James, Thanks for the assistance.
Adding a DeviceMention that uses EntityMention as the supertype worked. As you requested, I create JIRA 357: Adding support for mention of Medical Devices: https://issues.apache.org/jira/browse/CTAKES-357 Thanks, Bruce On Sun, May 3, 2015 at 5:59 AM, Masanz, James J. <masanz.ja...@mayo.edu> wrote: > I think the 'right way' would be to create a subtype of > org.apache.ctakes.typesystem.type.textsem.EntityMention (rather than what > you tried with a subtype of IdentifiedAnnotation) > I don't know where all the required changes would be beyond that. > > If you get that to work, please create a JIRA with the information so the > documentation can be updated. > > If I just wanted to get it to work, I would look at one of these options > - use the method you tried with EntityMention, and if you want to get > just the devices, loop through all EntityMention and check explicitly if > the type is EntityMention (and not a subtype of EntityMention) > - use the method you tried with either ProcedureMention or EntityMention, > and then in cases where you needed to know if it was a device, use the > _ref_ontologyConceptArr to find out the TUI associated with the annotation. > > > Regards, > James > > -----Original Message----- > From: Bruce Tietjen [mailto:bruce.tiet...@perfectsearchcorp.com] > Sent: Thursday, April 30, 2015 3:39 PM > To: dev@ctakes.apache.org > Subject: What is the correct way to enable cTakes to recognize and > annotate mentions of medical devices? > > Hi, > I am using the cTakes 3.2.0 code base and I have been trying to figure out > what would be the proper way to get cTakes to recognize and annotate > mentions of medical devices. > > I am using the AggregatePlaintextUMLSProcessor.xml because one of the main > requirements for the annotation is that it needs to to include subject, and > polarity, certainty, etc. > > First, I added TUI T074 to the procedureTuis in the LookupDesc_Db.xml. The > output from this provides mostly what I want, except it lumps the devices > as ProcedureMention where I would like them to be distinguished by their > own annotation. > > An example annotation created this way was: > <org.apache.ctakes.typesystem.type.textsem.ProcedureMention > _indexed="1" _id="35574" _ref_sofa="3" begin="472" end="481" id="32" > _ref_ontologyConceptArr="35569" typeID="8" segmentID="SIMPLE_SEGMENT" > discoveryTechnique="1" confidence="1.0" polarity="1" uncertainty="0" > conditional="false" generic="false" subject="patient" historyOf="0"/> > > I also tried adding code to classify devices as an EntityMention, and that > seemed to work too: > <org.apache.ctakes.typesystem.type.textsem.EntityMention _indexed="1" > _id="35574" _ref_sofa="3" begin="472" end="481" id="32" > _ref_ontologyConceptArr="35569" typeID="8" segmentID="SIMPLE_SEGMENT" > discoveryTechnique="1" confidence="1.0" polarity="1" uncertainty="0" > conditional="false" generic="false" subject="patient" historyOf="0"/> > > Again, that doesn't give devices their own unique annotation so I looked > further. Exploring the typesystem, I noticed the following types in > TypeSystem.xml: > org.apache.ctakes.typesystem.type.refsem.ProcedureDevice > org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier > > These seemed like the closest defined types to what I would expect so I > thought I would see if using them would generate what I wanted. I modified > the code to generate these annotations and the result was as follows: > <org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier > _indexed="1" _id="35587" _ref_sofa="3" begin="472" end="481" id="32" > typeID="0" segmentID="SIMPLE_SEGMENT" discoveryTechnique="0" > confidence="0.0" polarity="0" uncertainty="0" conditional="false" > generic="false" subject="patient" historyOf="0" > _ref_normalizedForm="35574"/> > <org.apache.ctakes.typesystem.type.refsem.ProcedureDevice _id="35574" > id="0" _ref_ontologyConcept="35542" discoveryTechnique="1" confidence="0.0" > conditional="false" generic="false" polarity="0" uncertainty="0" > historyOf="0"/> > > The problem with this approach was that confidence, polarity, and > uncertainty did not get filled in. I tried adding these to the inputs and > outputs of the AssertionMiniPipelineAnalysisEngine, but that didn't seem to > have any effect. Perhaps I didn't do it right? or maybe it isn't even the > right pipeline component to try to modify? > > Since ProcedureDevice and ProcedureDeviceModifer have different supertypes > than ProcedureMention, I also tried creating a new type in > TypeSystem.xml: > <typeDescription> > <name>org.apache.ctakes.typesystem.type.textsem.DeviceMention</name> > > > <supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</supertypeName> > <features> > <featureDescription> > <name>entity</name> > <description/> > > > <rangeTypeName>org.apache.ctakes.typesystem.type.refsem.Entity</rangeTypeName> > </featureDescription> > </features> > </typeDescription> > > Modifying the code to create this type, the result was: > <org.apache.ctakes.typesystem.type.textsem.DeviceMention _indexed="1" > _id="35574" _ref_sofa="3" begin="472" end="481" id="32" > _ref_ontologyConceptArr="35569" typeID="8" segmentID="SIMPLE_SEGMENT" > discoveryTechnique="1" confidence="0.0" polarity="0" uncertainty="0" > conditional="false" generic="false" subject="patient" historyOf="0"/> > > Again the problem here is that confidence, polarity and uncertainty are not > filled in. > > So, I am left wondering: > 1) Which of the methods I tried would be the best "cTakes way"? > 2) What do I need to modify to get confidence, polarity and uncertainty to > be filled in? > > Thanks, > Bruce >
