Abilash, The org.apache.uima.fit.util.JCasUtil methods selectCovered and indexCovered may be what you're looking for here.
If you run cTAKES on the following text: "Sodium Latest Range: 135-145 mmol/L 138" note that "135-145" is covered by a RangeAnnotation; "135" and "145" are covered by NumTokens; and "-" is covered by a PunctuationToken. Similarly, "21.1 L" is covered by a MeasurementAnnotation, in which "21.1" is covered by both a FractionAnnotation and a NumToken, and "L" by a WordToken. Have you used the CAS Visual Debugger? https://uima.apache.org/d/uimaj-current/tools.html#ugr.tools.cvd It will show you all the annotations covering a given stretch of text -- very helpful. On Wed, Feb 28, 2018 at 6:51 AM, <abilash.mat...@cognizant.com> wrote: > Kean, > > I was able to get the annotation tagged as Range and measurement > annotations as shown below. As a next step, I would like to get the > individual token like 42 ,52 and 21 etc. I know I can try a pattern or > index based search to extract the information, but I am trying to see if > any options currently available in CTAKES to do the same. > > 28 Feb 2018 15:04:04 INFO LabValueFinder - Set to value: > LabMention(349-352): HCT > > 28 Feb 2018 15:04:04 INFO LabValueFinder - Set to value: > RangeAnnotation(365-370): 42-52 > > 28 Feb 2018 15:04:04 INFO LabValueFinder - Set to value: > MeasurementAnnotation(354-360): 21.1 L > > > > Thanks, > > Abilash Mathew > > *From:* Kean Kaufmann [mailto:k...@recordsone.com] > *Sent:* Monday, February 12, 2018 8:44 PM > *To:* Mathew, Abilash (Cognizant) <abilash.mat...@cognizant.com> > *Subject:* Re: Lab Value - Range finder > > > > > I could see setReferenceRangeNarrative method in LabMention class. Is > that the one are you referring? > > > > Yes -- that's the setter method generated from the type system: > https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-type- > system/src/main/resources/org/apache/ctakes/typesystem/ > types/TypeSystem.xml > > Feature: referenceRangeNarrative > > Value type: org.apache.ctakes.typesystem.type.textsem. > LabReferenceRangeModifier > > > > > Also, what is your suggestion to create new class similar to > LabValueFinder? > > > > Well, if the LabValueFinder suits your needs, then I'd suggest using its > annotations as starting points. > > Run the LabValueFinder and inspect the LabMentions it creates. > > If getLabValue() gives you a RangeAnnotation, it's probably the reference > range, > > which the LabValueFinder fell back to because it couldn't find a value. > > Otherwise, search for RangeAnnotations nearby. > > You may find various org.apache.uima.fit.util.JCasUtil > <https://uima.apache.org/d/uimafit-current/api/org/apache/uima/fit/util/JCasUtil.html> > methods > useful, e.g. selectBetween, selectPreceding, selectFollowing. > > In my data, the range could often be found between the LabMention and the > LabValue; your data may vary. > > For a general-purpose annotator, you'd want to make that configurable. > > > > Also, make you're getting the RangeAnnotations you expect. > > Last year, I found it expedient to write a quick-fix regular-expression > annotator to pick up decimal ranges like the ones below. > > It would be more civic-minded to change the annotator that generates > RangeAnnotations > > (the ContextDependentTokenizerAnnotator? Not sure offhand). > > > > "Potassium Latest Range: > 3.5-5.3 mmol/L 3.8\n" + // range not annotated > "TSH, High Sensitivity Latest > Range: 0.450-5.100 uIU/mL 1.939\n" + // range not annotated > > > > > > On Mon, Feb 12, 2018 at 6:24 AM, <abilash.mat...@cognizant.com> wrote: > > Thanks Kean for the suggestions. I could see setReferenceRangeNarrative > method in LabMention class. Is that the one are you referring? Also, what > is your suggestion to create new class similar to LabValueFinder? > > Regards, > Abilash Mathew > > -----Original Message----- > From: Kean Kaufmann [mailto:k...