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Document Information
Author: Craig Stancl

Team: LexEVS
Contract: S13-500 MOD4
Client: NCI CBIIT
National Institutes of Heath
US Department of Health and Human Services

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Overview

Loading OWL2 sources is part of an ongoing project to create a viable mapping of OWL2 sources into the LexGrid model.  Challenges presented by this mapping include the punning of some owl classes into individuals and providing a mapping of annotations properties into a variety of LexEVS objects depending on the nature of the OWL2 annotation property.  In some cases drilling down into the NAry structure of boolean sentences to construct relationships that are otherwise hidden by the nature of anonymous class was necessary.  Individual examples of these issues have been detailed in the spread sheet below.  

 

LEXEVS-583 - Getting issue details... STATUS

LEXEVS-614 - Getting issue details... STATUS

 

Design

JIRAentitiestest entitytest annotationcommentLbGUI StructureLbGUI annotationPriorityLexEVS Team Comments0.1.20.1.10.1.30.1.0
LEXEVS-775Ontology metadata     1Make sure the OWL:Ontology tag contents are expressed as coding scheme metadataYesYesYesYes
 special classC123 (Gene)  + 0 N/A   
LEXEVS-776external classhttp://purl.obolibrary.org/obo/CL_0000000 (Cell) http://purl.obolibrary.org/obo/CL_0000148 (melanocyte) entity code missing "http:" portion? 5 (?)the issue is that depending on the context, the "http" might be present, raising the question of whether the references can be trusted. See e.g. item 85 vs 97YesYesYesYes
LEXEVS-777datatype propertyhas_physical_location in_organism semanticType no datatype ranges are shown in lbgui (in_organism and semanticType)+/- 1Some properties will be treated as first class entity. Range one of would be treated as flattened list. See sematic type. See also in_organism where we'd add provenance and definitionYesYesYesYes
LEXEVS-778annotation propertyAssociationLIT AssociationSTR AssociationURI AssociationV1 date definition note provenance semanticType source term term_type only AssociationV1 and semanticType show up in primitive-unannotated (dual definitions with ranges)- 2lexevs has built-in properties for various things, e.g. definitions. But there are other properties that are not built into the lexevs model that might still be needed to be exposed to the end-user. Properties to be attached to the enitity such as in_organizm.YesYesN/AN/A
LEXEVS-779anonymous class (test with unattached restriction)Patient_Has_Finding some Finding SubClassOf SickPatient express in LexEVS? Yes.- 3Left hand side is anon node subClass is the association. The intersection does not seem to be expressed in the annotated primitives. Assuming it is acceptably resolved for the defined annotated.YesYesYesYes
LEXEVS-780association, annotation (literal)AssociationLIT  - 1 Yes N/AN/A
LEXEVS-781association, annotation (anyURI)AsoociationURI  - 1 YesYesN/AN/A
LEXEVS-782association, annotation (string)AssociationSTR  - 1 YesYesN/AN/A
             
 annotations on entities (declaration)           
LEXEVS-783annotation on anonymous class (test with unattached restriction)Patient_Has_Finding some Finding SubClassOf SickPatientnote, provenance, sourceexpose in lexevs? Yes. See above for priority.-+3 YesYesN/AN/A
LEXEVS-784annotation on association, object + annotation (v1)term not consistent with other properties-+1not specific to these "association" properties, their metadata should be included as if they were first class citizens. Referring to the annotations in 10-12YesYesN/AN/A
LEXEVS-785annotation on association, annotation (literal)term not consistent with other properties-+1Not to be loaded as assoc entity -- only as a property on a class. This because the filler type is not anyURI.YesYesN/AN/A
LEXEVS-786annotation on association, annotation (anyURI)term not consistent with other properties-+1Needs Entity description. Annotated onYesYesN/AN/A
LEXEVS-787annotation on association, annotation (string)term not consistent with other properties-+1Not to be loaded as assoc entity -- only as a property on a class. This because the filler type is not anyURI.YesYesN/AN/A
             
