Sorry I miss-typed > So I changed it to UmlsOverlapLookupAnnotator descriptor as .... I meant UmlsLookupAnnotator instead of UmlsOverlapLookupAnnotator
Warm Regards, Sana Riaz AI/ML Engineer, xFlow Research Inc. +92-334-1172416 [email protected] www.xflowresearch.com On Fri, Jan 11, 2019 at 1:29 AM Sana Riaz <[email protected]> wrote: > Hi Sean > Thanks For responding. > Yes, I am using xml descriptor in ctakes-dictionary-lookup-fast. I tried > the fix you mentioned but it changed nothing. > To answer your second question, I have build the pipeline using xml > descriptors in java and am testing in java. Initially i was using > DefaultJCasTermAnnotator with The resource (dictionary) configuration file > resources/.../dictionary/lookup/fast/sno_rx_16ab.xml as following > > AggregateBuilder builder = new AggregateBuilder(); >> ... >> //other pipeline components// >> ... >> AnalysisEngineDescription dictionarylookup_desc = >> AnalysisEngineFactory.createEngineDescription( >> DefaultJCasTermAnnotator.class, >> AbstractJCasTermAnnotator.PARAM_WINDOW_ANNOT_KEY, >> "org.apache.ctakes.typesystem.type.textspan.Sentence", >> JCasTermAnnotator.DICTIONARY_DESCRIPTOR_KEY, >> >> "org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml"); >> builder.add(dictionarylookup_desc); >> ... >> //other pipeline components// >> ... >> builder.createAggregateDescription(); > > > This was working fine for plaintext but cuased the mentioned problem when > I processed the CDA document after adding CdaCasInitializer annotator to > the pipeline. So I changed it to UmlsOverlapLookupAnnotator descriptor as > > builder.add( AnalysisEngineFactory.createEngineDescription( >> "desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator") >> ); > > > > BTW, I experimented with the AggregateCdaUMLSProcessor.xml > (ctakes-clinical-pipeline) and changed the DictionaryLookupAnnotatorUmls > (original dictionary-lookup ) to UmlsLookupAnnotator . This also doesn't > give the the mentioned annotations. So this gaveme the hint that problem is > with UmlsLookupAnnotator maybe. > What do you suggest? > > >The java implementation pointed to in that descriptor, > DefaultJCasTermAnnotator does provide the various semantically-distinct > annotation types that you mention. > > I am a little confuse there; Do i have to enable the annotations types in > the DefaultJCasTermAnnotator class or something like that? becuase i didnt > had to do anything like that for the plaintext. Can you please elaborate > this point too, I am really naive to cTAKES yet so i might be not getting > it right. > > PS I am not getting any error or warning related to this in the compiling > logs. > > Warm Regards > > Sana Riaz > > > > On Thu, Jan 10, 2019 at 8:25 PM Finan, Sean < > [email protected]> wrote: > >> Hi Sana, >> >> When you say: >> >i want to use dictionary_lookup "UmlsLookupAnnotator" >> are you talking about the xml descriptor in >> ctakes-dictionary-lookup-fast? If so that is great. >> >> >The problem is that identifiedAnnotation given by UmlsLookupAnnotator >> does >> not include Sign/Symptoms, Disease/Disorder or Procedure Mentions etc. >> >> How are you testing this? The java implementation pointed to in that >> descriptor, DefaultJCasTermAnnotator does provide the various >> semantically-distinct annotation >> types that you mention. I use it every day without problem*. Are you >> seeing any errors at the top of the log? >> >> I just looked at the descriptor UmlsLookupAnnotator.xml and it may have a >> problem: >> >> <annotatorImplementationName>org.apache.ctakes.dictionary.lookup2.ae >> .DefaultJCasTermAnnotator >> </annotatorImplementationName> >> >> Notice that the end tag </annotatorImplementationName> is on a second >> line in the file. I have seen this cause problems in uima/ctakes. I think >> that the xml parser assumes that whitespace is part of the information - >> which in this case is not true. >> >> Try putting the end tag on the same line and running again. >> >> * I never use xml descriptors anymore. I use piper files. So, even >> though I use that implementation every day I do not load it in the same >> manner. >> https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files >> >> Please try the fix I mention and let me know what happens. >> >> Sean >> >> >> >> ________________________________________ >> From: Sana Riaz <[email protected]> >> Sent: Thursday, January 10, 2019 6:13 AM >> To: [email protected] >> Subject: UmlsLookupAnnotator.xml does not give sign/symptom, >> disease/disorder in identifiedAnnotation for CDA documents [EXTERNAL] >> >> Hi, I am doing NLP research on some clinical documents using cTAKES and I >> am a little stuck at a point. >> I have created a pipeline in java similar to "AggregateCdaUMLSProcessor" >> in >> which i want to use dictionary_lookup "UmlsLookupAnnotator" instead of >> "DictionaryLookupAnnotatorUmls". >> The problem is that identifiedAnnotation given by UmlsLookupAnnotator does >> not include Sign/Symptoms, Disease/Disorder or Procedure Mentions etc. I >> have done required sofa Mapping in java . The pipeline works fine for >> plaintext document but doesn't give the above mentioned annotations for >> CDA. I have tested the CDA document using AggregateCdaUMLSProcessor.xml >> descriptor and it gives the above mentioned annotations (except >> MedicationMention which I also need) . Can you give me any suggestion >> about >> what can I try or what is wrong? >> Looking forward to hearing from you. >> >> Warm Regards, >> >> Sana Riaz >> >
