Hi Vijay - I am at the same impasse as Mr Lee and Mr Abhishek, and I didnt come across any other solutions in the archives.
Through intuition I figured out what you mention in this post on my own, and tried it. It didnt work. It seems to revolve around this line: Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM @[email protected]_snomed_fword_lookup WHERE fword = ?] It seems the query is coming from LookupDesc_SNOMED.xml, but I cant find the @db.schema@... is this a windows/linux issue? Before Vijay spends his precious time on answering this, did anyone else get resolution on this? Best, JG On Wed, Jun 18, 2014 at 10:11 AM, vijay garla <[email protected]> wrote: > The YTEX AggregatePlaintextUMLSProcessor differs from the default > AggregatePlaintextUMLSProcessor in the following a ways: > * Use SegmentRegexAnnotator instead of SimpleSegmentAnnotator > * Use SentenceDetectorAnnotator without splitting on newlines > * Added SenseDisambiguatorAnnotator > ** Use YTEX DictionaryLookupAnnotatorDB instead of cTAKES > DictionaryLookupAnnotatorDB* > > The YTEX dictionary lookup is different from cTAKES': > * uses the old dictionary lookup > * uses a single dictionary > * uses a single lookup consumer that creates plain-vanilla EntityMention > annotations (none of the subtypes) > > I think that if you change the YTEX AggregatePlaintextUMLSProcessor to > point at the cTAKES dictionary lookup, you will get approximately same > annotations (probably more if sentences do not end on newlines, as > dictionary lookup is not performed across sentences) > > could you try the following please: > In > desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml > change > <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB"> > <import location="./DictionaryLookupAnnotator.xml" /> > </delegateAnalysisEngine> > To > <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB"> > <import > location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/> > </delegateAnalysisEngine> > > And re-run. You should get the same results (keep in mind the newline > thing). > > > > > > On Wed, Jun 18, 2014 at 9:46 AM, Lee, Richard A. [USA] < > [email protected]> wrote: > >> Yes, that exactly the problem I’ve been reporting. I think you’ll see >> that it you still get the non-Medical annotations, like Date, RomanNumeral, >> et al, but not DiseaseDisorderMention and the other Medical ones, right? >> >> >> >> I’m still hoping someone can assist with this. >> >> >> >> *From:* Abhishek Raj [mailto:[email protected]] >> *Sent:* Wed, 18 Jun, 2014 04:43 >> *To:* [email protected] >> *Subject:* Re: [External] Re: Cannot load >> AggregatePlainTextUmlsProcessor.xml >> >> >> >> Found a fix. Will post it here in case it helps someone. When using >> ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from " >> CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/ >> AggregatePlaintextUMLSProcessor.xml" and not from the usual " >> CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/ >> AggregatePlaintextUMLSProcessor.xml" as given here >> <https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide>. >> >> However strangely, >> "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml" >> produced even less annotations than " >> ctakes-clinical-pipeline/desc/analysis_engine/ >> AggregatePlaintextUMLSProcessor.xml". >> >> I expected ytex-specific AE to produce better results. But clearly that's >> not the case. >> >> >> >> On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <[email protected]> >> wrote: >> >> Hi. Thanks for the reply. >> I have a file named LookupDesc_Db.xml which has the line <jdbcImpl >> tableName="@[email protected]_snomed_fword_lookup"/> >> >> instead of LookupDesc_SNOMED.*template*.xml. Also, my ytex.properties >> file seems fine. I have attached the file for your reference. >> And yes, when running the ant setup by following #7 on this >> <https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation> link, >> it sends the output to "setup.out". The build was successful though. I >> didn't see any errors. I am attaching the file for your reference as well. >> Please have a look and let me know. >> >> >> > >
