Hi All,
I have done the below code for finding medical terms from String
information.
step 1 :
public static AnalysisEngineDescription getUMLPipeline() throws
ResourceInitializationException, URISyntaxException{
AggregateBuilder builder = new AggregateBuilder();
builder.add(SimpleSegmentAnnotator.createAnnotatorDescription());
builder.add(SentenceDetector.createAnnotatorDescription());
builder.add(TokenizerAnnotatorPTB.createAnnotatorDescription());
builder.add(POSTagger.createAnnotatorDescription());
builder.add(ClinicalPipelineFactory.getNpChunkerPipeline());
builder.add(LvgAnnotator.createAnnotatorDescription());
try {
builder.add( AnalysisEngineFactory.createEngineDescription(
DefaultJCasTermAnnotator.class,
AbstractJCasTermAnnotator.PARAM_WINDOW_ANNOT_PRP,
"org.apache.ctakes.typesystem.type.textspan.Sentence",
JCasTermAnnotator.DICTIONARY_DESCRIPTOR_KEY,
ExternalResourceFactory.createExternalResourceDescription(
FileResourceImpl.class,
FileLocator.locateFile(
"org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml" ) )
) );
} catch ( FileNotFoundException e ) {
e.printStackTrace();
throw new ResourceInitializationException( e );
}
return builder.createAggregateDescription();
}
step 2:
final JCas jcas = JCasFactory.createJCas();
jcas.setDocumentText( nextLine[0] );
SimplePipeline.runPipeline(jcas, getUMLPipeline());
for ( IdentifiedAnnotation entity : JCasUtil.select( jcas,
IdentifiedAnnotation.class ) ) {
if(entity.getOntologyConceptArr() != null){
add.append(entity.getCoveredText()+ ",");
}
}
its working Fine..
But i have two quires..
1. step1 , i am using Annotator step by step ... that time its taking more
time load the all fuctions
how can execute the single function to run all this jobs in short
time...
2. how can i find sentence vised Dictionary words from string, give me a
solution for this..
...please give me a solutions for this issues....
regards,
shyam k.
On Thu, Dec 8, 2016 at 1:59 AM, Mullane, Sean *HS <
sp...@hscmail.mcc.virginia.edu> wrote:
> I'm reviving this thread with reference to negation detection. I
> previously posted about this to the User list but this is probably a more
> appropriate venue.
>
> The way the sentences are split on ":" makes the negation annotator miss
> negation in lists of this form:
>
> Hyperlipidemia: Yes
> Hypercholesterolemia: No
> Chronic Renal Insufficiency: N/A
>
> I tried reversing order and removing ":"s and found that the negation for
> Hypercholesterolemia is detected when in this form:
>
> Yes Hyperlipidemia
> No Hypercholesterolemia
> N/A Chronic Renal Insufficiency
>
> Our notes have quite a few places with this sort of list where good
> negation detection is important but I haven't very good results. The
> sentence segmentator sees this as 12 separate sentences, but I would think
> proper behavior would be to consider this as 6 sentences (breaking
> sentences on line break but not on colons). I see previous discussion on
> the list about the sentence segmentator breaking on newlines but little
> regarding colons. I would think in most cases it would be more useful not
> to break on ":". Or is there an overriding reason for the current behavior?
> If changing the sentence segmentator isn't an option is there a different
> way to configure the negation detection annotator that would avoid this
> issue?
>
> Thanks,
> Sean
>
>
>
> Hi,
>
> I am interested in the design decision of the sentence detector.
>
> Why does it split a sentence of the form "WORD1: WORD2 WORD3." into two
> sentences "WORD1:" and "WORD2 WORD3."? Do other components of cTAKES
> require
> such a sentence splitting?
>
> It would seem to me that it should remain one sentence. For example, the
> smoking
> status detector has its own SentenceAdjuster that merges some of such
> sentences
> back into one, because of this design.
>
> Thanks, Tomasz
>
> ________________________________________ From: Finan, Sean [
> sean...@childrens.harvard.edu] Sent: Friday, July 10, 2015 3:20 PM To:
> de...@ctakes.apache.org Subject: RE: Allergy Annotator
>
> Hi Tom,
>
> It is exactly because the sentence detector splits "KEY:" from "VALUE"
> that I
> didn't suggest using sentences. Instead, I would just iterate over the
> whole
> cas collection of medication events and attempt to match allergy phrases
> ("allergic to medication") with text the note spanning from event.begin-15
> to
> event.end+15 or whatever window size you prefer.
>
> Sean
>
> -----Original Message----- From: Tom Devel [mailto:deve...@gmail.com]
> Sent: Friday, July 10, 2015 4:12 PM To: de...@ctakes.apache.org Subject:
> Re: Allergy Annotator
>
> Sean and Dima, these are great suggestions, thanks so far.
