Team: LexEVS
Contract: S13-500 MOD4
Client: NCI CBIIT
National Institutes of Heath
US Department of Health and Human Services
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
JIRA entities test entity test annotation comment LbGUI Structure LbGUI annotation Priority LexEVS Team Comments 0.1.2 0.1.1 0.1.3 0.1.0 LEXEVS-775 Ontology metadata 1 Make sure the OWL:Ontology tag contents are expressed as coding scheme metadata Yes Yes Yes Yes special class C123 (Gene) + 0 N/A LEXEVS-776 external class http://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 97 Yes Yes Yes Yes LEXEVS-777 datatype property has_physical_location
in_organism
semanticType no datatype ranges are shown in lbgui (in_organism and semanticType) +/- 1 Some 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 definition Yes Yes Yes Yes LEXEVS-778 annotation property AssociationLIT
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) - 2 lexevs 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. Yes Yes N/A N/A LEXEVS-779 anonymous class (test with unattached restriction) Patient_Has_Finding some Finding SubClassOf SickPatient express in LexEVS? Yes. - 3 Left 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. Yes Yes Yes Yes LEXEVS-780 association, annotation (literal) AssociationLIT - 1 Yes N/A N/A LEXEVS-781 association, annotation (anyURI) AsoociationURI - 1 Yes Yes N/A N/A LEXEVS-782 association, annotation (string) AssociationSTR - 1 Yes Yes N/A N/A annotations on entities (declaration) LEXEVS-783 annotation on anonymous class (test with unattached restriction) Patient_Has_Finding some Finding SubClassOf SickPatient note, provenance, source expose in lexevs? Yes. See above for priority. - + 3 Yes Yes N/A N/A LEXEVS-784 annotation on association, object + annotation (v1) term not consistent with other properties - + 1 not specific to these "association" properties, their metadata should be included as if they were first class citizens. Referring to the annotations in 10-12 Yes Yes N/A N/A LEXEVS-785 annotation on association, annotation (literal) term not consistent with other properties - + 1 Not to be loaded as assoc entity -- only as a property on a class. This because the filler type is not anyURI. Yes Yes N/A N/A LEXEVS-786 annotation on association, annotation (anyURI) term not consistent with other properties - + 1 Needs Entity description. Annotated on Yes Yes N/A N/A LEXEVS-787 annotation on association, annotation (string) term not consistent with other properties - + 1 Not to be loaded as assoc entity -- only as a property on a class. This because the filler type is not anyURI. Yes Yes N/A N/A axioms, annotated N/A LEXEVS-788 subclassOf, external named class Epithelial_Cell isa Cell = definition on subclass axiom "http" of external class, missing? +/- + 5 (?) Yes Yes Yes Yes subclassOf, intersection named classes TotalPerson isa Person and PersonRole note on subclass axiom PersonRole not extracted - + 5 question: should we also present the standalone conjuntion. Dup? subclassOf, union named classes Prognosis isa (PrognosisGood or PrognosisBad), SickPatient isa Patient and (CancerPatient or MildlySickPatient or VerySickPatient) note on subclass axiom unions anon classes appear parsed because the subclasses are "[R]subClassOf" +/= + 0 Dup? subclassOf, union named disjoint classes Gene isa disjointunion(Braf or Brca1 or Erbb2 or Mefv or OncogeneTim or Ras or Actin) note on disjoint union the classes in the disjoint union appear parsed, but it's because they are also subclasses (see above) +/- - 5 Dup? subclassOf, complement named class HealthyPatient not(SickPatient) note on subclass axiom anon class not parsed - + 3 representation issue Dup? subclassOf, one of Finding one of (Fever, PaleSkin, ShallowBreathing) [individuals] note on subclass axiom anon class appears parsed because the individuals have [R]type relations N/A + 0 Dup? Dup? subclassOf, some datatype restriction ras isa gene and has_physical_location some positiveInteger note on subclass axiom anon class not parsed - + 3 representation issue Dup? subclassOf, all datatype restriction k-ras isa gene and has_physical_location all positiveInteger note on subclass axiom anon class not parsed - + 3 representation issue Dup? subclassOf, datatype hasValue oncogeneTim isa gene and has_physical_location value 12345 note on subclass axiom anon class not parsed - + 3 representation issue Dup? subclassOf, some objectype restriction SOS isa gene and gene_related_to_disease some NeoplasticDisease note on subclass axiom anon class not parsed - + 5 Dup? subclassOf, some objectype restriction external class braf isa gene and gene_expressed_in some melanocyte note on subclass axiom anon class not parsed. "http" present in class IRI - + 5 Dup? subclassOf, all