I believe that I am in fact using the UMLS, since I run the bin/runClinicalPipeline.sh with my UMLS credentials and I have added my credentials to the bin/runctakesCVD.sh script as recommended by the user installation guide ( https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide#cTAKES4.0UserInstallGuide-(Recommended)AddUMLSaccessrights ). Also thanks for pointing out my Polarity=negation confusion, just started reading through the Component Use documentation ( https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Assertion#cTAKES4.0-Assertion-Negationattributeannotator ).
On Fri, Mar 23, 2018 at 6:04 AM, Schenk, Gundolf <[email protected]> wrote: > Hi Reed, > > > > Did you enable UMLS? > > > > I am also not quite happy with the result. When I run this test sentence > in the DefaultClinicalPipeline I am getting 4 IdentifiedAnnotation > (AnnotationIndex -> uima.tcas.Annotation -> org.apache.ctakes.typesystem. > type.textsem.IdentifiedAnnotation). > > Namely, ProcedureMention (“scan”), RomanNumericalAnnotation (“did”), > SignSymptomAnnotation (“lesions”) and AnatomicalSiteMention (“liver”). > “lesions” is negated as indicated by Polarity=-1. > > > > This does not seem error-free to me, still. Could anyone confirm this is > the expected result, please? > > > > Cheers, > > Gundolf. > > > > > > *From: *Reed Villanueva <[email protected]> > *Reply-To: *"[email protected]" <[email protected]> > *Date: *Friday, March 23, 2018 at 01:54 > *To: *"[email protected]" <[email protected]> > *Subject: *Default clinical pipeline does not appear to work as > advertised by the docs' graphic showing its use, how to get there? > > > > Running the exact same test ("The patient underwent a CT scan in April > which did not reveal lesions in his liver") as shown for the default > clinical pipeline (https://cwiki.apache.org/confluence/display/CTAKES/ > Default+Clinical+Pipeline) and examining the XMI output in the ctakesCVD, > does not seem to extract the same information as shown in the graphic in > the docs demonstrating what information is taken from that same sentence. > > > > Eg. > > * The only detect EntityMention was "liver" and I could not find where it > had received a tag value of "Anatomy". > > * Looking at the AnnotationIndex.IdentifiedAnnotations, there seems to be > no "Entity Properties" data as implied in the docs (such as "lesions" > having the property of "negated"). > > > > I feel that I must have missed something here, am looking in the wrong > place, or something else? Please advise, thank you. >