>
> Sean, when looping over medication events as you say, I can see how it is
> possible to take the textspan.Sentence of this MedicationMention, and then
> do a
> regex check for the phrase structure as Dima said.
>
> But instead of textspan.Sentence, you mention "see any is included in a
> phrase".
> What cTAKES/UIMA class is related to this?
>
> Because if I would use textspan.Sentence, it would work for "The patient is
> allergic to penicillin.", but cTAKES splits "ALLERGIES: PENICILLIN, WHEAT"
> into two sentences, so that the MedicationMentions here would not be in the
> same
> sentence as the word "ALLERGIES".
>
> Thanks again, Tom
>
> On Fri, Jul 10, 2015 at 2:12 PM, Finan, Sean <
> sean...@childrens.harvard.edu>
> wrote:
>
> Hi Dima, Tom,
>
> I was thinking the same as Dima's first solution. Iterate through the
> medication events and see any is included in a phrase as mentioned in Tom's
> original email. Each phrase structure would have to be specified
> beforehand. However, assigning appropriate CUIs would require having a
> lookup table for each medication allergy. I think that would be the
> simplest solution.
>
> Sean
>
> -----Original Message----- From: Dligach, Dmitriy [mailto:
> dmit...@childrens.harvard.edu] Sent: Friday, July 10, 2015 2:50 PM To:
> cTAKES Developer list Subject: Re: Allergy Annotator
>
> Hi Tom,
>
> If the patters are pretty simple, you could just add a few rules on top of
> the cTAKES dictionary lookup output. Something of the kind "allergic to
> <medication>" or "allergies: <medication1>, <medication2>, <substance1>,
> ...".
>
> If these patterns are hard to express as rules, you should consider a
> machine learning based sequence labeling route (e.g. something similar to
> the cTAKES chunker).
>
> Dima
>
> -- Dmitriy (Dima) Dligach, Ph.D. Boston Children's Hospital and Harvard
> Medical School (617) 651-0397
>
> On Jul 10, 2015, at 13:40, Tom Devel <deve...@gmail.com<mailto:
> deve...@gmail.com>> wrote:
>
> Sean,
>
> It would be a wider net, such that if an allergy is mentioned in the
> clinical note, this is captured in the corresponding IdentifiedAnnotation
> (or alternatively, if the IdentifiedAnnotation class should not be changed
> with a new attribute, in a separate allergy
> annotation).
>
> This annotator would then have to of course run after the clinical
> pipeline has run and discovered all IdentifiedAnnotations.
>
> I am familiar with writing UIMA/cTAKES annotators, but not sure how a new
> ML method could be integrated here for detecting allergies. Do you have any
> thoughts about how to approach this in general?
>
> Thanks, Tom
>
> On Fri, Jul 10, 2015 at 11:54 AM, Finan, Sean <
> sean...@childrens.harvard.edu<mailto:Sean.Finan@childrens.harvard.e du>>
> wrote:
>
> Hi Tom,
>
> Are you interested in catching all allergies or just a few specific
> allergies for a study? If you are only concerned with a few then there is a
> (possibly) simple solution. If you are interested in throwing a wider net
> then I think that a new module would need to be created; does anybody
> reading this have an ML or regex style module?
>
> Sean
>
> -----Original Message----- From: Tom Devel [mailto:deve...@gmail.com]
> Sent: Friday, July 10, 2015 12:42 PM To: de...@ctakes.apache.org<mailto:
> de...@ctakes.apache.org> Subject: Allergy Annotator
>
> Hi,
>
> I would like to use/extend cTAKES to detect allergies.
>
> In the cTAKES publication (2010)
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ncbi.nlm.nih.g
> ov_pmc_articles_PMC2995668_&d=BQIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZM
> SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZApJmGKjz
> vFfNco5rRFVwSIyxmg4MRsxakfuXHbMZME&s=mGWu0XBCJqG2MI5qPlwIpGbQL5IYe7t5E
> WcvhPYW7Lo&e= there is the mention that: "Allergies to a given medication
> are handled by setting the negation attribute of that medication to 'is
> negated'."
>
> However, in a post here in 2014 (RE: Allergy Indication) it is said that
> cTAKES does not have a module for allergy discovery.
>
> 1. What is the current status of allergy detection in cTAKES?
>
> 2. I did some testing, while cTAKES discovers concepts about allegies
> ("wheat allergy" is found as C0949570), using "ALLERGIES: PENICILLIN,
> WHEAT" or "The patient is allergic to penicillin." does not give penicillin
> or wheat annotations allergy status.
>
> How would I go about detecting these allergy mentions?
>
> Thanks, Tom
>
>