objectype restriction external class erbb2 isa gene and gene_expressed_in only melanocyte note on subclass axiom anon class not parsed. "http" present in class IRI - + 5 Dup? subclassOf, all objectype restriction shh isa gene and gene_related_to_disease only NeoplasticDisease note on subclass axiom anon class not parsed - + 5 Dup? subclassOf, object hasValue Mefv isa Gene and gene_related_to_disease value Fever note on subclass axiom anon class not parsed. Individual present - + 5 Dup? subclassOf, intersection object restrictions MildlySickCancerPatient isa MildlySickPatient and (patient_has_finding some TumorBenign) and (patient_has_prognosis some PrognosisGood) note on subclass axiom anon class not parsed - + 5 Dup? subclassOf, union object restrictions VerySickCancerPatient isa VerySickPatient and (patient_has_finding some TumorMalignant) or (patient_has_prognosis some PrognosisBad) note on subclass axiom anon class not parsed - + 5 Dup? subclassOf, role group CancerPatient 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 axiom anon 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 - + 3 representation issue Dup? subclassOf, class expression (union object & datatype) actin isa gene and ((gene_expressedin some EpithelialCell) or (in_organism value "all Organisms")) anon class not parsed - + 3 representation issue Dup? LEXEVS-789 association 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 Yes Yes N/A N/A LEXEVS-790 association 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 Yes Yes N/A N/A LEXEVS-791 equivalentClass, external named class (external class does not have "http") - 5 (?) Yes Yes Yes Yes LEXEVS-792 equivalentClass, intersection named classes TotalPerson isa Person and PersonRole note anon class not parsed - + 5 Yes Yes Yes Yes LEXEVS-793 equivalentClass, union named disjoint classes Gene 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 Yes Yes Yes Yes LEXEVS-794 equivalentClass, complement named class HealthyPatient not(SickPatient) note anon class not parsed - + 3 Yes Yes Yes Yes LEXEVS-795 equivalentClass, some datatype restriction ras isa gene and has_physical_location some positiveInteger note anon class not parsed - + 3 representation issue: Must be designated as something other than a concept Yes Yes Yes Yes LEXEVS-796 equivalentClass, all datatype restriction k-ras isa gene and has_physical_location all positiveInteger note anon class not parsed - + 3 representation issue Yes Yes Yes Yes LEXEVS-797 equivalentClass, datatype hasValue (inconsistent class) oncogeneTim isa gene and has_physical_location value 12345 note anon class not parsed - + 3 representation issue Yes Yes Yes Yes LEXEVS-798 equivalentClass, some objectype restriction SOS isa gene and gene_related_to_disease some NeoplasticDisease note anon class not parsed + + 5 Yes Yes Yes Yes LEXEVS-799 equivalentClass, some objectype restriction external class braf isa gene and gene_expressed_in some melanocyte note anon class not parsed (external class has "http") - + 5 Yes Yes Yes Yes LEXEVS-800 equivalentClass, all objectype restriction external class erbb2 isa gene and gene_expressed_in only melanocyte note anon class not parsed - + 5 Yes Yes Yes Yes LEXEVS-801 equivalentClass, all objectype restriction shh isa gene and gene_related_to_disease only NeoplasticDisease note anon class not parsed - + 5 Yes Yes Yes Yes LEXEVS-802 equivalentClass, object hasValue Mefv isa Gene and gene_related_to_disease value Fever note anon class not parsed - + 5 Yes Yes Yes Yes LEXEVS-803 equivalentClass, intersection object restrictions MildlySickCancerPatient isa MildlySickPatient and (patient_has_finding some TumorBenign) and (patient_has_prognosis some PrognosisGood) note anon class not parsed - + 5 Yes Yes Yes Yes LEXEVS-804 equivalentClass, union object restrictions VerySickCancerPatient isa VerySickPatient and (patient_has_finding some TumorMalignant) or (patient_has_prognosis some PrognosisBad) note anon class not parsed - + 5 Yes Yes Yes Yes LEXEVS-805 equivalentClass, role group CancerPatient 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 anon class not parsed - + 5 Yes Yes Yes Yes LEXEVS-806 equivalentClass, class expression (intersection object & datatype) brca1 isa gene and ((gene_expressed_in some EpithelialCell) and (in_organism value "homo sapiens)) note anon class not parsed (SB, at the very least missing in_organism) - + 3 representation issue Yes Yes Yes Yes LEXEVS-807 equivalentClass, class expression (union object & datatype) actin isa gene and ((gene_expressedin some EpithelialCell) or (in_organism value "all Organisms")) note anon class not parsed(SB, at the very least missing in_organism) - - 3 representation issue Yes Yes Yes Yes not covered no cardinality no symmetry, reflexive, functional,…