTakes web-server code someone already wrote (who > wrote it btw?). Im running into deployment issues in eclipse with tomcat 7 > on mac... I can get into details but for now: is it in a working state? Im > learning as I go and it looks in order and the code is solid... > Also, Pei: did they check in an LVG version that is thread safe now? > Im really set on getting cTakes into a fluid RESTful interface. > JG
RE: Web server
And you did so with ctakes? Thats great, ill try it. JG — Sent from Mailbox for iPhone On Thu, Aug 21, 2014 at 12:46 PM, Finan, Sean wrote: >> Do you have experience with uima simple server? > A few months ago I set it up and ran it just for kicks. It is simple, but I > pondered that as such it could serve as a nice foundation. Well, maybe a > cornerstone. >> -Original Message- >> From: John Green [mailto:john.travis.gr...@gmail.com] >> Sent: Thursday, August 21, 2014 3:43 PM >> To: dev@ctakes.apache.org >> Cc: dev@ctakes.apache.org >> Subject: RE: Web server >> >> I have. I read the docs, it mentions more information but the tutorial was >> very >> short. >> >> >> It seems there are simple get requests with the xml ae for output built into >> the >> existing sandbox code, so I just wanted to hash that first before starting >> on a >> new thread. >> >> >> >> >> Do you have experience with uima simple server? >> >> >> >> >> JG >> — >> Sent from Mailbox for iPhone >> >> On Thu, Aug 21, 2014 at 12:10 PM, Finan, Sean >> wrote: >> >> > Hi John, >> > Have you (or another) thought about modifying the Uima Simple Server to run >> a cTakes pipeline? >> > http://uima.apache.org/sandbox.html#simple-server >> >> -Original Message- >> >> From: John Green [mailto:john.travis.gr...@gmail.com] >> >> Sent: Thursday, August 21, 2014 3:06 PM >> >> To: dev@ctakes.apache.org >> >> Subject: Web server >> >> >> >> Im trying to deploy the cTakes web-server code someone already wrote >> >> (who wrote it btw?). Im running into deployment issues in eclipse >> >> with tomcat 7 on mac... I can get into details but for now: is it in >> >> a working state? Im learning as I go and it looks in order and the code is >> solid... >> >> >> >> Also, Pei: did they check in an LVG version that is thread safe now? >> >> >> >> Im really set on getting cTakes into a fluid RESTful interface. >> >> >> >> JG
RE: Web server
> Do you have experience with uima simple server? A few months ago I set it up and ran it just for kicks. It is simple, but I pondered that as such it could serve as a nice foundation. Well, maybe a cornerstone. > -Original Message- > From: John Green [mailto:john.travis.gr...@gmail.com] > Sent: Thursday, August 21, 2014 3:43 PM > To: dev@ctakes.apache.org > Cc: dev@ctakes.apache.org > Subject: RE: Web server > > I have. I read the docs, it mentions more information but the tutorial was > very > short. > > > It seems there are simple get requests with the xml ae for output built into > the > existing sandbox code, so I just wanted to hash that first before starting on > a > new thread. > > > > > Do you have experience with uima simple server? > > > > > JG > — > Sent from Mailbox for iPhone > > On Thu, Aug 21, 2014 at 12:10 PM, Finan, Sean > wrote: > > > Hi John, > > Have you (or another) thought about modifying the Uima Simple Server to run > a cTakes pipeline? > > http://uima.apache.org/sandbox.html#simple-server > >> -Original Message- > >> From: John Green [mailto:john.travis.gr...@gmail.com] > >> Sent: Thursday, August 21, 2014 3:06 PM > >> To: dev@ctakes.apache.org > >> Subject: Web server > >> > >> Im trying to deploy the cTakes web-server code someone already wrote > >> (who wrote it btw?). Im running into deployment issues in eclipse > >> with tomcat 7 on mac... I can get into details but for now: is it in > >> a working state? Im learning as I go and it looks in order and the code is > solid... > >> > >> Also, Pei: did they check in an LVG version that is thread safe now? > >> > >> Im really set on getting cTakes into a fluid RESTful interface. > >> > >> JG
RE: Web server
