ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Sana Riaz <sana.r...@xflowresearch.com>
Subject Re: UmlsLookupAnnotator.xml does not give sign/symptom, disease/disorder in identifiedAnnotation for CDA documents [EXTERNAL]
Date Thu, 10 Jan 2019 20:29:56 GMT
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 <
Sean.Finan@childrens.harvard.edu> 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 <sana.riaz@xflowresearch.com>
> Sent: Thursday, January 10, 2019 6:13 AM
> To: dev@ctakes.apache.org
> 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
>

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message