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