             
 axioms, annotated           
             
         N/A   
LEXEVS-788subclassOf, external named classEpithelial_Cell isa Cell =definition on subclass axiom"http" of external class, missing?+/-+5 (?) YesYesYesYes
 subclassOf, intersection named classesTotalPerson isa Person and PersonRolenote on subclass axiomPersonRole not extracted-+5question: should we also present the standalone conjuntion.Dup?   
 subclassOf, union named classesPrognosis isa (PrognosisGood or PrognosisBad), SickPatient isa Patient and (CancerPatient or MildlySickPatient or VerySickPatient)note on subclass axiomunions anon classes appear parsed because the subclasses are "[R]subClassOf"+/=+0 Dup?   
 subclassOf, union named disjoint classesGene isa disjointunion(Braf or Brca1 or Erbb2 or Mefv or OncogeneTim or Ras or Actin)note on disjoint unionthe classes in the disjoint union appear parsed, but it's because they are also subclasses (see above)+/--5 Dup?   
 subclassOf, complement named classHealthyPatient not(SickPatient)note on subclass axiomanon class not parsed-+3representation issueDup?   
 subclassOf, one ofFinding one of (Fever, PaleSkin, ShallowBreathing) [individuals]note on subclass axiomanon class appears parsed because the individuals have [R]type relationsN/A+0 Dup?   
         Dup?   
 subclassOf, some datatype restrictionras isa gene and has_physical_location some positiveIntegernote on subclass axiomanon class not parsed-+3representation issueDup?   
 subclassOf, all datatype restrictionk-ras isa gene and has_physical_location all positiveIntegernote on subclass axiomanon class not parsed-+3representation issueDup?   
 subclassOf, datatype hasValueoncogeneTim isa gene and has_physical_location value 12345note on subclass axiomanon class not parsed-+3representation issueDup?   
 subclassOf, some objectype restrictionSOS isa gene and gene_related_to_disease some NeoplasticDiseasenote on subclass axiomanon class not parsed-+5 Dup?   
 subclassOf, some objectype restriction external classbraf isa gene and gene_expressed_in some melanocytenote on subclass axiomanon class not parsed. "http" present in class IRI-+5 Dup?   
 subclassOf, all objectype restriction external classerbb2 isa gene and gene_expressed_in only melanocytenote on subclass axiomanon class not parsed. "http" present in class IRI-+5 Dup?   
 subclassOf, all objectype restrictionshh isa gene and gene_related_to_disease only NeoplasticDiseasenote on subclass axiomanon class not parsed-+5 Dup?   
 subclassOf, object hasValueMefv isa Gene and gene_related_to_disease value Fevernote on subclass axiomanon class not parsed. Individual present-+5 Dup?   
 subclassOf, intersection object restrictionsMildlySickCancerPatient isa MildlySickPatient and (patient_has_finding some TumorBenign) and (patient_has_prognosis some PrognosisGood)note on subclass axiomanon class not parsed-+5 Dup?   
 subclassOf, union object restrictionsVerySickCancerPatient isa VerySickPatient and (patient_has_finding some TumorMalignant) or (patient_has_prognosis some PrognosisBad)note on subclass axiomanon class not parsed-+5 Dup?   
 subclassOf, role groupCancerPatient isa SickPatient and ((patient_has_finding some TumorBenign) and (patient_has_prognosis some PrognosisGood)) or ((patient_has_finding some TumorMalignant) and (patient_has_prognosis some PrognosisBad))note on subclass axiomanon class not parsed-+5 Dup?   
 subclassOf, class expression (intersection object & datatype)brca1 isa gene and ((gene_expressed_in some EpithelialCell) and (in_organism value "homo sapiens)) anon class not parsed-+3representation issueDup?   
 subclassOf, class expression (union object & datatype)actin isa gene and ((gene_expressedin some EpithelialCell) or (in_organism value "all Organisms")) anon class not parsed-+3representation issueDup?   
             
