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matentznanitacaronAnita Caron
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Removing danging logical axioms on obsoleted relations and add QC (#751)
* Update ro-edit.owl * add QC for obsolete relations * remove logical axioms from obsolete relations * update_repo --------- Co-authored-by: Anita Caron <anitacaron@users.noreply.github.com> Co-authored-by: Anita Caron <anitac@ebi.ac.uk>
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‎src/ontology/Makefile‎

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@@ -1,7 +1,7 @@
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# ----------------------------------------
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# Makefile for ro
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# Generated using ontology-development-kit
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# ODK Version: v1.4
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# ODK Version: v1.4.1
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# ----------------------------------------
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# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use ro.Makefile instead
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@@ -42,9 +42,9 @@ REPORT_FAIL_ON = ERROR
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REPORT_LABEL = -l true
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REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE)
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OBO_FORMAT_OPTIONS =
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SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by term-editor-uri dce
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SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by term-editor-uri dce obsolete-relation
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SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms
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ODK_VERSION_MAKEFILE = v1.4
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ODK_VERSION_MAKEFILE = v1.4.1
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TODAY ?= $(shell date +%Y-%m-%d)
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OBODATE ?= $(shell date +'%d:%m:%Y %H:%M')

‎src/ontology/ro-edit.owl‎

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@@ -1301,7 +1301,6 @@ AnnotationAssertion(cito:citesAsAuthority obo:RO_0000300 <http://www.ncbi.nlm.ni
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AnnotationAssertion(rdfs:comment obo:RO_0000300 "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).")
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AnnotationAssertion(rdfs:label obo:RO_0000300 "obsolete in neural circuit with"@en)
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AnnotationAssertion(owl:deprecated obo:RO_0000300 "true"^^xsd:boolean)
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TransitiveObjectProperty(obo:RO_0000300)
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# Object Property: obo:RO_0000301 (obsolete upstream in neural circuit with)
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@@ -1313,7 +1312,6 @@ AnnotationAssertion(cito:citesAsAuthority obo:RO_0000301 <http://www.ncbi.nlm.ni
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AnnotationAssertion(rdfs:comment obo:RO_0000301 "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).")
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AnnotationAssertion(rdfs:label obo:RO_0000301 "obsolete upstream in neural circuit with"@en)
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AnnotationAssertion(owl:deprecated obo:RO_0000301 "true"^^xsd:boolean)
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TransitiveObjectProperty(obo:RO_0000301)
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# Object Property: obo:RO_0000302 (obsolete downstream in neural circuit with)
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@@ -1325,23 +1323,17 @@ AnnotationAssertion(cito:citesAsAuthority obo:RO_0000302 <http://www.ncbi.nlm.ni
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AnnotationAssertion(rdfs:comment obo:RO_0000302 "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other).")
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AnnotationAssertion(rdfs:label obo:RO_0000302 "obsolete downstream in neural circuit with"@en)
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AnnotationAssertion(owl:deprecated obo:RO_0000302 "true"^^xsd:boolean)
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TransitiveObjectProperty(obo:RO_0000302)
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# Object Property: obo:RO_0001018 (obsolete contained in)
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AnnotationAssertion(obo:IAO_0000111 obo:RO_0001018 "contained in"@en)
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AnnotationAssertion(obo:IAO_0000116 obo:RO_0001018 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved.")
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AnnotationAssertion(obo:IAO_0000116 obo:RO_0001018 "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):"@en)
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AnnotationAssertion(obo:IAO_0000116 obo:RO_0001018 "Intended meaning:
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domain: material entity
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range: spatial region or site (immaterial continuant)
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"@en)
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AnnotationAssertion(obo:IAO_0000118 obo:RO_0001018 "contained_in"@en)
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AnnotationAssertion(rdfs:label obo:RO_0001018 "obsolete contained in")
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AnnotationAssertion(rdfs:seeAlso obo:RO_0001018 <https://github.com/oborel/obo-relations/issues/693>)
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AnnotationAssertion(owl:deprecated obo:RO_0001018 "true"^^xsd:boolean)
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ObjectPropertyDomain(obo:RO_0001018 obo:BFO_0000040)
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ObjectPropertyRange(obo:RO_0001018 obo:BFO_0000004)
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# Object Property: obo:RO_0001019 (obsolete contains)
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@@ -6940,7 +6932,6 @@ SubObjectPropertyOf(ObjectPropertyChain(obo:BFO_0000054 obo:RO_0002404) obo:RO_0
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SubObjectPropertyOf(Annotation(obo:RO_0002582 "true"^^xsd:boolean) ObjectPropertyChain(obo:RO_0000052 obo:BFO_0000050) obo:RO_0002314)
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SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0000052 obo:RO_0000058) obo:RO_0010001)
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SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0000059 obo:RO_0000053) obo:RO_0010002)
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SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0001025 obo:BFO_0000050) obo:RO_0001018)
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SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0001025 obo:BFO_0000050) obo:RO_0001025)
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SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0001025 ObjectInverseOf(obo:RO_0001025)) obo:RO_0002379)
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SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0002092 obo:BFO_0000063) obo:BFO_0000063)

‎src/ontology/ro-odk.yaml‎

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- multiple-replaced_by
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- term-editor-uri
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- dce
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- obsolete-relation

‎src/sparql/obsolete-relation-violation.sparql‎

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# # Obsolete relation with logical axioms
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#
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# **Problem:** A deprecated ObjectProperty with logical axioms. A deprecated property can be the child of another property (e.g., ObsoleteProperty), but it cannot have children or be used in blank nodes or equivalence statements. Additionally, a deprecated property should not have any equivalent properties.
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#
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# **Solution:** Remove the logical axioms.
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PREFIX obo: <http://purl.obolibrary.org/obo/>
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PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
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PREFIX owl: <http://www.w3.org/2002/07/owl#>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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SELECT DISTINCT ?entity ?property ?value WHERE {
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{
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VALUES ?property {
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owl:equivalentProperty
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rdfs:subPropertyOf
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owl:inverseOf
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rdfs:domain
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rdfs:range
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rdf:type
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}
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?entity a owl:ObjectProperty ;
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owl:deprecated true .
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?entity ?property ?value1 .
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FILTER (?value1 != owl:ObjectProperty)
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}
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UNION
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{
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VALUES ?property {
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owl:equivalentProperty
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rdfs:subPropertyOf
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}
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?entity a owl:DatatypeProperty ;
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owl:deprecated true .
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?entity ?property ?value1 .
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}
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UNION
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{
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?property owl:deprecated true .
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?value1 ?property ?entity .
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}
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UNION
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{
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?property owl:deprecated true .
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?entity ?x ?value1 .
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?value1 a owl:Restriction ;
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owl:onProperty ?property .
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}
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BIND (if(isIRI(?value1), ?value1, "blank node" ) as ?value)
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}
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ORDER BY ?entity

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