I have. I read the docs, it mentions more information but the tutorial was very short. It seems there are simple get requests with the xml ae for output built into the existing sandbox code, so I just wanted to hash that first before starting on a new thread. Do you have experience with uima simple server? JG — Sent from Mailbox for iPhone On Thu, Aug 21, 2014 at 12:10 PM, Finan, Sean wrote: > Hi John, > Have you (or another) thought about modifying the Uima Simple Server to run a > cTakes pipeline? > http://uima.apache.org/sandbox.html#simple-server >> -Original Message- >> From: John Green [mailto:john.travis.gr...@gmail.com] >> Sent: Thursday, August 21, 2014 3:06 PM >> To: dev@ctakes.apache.org >> Subject: Web server >> >> Im trying to deploy the cTakes web-server code someone already wrote (who >> wrote it btw?). Im running into deployment issues in eclipse with tomcat 7 >> on mac... I can get into details but for now: is it in a working state? Im >> learning as I go and it looks in order and the code is solid... >> >> Also, Pei: did they check in an LVG version that is thread safe now? >> >> Im really set on getting cTakes into a fluid RESTful interface. >> >> JG
RE: Web server
Hi John, Have you (or another) thought about modifying the Uima Simple Server to run a cTakes pipeline? http://uima.apache.org/sandbox.html#simple-server > -Original Message- > From: John Green [mailto:john.travis.gr...@gmail.com] > Sent: Thursday, August 21, 2014 3:06 PM > To: dev@ctakes.apache.org > Subject: Web server > > Im trying to deploy the cTakes web-server code someone already wrote (who > wrote it btw?). Im running into deployment issues in eclipse with tomcat 7 > on mac... I can get into details but for now: is it in a working state? Im > learning as I go and it looks in order and the code is solid... > > Also, Pei: did they check in an LVG version that is thread safe now? > > Im really set on getting cTakes into a fluid RESTful interface. > > JG
Acronym annotator
Are there any acronym annotators and disambiguators? What are people doing in production elsewhere? Im learning the heart of cTakes and UIMA by the numbers right now and I think writing an annotator of my own will be the best way to solidify the information. If no one has it done already, I thought Id write a simple acronym annotator and disambiguator. The disambiguation would just be a co-occurance over a lookup window across a private corpus I have access to, e.g., word1 word 2 word3 acronym1 word4 word5 word6. I would provide specificity by excluding words that tend to occur frequently across instances of the acronyms with the same abbreviation. But, if someone has already done it and is planning on releasing it, I hate to reproduce wheels... JG
Web server
Im trying to deploy the cTakes web-server code someone already wrote (who wrote it btw?). Im running into deployment issues in eclipse with tomcat 7 on mac... I can get into details but for now: is it in a working state? Im learning as I go and it looks in order and the code is solid... Also, Pei: did they check in an LVG version that is thread safe now? Im really set on getting cTakes into a fluid RESTful interface. JG
Re: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup
Awesome. This is just what I needed for the longest time. I'm having a slight issue. When running either the ytex pipeline or ytex version of the AggregatePlaintextUMLSProcessor I get an error during initialization. My DictionaryLookupAnnotator.xml is raising a org.apache.uima.resource.ResourceInitializationException causedby: java.lang.ClassNotFoundException: edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl I feel like I may have drifted away from what I need, though, because before this the CPE was complaining about a lack of LookupDesc_SNOMED.xml file. I found a ytex version of this on a google code site somewhere and pasted it where the CPE was looking for it. Now this error is coming up. Could my problem be solved with just a re-run of the ant script (was just trying to avoid since it takes ages) or is it a different issue? On