From 3e09daab14f47a4ae83617229a59925800c4c927 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Tue, 21 Jun 2022 10:52:18 +0100 Subject: [PATCH 1/3] add axioms and create id for `has_start_point` --- src/ontology/bspo-edit.owl | 35 ++++++++++++++++++++++------------- 1 file changed, 22 insertions(+), 13 deletions(-) diff --git a/src/ontology/bspo-edit.owl b/src/ontology/bspo-edit.owl index f5bc29e..a016fe1 100644 --- a/src/ontology/bspo-edit.owl +++ b/src/ontology/bspo-edit.owl @@ -223,10 +223,11 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -652,6 +653,7 @@ AnnotationAssertion( "in lateral side of"^^xsd:string) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) SubObjectPropertyOf( ) +DisjointObjectProperties( ) # Object Property: (in superficial part of) @@ -867,6 +869,7 @@ AnnotationAssertion( "immediately_posterior_to"^^xsd:string) AnnotationAssertion(rdfs:label "immediately posterior to"^^xsd:string) SubObjectPropertyOf( ) +SubObjectPropertyOf( ) # Object Property: (immediately proximal to) @@ -887,6 +890,7 @@ AnnotationAssertion( "immediately_superficial_to"^^xsd:string) AnnotationAssertion(rdfs:label "immediately superficial to"^^xsd:string) SubObjectPropertyOf( ) +SubObjectPropertyOf( ) # Object Property: (immediately ventral to) @@ -959,6 +963,23 @@ AnnotationAssertion( "aboral to"^^xsd:string) TransitiveObjectProperty() +# Object Property: (in central side of) + +AnnotationAssertion( "BSPO:0020001") +AnnotationAssertion(rdfs:label "in central side of") + +# Object Property: (has start point) + +AnnotationAssertion(Annotation( "BSPO:cjm"^^xsd:string) "A relation between an axis and a part of an organism, in which the part defines the initial point of the axis."^^xsd:string) +AnnotationAssertion( ":has_start_point"^^xsd:string) +AnnotationAssertion( "spatial"^^xsd:string) +AnnotationAssertion( "has_start_point"^^xsd:string) +AnnotationAssertion( "has_start_point"^^xsd:string) +AnnotationAssertion(rdfs:comment "Axes can be defined in a given species by subtyping the relevant axis type and stating a start and end point."^^xsd:string) +AnnotationAssertion(rdfs:label "has start point"^^xsd:string) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (preaxial to) AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/preaxial"^^xsd:string) "x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the front."^^xsd:string) @@ -991,18 +1012,6 @@ AnnotationAssertion( "adjacent to"^^xsd:string) SymmetricObjectProperty() -# Object Property: (has start point) - -AnnotationAssertion(Annotation( "BSPO:cjm"^^xsd:string) "A relation between an axis and a part of an organism, in which the part defines the initial point of the axis."^^xsd:string) -AnnotationAssertion( ":has_start_point"^^xsd:string) -AnnotationAssertion( "spatial"^^xsd:string) -AnnotationAssertion( "has_start_point"^^xsd:string) -AnnotationAssertion( "has_start_point"^^xsd:string) -AnnotationAssertion(rdfs:comment "Axes can be defined in a given species by subtyping the relevant axis type and stating a start and end point."^^xsd:string) -AnnotationAssertion(rdfs:label "has start point"^^xsd:string) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - # Object Property: (parallel to) AnnotationAssertion(Annotation( "BSPO:curators"^^xsd:string) "x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross."^^xsd:string) From dad54ff61c4b27ecf85dec919d844bffdbb6cf69 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Wed, 22 Jun 2022 15:43:15 +0100 Subject: [PATCH 2/3] add metadata --- src/ontology/bspo-edit.owl | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/ontology/bspo-edit.owl b/src/ontology/bspo-edit.owl index a016fe1..8fe055c 100644 --- a/src/ontology/bspo-edit.owl +++ b/src/ontology/bspo-edit.owl @@ -230,11 +230,13 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty(dce:description)) Declaration(AnnotationProperty(dce:title)) +Declaration(AnnotationProperty(dcterms:contributor)) Declaration(AnnotationProperty(dcterms:license)) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -651,6 +653,7 @@ AnnotationAssertion( "in_lateral_side_of"^^xsd:string) AnnotationAssertion( "in_lateral_side_of"^^xsd:string) AnnotationAssertion(rdfs:label "in lateral side of"^^xsd:string) +AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/2453"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) SubObjectPropertyOf( ) DisjointObjectProperties( ) @@ -965,12 +968,14 @@ TransitiveObjectProperty() # Object Property: (in central side of) -AnnotationAssertion( "BSPO:0020001") +AnnotationAssertion( "This was migrated from http://purl.obolibrary.org/obo/uberon/core#in_central_side_of in Uberon."^^xsd:string) +AnnotationAssertion(dcterms:contributor ) AnnotationAssertion(rdfs:label "in central side of") # Object Property: (has start point) AnnotationAssertion(Annotation( "BSPO:cjm"^^xsd:string) "A relation between an axis and a part of an organism, in which the part defines the initial point of the axis."^^xsd:string) +AnnotationAssertion( "This relationship was originally called http://purl.obolibrary.org/obo/#_has_start_point, but was renamed because of the non-standard IRI syntax."^^xsd:string) AnnotationAssertion( ":has_start_point"^^xsd:string) AnnotationAssertion( "spatial"^^xsd:string) AnnotationAssertion( "has_start_point"^^xsd:string) From 654a2506ce87bde0050f5bd874cbbf4191ce2ab9 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Thu, 23 Jun 2022 14:40:40 +0100 Subject: [PATCH 3/3] add axioms from uberon to `in central side of` --- src/ontology/bspo-edit.owl | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/ontology/bspo-edit.owl b/src/ontology/bspo-edit.owl index 8fe055c..abd1777 100644 --- a/src/ontology/bspo-edit.owl +++ b/src/ontology/bspo-edit.owl @@ -653,7 +653,7 @@ AnnotationAssertion( "in_lateral_side_of"^^xsd:string) AnnotationAssertion( "in_lateral_side_of"^^xsd:string) AnnotationAssertion(rdfs:label "in lateral side of"^^xsd:string) -AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/2453"^^xsd:anyURI) +AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^xsd:anyURI) SubObjectPropertyOf( ) DisjointObjectProperties( ) @@ -871,6 +871,7 @@ AnnotationAssertion( "immediately_posterior_to"^^xsd:string) AnnotationAssertion( "immediately_posterior_to"^^xsd:string) AnnotationAssertion(rdfs:label "immediately posterior to"^^xsd:string) +AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -892,6 +893,7 @@ AnnotationAssertion( "immediately_superficial_to"^^xsd:string) AnnotationAssertion( "immediately_superficial_to"^^xsd:string) AnnotationAssertion(rdfs:label "immediately superficial to"^^xsd:string) +AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -968,9 +970,13 @@ TransitiveObjectProperty() # Object Property: (in central side of) +AnnotationAssertion(Annotation( "BSPO:cjm"^^xsd:string) "X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides."^^xsd:string) AnnotationAssertion( "This was migrated from http://purl.obolibrary.org/obo/uberon/core#in_central_side_of in Uberon."^^xsd:string) AnnotationAssertion(dcterms:contributor ) AnnotationAssertion(rdfs:label "in central side of") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) # Object Property: (has start point)