LEXEVS-789association internal class (PrognosisGood)HappyPatientDrivingAround: Associations V1, STR, URI, LIT, and URI as resource type=anyURI is not being used for the association (V1 unannotated, OWLAPI issue)-+5 YesYesN/AN/A
LEXEVS-790association external class (melanocyte)HappyPatientWalkingAround: Associations V1, STR, URI, LIT, and URI as resource 1) as above, 2) "http" not present in the external class' URI, 3) annotation on V1 belongs to another property-+5 YesYesN/AN/A
             
LEXEVS-791equivalentClass, external named class  (external class does not have "http")- 5 (?) YesYesYesYes
LEXEVS-792equivalentClass, intersection named classesTotalPerson isa Person and PersonRolenoteanon class not parsed-+5 YesYesYesYes
LEXEVS-793equivalentClass, union named disjoint classesGene isa disjointunion(Braf or Brca1 or Erbb2 or Mefv or OncogeneTim or Ras or Actin)note; (already a defined class)anon class not displayed, can't confirm. (SB, I don't see OncogeneTim or Brca1 in Protégé or the source. I'm leaving them out of the test case and putting in SHH, k-Ras and SOS.)++5 YesYesYesYes
LEXEVS-794equivalentClass, complement named classHealthyPatient not(SickPatient)noteanon class not parsed-+3 YesYesYesYes
             
LEXEVS-795equivalentClass, some datatype restrictionras isa gene and has_physical_location some positiveIntegernoteanon class not parsed-+3representation issue: Must be designated as something other than a conceptYesYesYesYes
LEXEVS-796equivalentClass, all datatype restrictionk-ras isa gene and has_physical_location all positiveIntegernoteanon class not parsed-+3representation issueYesYesYesYes
LEXEVS-797equivalentClass, datatype hasValue (inconsistent class)oncogeneTim isa gene and has_physical_location value 12345noteanon class not parsed-+3representation issueYesYesYesYes
LEXEVS-798equivalentClass, some objectype restrictionSOS isa gene and gene_related_to_disease some NeoplasticDiseasenoteanon class not parsed++5 YesYesYesYes
LEXEVS-799equivalentClass, some objectype restriction external classbraf isa gene and gene_expressed_in some melanocytenoteanon class not parsed (external class has "http")-+5 YesYesYesYes
LEXEVS-800equivalentClass, all objectype restriction external classerbb2 isa gene and gene_expressed_in only melanocytenoteanon class not parsed-+5 YesYesYesYes
LEXEVS-801equivalentClass, all objectype restrictionshh isa gene and gene_related_to_disease only NeoplasticDiseasenoteanon class not parsed-+5 YesYesYesYes
LEXEVS-802equivalentClass, object hasValueMefv isa Gene and gene_related_to_disease value Fevernoteanon class not parsed-+5 YesYesYesYes
LEXEVS-803equivalentClass, intersection object restrictionsMildlySickCancerPatient isa MildlySickPatient and (patient_has_finding some TumorBenign) and (patient_has_prognosis some PrognosisGood)noteanon class not parsed-+5 YesYesYesYes
LEXEVS-804equivalentClass, union object restrictionsVerySickCancerPatient isa VerySickPatient and (patient_has_finding some TumorMalignant) or (patient_has_prognosis some PrognosisBad)noteanon class not parsed-+5 YesYesYesYes
LEXEVS-805equivalentClass, role groupCancerPatient isa SickPatient and ((patient_has_finding some TumorBenign) and (patient_has_prognosis some PrognosisGood)) or ((patient_has_finding some TumorMalignant) and (patient_has_prognosis some PrognosisBad))noteanon class not parsed-+5 YesYesYesYes
LEXEVS-806equivalentClass, class expression (intersection object & datatype)brca1 isa gene and ((gene_expressed_in some EpithelialCell) and (in_organism value "homo sapiens))noteanon class not parsed (SB, at the very least missing in_organism)-+3representation issueYesYesYesYes
LEXEVS-807equivalentClass, class expression (union object & datatype)actin isa gene and ((gene_expressedin some EpithelialCell) or (in_organism value "all Organisms"))noteanon class not parsed(SB, at the very least missing in_organism)--3representation issueYesYesYesYes
             
             
 not covered           
 no cardinality           
 no symmetry, reflexive, functional,…