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Update SHACL rules
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Incorporate changes to the SHACL rules based on an update to the SBOL3
RDF files in SynBioDex/sbol-shacl. These changes remove
VariableComponent and add VariableFeature. Include a new test case
since the SBOLTestSuite does not contain any files with
VariableFeature or VariableComponent.
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@tcmitchell
tcmitchell committed May 28, 2021
1 parent e9495c0 commit 9f63b3d
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Showing 3 changed files with 737 additions and 42 deletions.
97 changes: 55 additions & 42 deletions sbol3/rdf/sbol3-shapes.ttl
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
@prefix dash: <http://datashapes.org/dash#> .
@prefix om: <http://www.ontology-of-units-of-measure.org/resource/om-2/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
Expand All @@ -22,10 +21,10 @@ sbol:CombinatorialDerivation a rdfs:Class,
sh:NodeShape ;
rdfs:label "CombinatorialDerivation"@en ;
tawny:name "CombinatorialDerivation"@en ;
rdfs:comment "The purpose of the CombinatorialDerivation class is to specify combinatorial genetic designs without having to specify every possible design variant. For example, a CombinatorialDerivation can be used to specify a library of reporter gene variants that include different promoters and RBSs without having to specify a ComponentDefinition for every possible combination of promoter, RBS, and CDS in the library. ComponentDefinition objects that realize a CombinatorialDerivation can be derived in accordance with the class properties template, variableComponents, and strategy."@en ;
rdfs:comment "The purpose of the CombinatorialDerivation class is to specify combinatorial genetic designs without having to specify every possible design variant. For example, a CombinatorialDerivation can be used to specify a library of reporter gene variants that include different promoters and RBSs without having to specify a ComponentDefinition for every possible combination of promoter, RBS, and CDS in the library. ComponentDefinition objects that realize a CombinatorialDerivation can be derived in accordance with the class properties template, variableFeatures, and strategy."@en ;
rdfs:subClassOf sbol:TopLevel ;
sh:property sbol:CombinatorialDerivation-template,
sbol:CombinatorialDerivation-variableComponent .
sbol:CombinatorialDerivation-variableFeature .

sbol:Component a rdfs:Class,
owl:Class,
Expand Down Expand Up @@ -67,20 +66,21 @@ sbol:Identified a rdfs:Class,
sbol:Identified-hasMeasure,
sbol:Identified-name .

sbol:VariableComponent a rdfs:Class,
sbol:VariableFeature a rdfs:Class,
owl:Class,
sh:NodeShape ;
rdfs:label "VariableComponent"@en ;
tawny:name "VariableComponent"@en ;
rdfs:comment "The VariableComponent class can be used to specify a choice of ComponentDefinition objects for any new 35 Component derived from a template Component in the template ComponentDefinition."@en ;
rdfs:label "VariableFeature"@en ;
tawny:name "VariableFeature"@en ;
rdfs:comment "The VariableFeature class can be used to specify a choice of ComponentDefinition objects for any new 35 Component derived from a template Component in the template ComponentDefinition."@en ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty sbol:variable ;
owl:someValuesFrom sbol:Component ],
owl:someValuesFrom sbol:Feature ],
sbol:Identified ;
sh:property sbol:VariableComponent-variable,
sbol:VariableComponent-variant,
sbol:VariableComponent-variantCollection,
sbol:VariableComponent-variantDerivation .
sh:property sbol:VariableFeature-variable,
sbol:VariableFeature-variant,
sbol:VariableFeature-variantCollection,
sbol:VariableFeature-variantDerivation,
sbol:VariableFeature-variantMeasure .

om:Measure a rdfs:Class,
owl:Class,
Expand All @@ -107,13 +107,16 @@ sbol:LocalSubComponent a owl:Class ;
sbol:SequenceFeature a owl:Class ;
rdfs:subClassOf sbol:Feature .

sbol:SubComponent a owl:Class ;
rdfs:subClassOf sbol:Feature .

sbol:hasMeasure-shape a sh:NodeShape ;
sh:class sbol:Identified ;
sh:targetSubjectsOf sbol:hasMeasure .

sbol:hasVariableComponent a owl:ObjectProperty ;
rdfs:label "hasVariableComponent" ;
tawny:name "hasVariableComponent" .
sbol:hasVariableFeature a owl:ObjectProperty ;
rdfs:label "hasVariableFeature" ;
tawny:name "hasVariableFeature" .

sbol:isMemberOf a owl:ObjectProperty ;
rdfs:label "isMemberOf"@en ;
Expand All @@ -130,25 +133,29 @@ sbol:template-shape a sh:NodeShape ;
sh:targetSubjectsOf sbol:template .

sbol:variable-shape a sh:NodeShape ;
sh:class sbol:VariableComponent ;
sh:class sbol:VariableFeature ;
sh:targetSubjectsOf sbol:variable .

sbol:variableComponent-shape a sh:NodeShape ;
sbol:variableFeature-shape a sh:NodeShape ;
sh:class sbol:CombinatorialDerivation ;
sh:targetSubjectsOf sbol:variableComponent .
sh:targetSubjectsOf sbol:variableFeature .

sbol:variant-shape a sh:NodeShape ;
sh:class sbol:VariableComponent ;
sh:class sbol:VariableFeature ;
sh:targetSubjectsOf sbol:variant .

sbol:variantCollection-shape a sh:NodeShape ;
sh:class sbol:VariableComponent ;
sh:class sbol:VariableFeature ;
sh:targetSubjectsOf sbol:variantCollection .

