> (diseaseDisorder entity : JCasUtil.select(jcas,
DiseaseDisorderMention.class))
Justin, you might also want to check out the JCasUtil
selectCovering/Covered and indexCovering/Covered methods: e.g., in your
example, I *think* this would work to remove "arterial":
JCasUtil.indexCovered(jcas, AnatomicalSiteMention.class,
DiseaseDisorderMention.class).keySet().forEach(diseaseCoveredBodypart ->
diseaseCoveredBodypart.removeFromIndexes());
or, less drastically:
Map<ASM.class,Collection<DDM.class>> diseaseCoveredBodyparts =
JCasUtil.indexCovered(jCas, ASM.class, DDM.class);
for (ASM bodypart : JCasUtil.select(jcas, ASM.class) {
if (!diseaseCoveredBodyparts.containsKey(bodypart)) {
...
}
}
On Fri, Jul 14, 2017 at 4:23 PM, Finan, Sean <
[email protected]> wrote:
> Hi Justin,
>
> > To accomplish this I'm using a modified version of the FastPipeline.
> >And in the sno_rx_2016ab.xml, instead of DefaultTermConsumer, I'm using
> the PrecisionTermConsumer.
>
> This is the correct approach for your stated goal.
>
> > cTakes picks up "peripheral arterial disease" but it also picks up
> "arterial".
>
> cTakes is doing exactly what it is supposed to do. Overlapping words of
> different semantic types will all be kept:
> https://cwiki.apache.org/confluence/display/CTAKES/
> cTAKES+3.2+-+Fast+Dictionary+Lookup#cTAKES3.2-FastDictionaryLookup-
> MostPreciseTermsPersistence
> Check to see if "arterial" is something other than a disease/disorder.
> According to my search it is an anatomical site. It is important that
> ctakes does pick up both the disease and site.
>
> > So is there an even more precise PrecisionTermConsumer or do I need to
> make my own custom TermConsumer?
>
> No there is not. However, you can fetch or ignore terms of semantic types
> that are desired.
> You can create your own TermConsumer to perform filtering, but my advice
> is that you only perform filtering/fetching when writing output. You can
> do this by changing your
> >for (IdentifiedAnnotation entity : JCasUtil.select(jcas,
> IdentifiedAnnotation.class))
> To:
> for (diseaseDisorder entity : JCasUtil.select(jcas,
> DiseaseDisorderMention.class))
>
> Or if you want more than one semantic type, something like:
> JCasUtil.select(jcas, IdentifiedAnnotation.class).stream().filter(
> myTypes.contains( Object::getClass ) )
> Where myTypes is a collection of your desired semantic types.
>
> Sean
>
>
>
> -----Original Message-----
> From: Justin Brown [mailto:[email protected]]
> Sent: Friday, July 14, 2017 2:54 PM
> To: [email protected]
> Cc: Daya Sharma
> Subject: Problem with the PrecisionTermConsumer [EXTERNAL]
>
> I'm using the dev version of ctakes 4.0. I'm trying to match a phrase, and
> ignore all subcomponents of the phrase. For instance, if the note is, "Very
> severe peripheral arterial disease." cTakes should pick up only "peripheral
> arterial disease" and not "arterial", "disease", "arterial disease" etc....
>
> To accomplish this I'm using a modified version of the FastPipeline.
> Instead of using the DefaultJCasTermAnnotator, I'm using
> OverlapJCasTermAnnotator. And in the sno_rx_2016ab.xml, instead of
> DefaultTermConsumer, I'm using the PrecisionTermConsumer. In theory, the
> overlap annotator and the PrecisionTermConsumer combined should solve the
> problem.
>
> The problem is, when the note is "Very severe peripheral arterial disease."
> cTakes picks up "peripheral arterial disease" but it also picks up
> "arterial".
>
> So is there an even more precise PrecisionTermConsumer or do I need to
> make my own custom TermConsumer? I also tried the
> SemanticCleanupTermConsumer, but it gave the same results.
>
> Here's the code I'm using to extract phrases:
>
> JCas jcas = JCasFactory.createJCas();
> jcas.setDocumentText(note);
> AggregateBuilder builder = new AggregateBuilder(); builder.add(
> ClinicalPipelineFactory.getFastPipeline());
> SimplePipeline.runPipeline(jcas, builder.createAggregateDescription());
>
> for (IdentifiedAnnotation entity : JCasUtil.select(jcas,
> IdentifiedAnnotation.class)) {
> ...
> }
>
>
> Any help is appreciated.
>
> Thank you,
> Justin
>
--
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