ernestojimenezruiz
commented
4 years ago For some reason I was not getting the notifications from the issues.
The versions are different. The one in the Web service was deployed in 2013 or 2014.
The problem with ELK seems to be a internal problem with the reasoner.
The missing mapping was borderline and may have not passed the cut in the new version depending on the neighborhood information.
Ernesto
Both the below scenarios work perfect with the web version. Finds the match for Dim_patient http://krrwebtools.cs.ox.ac.uk/logmap/output/matching_07_04_2020__20_47_14_29/mappings.txt
http://hl7.org/fhir/integer|http://watsonhealth.ibm.com/cro/integer|=|0.7|CLS http://hl7.org/fhir/string|http://watsonhealth.ibm.com/cro/string|=|0.7|CLS http://hl7.org/fhir/boolean|http://watsonhealth.ibm.com/cro/boolean|=|0.7|CLS http://hl7.org/fhir/Patient|http://watsonhealth.ibm.com/cro/Dim_Patient|=|0.52|CLS http://hl7.org/fhir/value|http://watsonhealth.ibm.com/cro/value|=|1.0|DPROP
Standalone (build from Github)
with ELK reasoner turned on in parameters.txt I get Running LogMap Matcher .... SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. org.semanticweb.owlapi.model.OWLRuntimeException: No current axiom; is the walker being used outside of an ontology visit? at org.semanticweb.owlapi.util.OWLOntologyWalkerVisitor.getCurrentAxiom(OWLOntologyWalkerVisitor.java:48) at org.semanticweb.owlapi.profiles.OWL2DLProfile$OWL2DLProfileObjectVisitor.visit(OWL2DLProfile.java:477) at uk.ac.manchester.cs.owl.owlapi.OWLAnnotationPropertyImpl.accept(OWLAnnotationPropertyImpl.java:83) at org.semanticweb.owlapi.util.OWLObjectWalker.passToVisitor(OWLObjectWalker.java:137) at org.semanticweb.owlapi.util.StructureWalker.process(StructureWalker.java:87) at org.semanticweb.owlapi.util.StructureWalker.visit(StructureWalker.java:687) at uk.ac.manchester.cs.owl.owlapi.OWLAnnotationPropertyImpl.accept(OWLAnnotationPropertyImpl.java:83) at org.semanticweb.owlapi.profiles.OWLOntologyProfileWalker$1.visit(OWLOntologyProfileWalker.java:56) at uk.ac.manchester.cs.owl.owlapi.OWLAnnotationImpl.accept(OWLAnnotationImpl.java:141) at org.semanticweb.owlapi.util.StructureWalker.process(StructureWalker.java:101) at org.semanticweb.owlapi.util.StructureWalker.visit(StructureWalker.java:116) at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.accept(OWLImmutableOntologyImpl.java:852) at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyImpl.accept(ConcurrentOWLOntologyImpl.java:396) at org.semanticweb.owlapi.util.OWLObjectWalker.walkStructure(OWLObjectWalker.java:181) at org.semanticweb.owlapi.profiles.OWL2DLProfile.checkOntology(OWL2DLProfile.java:146) at org.semanticweb.owlapi.profiles.OWL2ELProfile.checkOntology(OWL2ELProfile.java:106) at uk.ac.ox.krr.logmap2.reasoning.profiles.CheckOWL2Profile.isInOWL2ELProfile(CheckOWL2Profile.java:59) at uk.ac.ox.krr.logmap2.indexing.OntologyProcessing.setUpReasoner_ELK(OntologyProcessing.java:2809) at uk.ac.ox.krr.logmap2.indexing.OntologyProcessing.setTaxonomicData(OntologyProcessing.java:2625) at uk.ac.ox.krr.logmap2.LogMap2Core.IndexLexiconAndStructure(LogMap2Core.java:942) at uk.ac.ox.krr.logmap2.LogMap2Core.IndexLexiconAndStructure(LogMap2Core.java:886) at uk.ac.ox.krr.logmap2.LogMap2Core.(LogMap2Core.java:421)
at uk.ac.ox.krr.logmap2.LogMap2Core.(LogMap2Core.java:214)
at uk.ac.ox.krr.logmap2.LogMap2_Matcher.(LogMap2_Matcher.java:63)
at uk.ac.ox.krr.logmap2.LogMap2_CommandLine.main(LogMap2_CommandLine.java:106)
With HemiT
It just simply ignores the custom datatypes
http://hl7.org/fhir/string|http://watsonhealth.ibm.com/cro/string|=|0.7|CLS http://hl7.org/fhir/boolean|http://watsonhealth.ibm.com/cro/boolean|=|0.7|CLS http://hl7.org/fhir/integer|http://watsonhealth.ibm.com/cro/integer|=|0.7|CLS http://hl7.org/fhir/value|http://watsonhealth.ibm.com/cro/value|=|1.0|DPROP