Tue, Aug 19, 2014 at 12:58 PM, Tim O'Connell wrote: > Hi John, > > I'm not sure what was going on with the @db.schema@ error, although I was > getting it as well before with my prior build of 3.1.2 - I assume that > you've fixed something (thank you!) to make this go away. I rebuilt > everything from scratch and it's working now. > > I think one other thing I had to change was that after I had finished the > install/build, the cTakes version of LookupDesc_Db.xml doesn't work (in > resources\org\apache\ctakes\dictionary\lookup) - I'm pretty sure I had to > copy in an older version of the file from 3.1.1 to get the default cTakes > AggregatePlaintextUMLSProcessor pipeline working, although please > double-check that as my memory is a little foggy. > > But yes, here's what I have working since re-building: > 1. ytex-pipeline.xml > 2. ytex version of AggregatePlaintextUMLSProcessor.xml > 3. cTakes version of AggregatePlaintextUMLSProcessor.xml (with swapping the > LookupDesc_Db.xml file as above) > > I've even made modifications to the ytex version of LookupDesc_SNOMED.xml > to get it tagging Disease Disorders, along with database modifications to > have it store these entries as well, which is working great. Literally, > everything is working perfectly now. > > Still so much for me to learn! Let me know if you need any more details. > > All the best, > Tim > > > > On Tue, Aug 19, 2014 at 4:31 AM, John Green > wrote: > > > I have not had time to implement this - to clarify out of curiosity, does > > this clear up the @db.schema@ error Tim? And did you successfully run > > ytex with the ctakes dictionary-lookup? > > > > > > JG > > — > > Sent from Mailbox for iPhone > > > > On Sat, Aug 16, 2014 at 2:53 AM, Tim O'Connell > > wrote: > > > > > Hi folks, > > > I was having an issue with the current build (from svn) of ctakes/ytex > > not > > > identifying any annotations as some folks on this board. I traced it > to > > > the fact that the UMLS database has at sometime in the relatively > recent > > > past changed the SAB tag in the MRCONSO table for SNOMED terms from > > > SNOMEDCT to SNOMEDCT_US. I just had a newer version of UMLS that uses > > > SNOMEDCT_US. Thus when the install script tried to create the > > > v_snomed_fword_lookup table, it wasn't finding any of the SNOMEDCT > terms, > > > thus nothing was getting annotated. > > > The ytex install script was just looking for things in MRCONSO with the > > > SNOMEDCT SAB tag when it created the ytex lookup table - so, by > changing > > > this to SNOMEDCT_US in the file > > > > > > CTAKES_HOME/bin/ctakes-ytex/scripts/data/mysql/umls/insert_view_template.sql > > > it now works (for mysql users) to find the annotations. You can just > > re-run > > > the ytex setup script, but that takes hours - instead, I just deleted > all > > > the data from the v_snomed_fword_lookup table and basically ran the sql > > > command to repopulate the table and it worked fine. Here's the code, > n.b. > > > my schema name for my umls database is 'umls' - change the code below > if > > > yours is different. > > > delete from v_snomed_fword_lookup; > > > insert into v_snomed_fword_lookup (cui, tui, fword, fstem, tok_str, > > > stem_str) > > > select mrc.cui, t.tui, c.fword, c.fstem, c.tok_str, c.stem_str > > > from umls_aui_fword c > > > inner join umls.MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in ( > > > 'SNOMEDCT_US', 'RXNORM') > > > inner join > > > ( > > > select cui, min(tui) tui > > > from umls.MRSTY sty > > > where sty.tui in > > > ( > > >'T019', 'T020', 'T037', 'T046', 'T047', 'T048', 'T049', 'T050', > > > 'T190', 'T191', 'T033', > > >'T184', > > >'T017', 'T029', 'T023', 'T030', 'T031', 'T022', 'T025', 'T026', > > >'T018', 'T021', 'T024', > > > 'T116', 'T195', 'T123', 'T122', 'T118', 'T103', 'T120', 'T104', > > >'T200', 'T111', 'T196', 'T126', 'T131', 'T125', 'T129', 'T130', > > >'T197', 'T119', 'T124', 'T114', 'T109', 'T115', 'T121', 'T192', > > >'T110', 'T127', > > >'T060', 'T065', 'T058', 'T059', 'T063', 'T062', 'T061', > > >'T074', 'T075', > > >'T059'