@recordsone.com] > Sent: Friday, February 9, 2018 10:35 PM > To: dev@ctakes.apache.org > Subject: Re: Lab Value - Range finder > > Hi Abilash, > > By design, the Lab Value annotator avoids ranges if possible: > > https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core/ > src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java > > // prefer non-range values, if any > > value = candidateList.stream() > > .filter( a -> !(a instanceof RangeAnnotation) ) > > .findFirst() > > .orElse( candidateList.get( 0 ) ); > > > The design is intended to cope with the widest possible variety of > formats, and avoid confusion. > > If you know where the reference ranges are going to be in your data, I'd > suggest annotating those separately, using the referenceRangeNarrative > feature with LabReferenceRange values rather than conflating them with > labValue / LabMention. > > https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-type- > system/src/main/resources/org/apache/ctakes/typesystem/ > types/TypeSystem.xml > > Caveat: When I wrote this last year, the range annotator didn't seem to be > picking up on decimal points. So, below, the first two got > RangeAnnotations, and the second two didn't. > > "Sodium Latest Range: 135-145 mmol/L 138\n" + > > "Anion Gap Latest Range: 13-16 mmol/L\n" + "Potassium Latest Range: > > 3.5-5.3 mmol/L 3.8\n" + // range not annotated "TSH, High Sensitivity > > Latest Range: 0.450-5.100 uIU/mL 1.939\n" + // range not annotated > > > > > On Wed, Feb 7, 2018 at 6:46 AM, <abilash.mat...@cognizant.com> wrote: > > > Hi All, > > > > I am trying to extend the current Lab Value finder annotator to > > include the Range annotation also. > > > > "Blood Urea Nitrogen (BUN) 10 mg/dL 8-23" > > > > Using current module , I am able to pull lab value as " BUN 10 mg" > > from above text and trying to tag "8-23" as reference range. > > > > final Map<Annotation, List<IdentifiedAnnotation>> subsumeMap = > > createCoveringMap( jCas, valueClasses, > > Arrays.asList( FractionAnnotation.class, > > RangeAnnotation.class, MeasurementAnnotation.class ) ); > > > > The range annotator is already added in the Labvalue finder class, but > > only MeasurementAnnotation is getting tagged in the output. Can anyone > > help here? > > > > > > Thanks, > > Abilash Mathew > > This e-mail and any files transmitted with it are for the sole use of > > the intended recipient(s) and may contain confidential and privileged > > information. If you are not the intended recipient(s), please reply to > > the sender and destroy all copies of the original message. Any > > unauthorized review, use, disclosure, dissemination, forwarding, > > printing or copying of this email, and/or any action taken in reliance > > on the contents of this e-mail is strictly prohibited and may be > > unlawful. Where permitted by applicable law, this e-mail and other > > e-mail communications sent to and from Cognizant e-mail addresses may be > monitored. > > > This e-mail and any files transmitted with it are for the sole use of the > intended recipient(s) and may contain confidential and privileged > information. If you are not the intended recipient(s), please reply to the > sender and destroy all copies of the original message. Any unauthorized > review, use, disclosure, dissemination, forwarding, printing or copying of > this email, and/or any action taken in reliance on the contents of this > e-mail is strictly prohibited and may be unlawful. Where permitted by > applicable law, this e-mail and other e-mail communications sent to and > from Cognizant e-mail addresses may be monitored. > > > This e-mail and any files transmitted with it are for the sole use of the > intended recipient(s) and may contain confidential and privileged > information. If you are not the intended recipient(s), please reply to the > sender and destroy all copies of the original message. Any unauthorized > review, use, disclosure, dissemination, forwarding, printing or copying of > this email, and/or any action taken in reliance on the contents of this > e-mail is strictly prohibited and may be unlawful. Where permitted by > applicable law, this e-mail and other e-mail communications sent to and > from Cognizant e-mail addresses may be monitored. >