sbol:variantDerivation-shape a sh:NodeShape ;
sh:class sbol:VariableComponent ;
sh:class sbol:VariableFeature ;
sh:targetSubjectsOf sbol:variantDerivation .

sbol:variantMeasure-shape a sh:NodeShape ;
sh:class sbol:VariableFeature ;
sh:targetSubjectsOf sbol:variantMeasure .

tawny:name a owl:AnnotationProperty .

sbol:Collection-member a sh:PropertyShape ;
Expand All @@ -159,9 +166,9 @@ sbol:CombinatorialDerivation-template a sh:PropertyShape ;
sh:class sbol:Component ;
sh:path sbol:template .

sbol:CombinatorialDerivation-variableComponent a sh:PropertyShape ;
sh:class sbol:VariableComponent ;
sh:path sbol:variableComponent .
sbol:CombinatorialDerivation-variableFeature a sh:PropertyShape ;
sh:class sbol:VariableFeature ;
sh:path sbol:variableFeature .

sbol:Component-type a sh:PropertyShape ;
sh:minCount 1 ;
Expand Down Expand Up @@ -189,32 +196,32 @@ sbol:Identified-name a sh:PropertyShape ;
sh:maxCount 1 ;
sh:path sbol:name .

sbol:VariableComponent-variable a sh:PropertyShape ;
dash:hasValueWithClass sbol:Component ;
sh:class sbol:SubComponent ;
sbol:VariableFeature-variable a sh:PropertyShape ;
sh:class sbol:Feature ;
sh:minCount 1 ;
sh:path sbol:variable .

sbol:VariableComponent-variant a sh:PropertyShape ;
sbol:VariableFeature-variant a sh:PropertyShape ;
sh:class sbol:Component ;
sh:path sbol:variant .

sbol:VariableComponent-variantCollection a sh:PropertyShape ;
sbol:VariableFeature-variantCollection a sh:PropertyShape ;
sh:class sbol:Collection ;
sh:path sbol:variantCollection .

sbol:VariableComponent-variantDerivation a sh:PropertyShape ;
sbol:VariableFeature-variantDerivation a sh:PropertyShape ;
sh:class sbol:CombinatorialDerivation ;
sh:path sbol:variantDerivation .

sbol:VariableFeature-variantMeasure a sh:PropertyShape ;
sh:class om:Measure ;
sh:path sbol:variantMeasure .

om:Measure-http___www.ontology-of-units-of-measure.org_resource_om-2_hasNumericalValue a sh:PropertyShape ;
sh:maxCount 1 ;
sh:minCount 1 ;
sh:path om:hasNumericalValue .

sbol:SubComponent a owl:Class ;
rdfs:subClassOf sbol:Feature .

sbol:hasFeature a owl:ObjectProperty ;
rdfs:label "hasFeature" ;
tawny:name "hasFeature" ;
Expand All @@ -238,30 +245,36 @@ sbol:type a owl:ObjectProperty ;
tawny:name "type"@en ;
rdfs:comment "Specifies the category of biochemical or physical entity. For example DNA, protein, or small molecule that a ComponentDefinition object abstracts for the purpose of engineering design. For DNA or RNA entities, additional types fields are used to describe nucleic acid topology (circular / linear) and strandedness (double- or single-stranded)."@en .

sbol:variableComponent a owl:ObjectProperty ;
rdfs:label "variableComponent"@en ;
tawny:name "variableComponent"@en ;
sbol:variableFeature a owl:ObjectProperty ;
rdfs:label "variableFeature"@en ;
tawny:name "variableFeature"@en ;
rdfs:domain sbol:CombinatorialDerivation ;
rdfs:range sbol:VariableComponent .
rdfs:range sbol:VariableFeature .

sbol:variant a owl:ObjectProperty ;
rdfs:label "variant"@en ;
tawny:name "variant"@en ;
rdfs:domain sbol:VariableComponent ;
rdfs:domain sbol:VariableFeature ;
rdfs:range sbol:Component .

sbol:variantCollection a owl:ObjectProperty ;
rdfs:label "variantCollection"@en ;
tawny:name "variantCollection"@en ;
rdfs:domain sbol:VariableComponent ;
rdfs:domain sbol:VariableFeature ;
rdfs:range sbol:Collection .

sbol:variantDerivation a owl:ObjectProperty ;
rdfs:label "variantDerivation"@en ;
tawny:name "variantDerivation"@en ;
rdfs:domain sbol:VariableComponent ;
rdfs:domain sbol:VariableFeature ;
rdfs:range sbol:CombinatorialDerivation .

sbol:variantMeasure a owl:ObjectProperty ;
rdfs:label "variantMeasure"@en ;
tawny:name "variantMeasure"@en ;
rdfs:domain sbol:VariableFeature ;
rdfs:range om:Measure .

sbol:member a owl:ObjectProperty ;
rdfs:label "member"@en ;
tawny:name "member"@en ;
Expand All @@ -273,8 +286,8 @@ sbol:variable a owl:FunctionalProperty,
owl:ObjectProperty ;
rdfs:label "variable"@en ;
tawny:name "variable"@en ;
rdfs:domain sbol:VariableComponent ;
rdfs:range sbol:SubComponent .
rdfs:domain sbol:VariableFeature ;
rdfs:range sbol:Feature .

sbol:TopLevel a owl:Class ;
rdfs:label "TopLevel"@en ;
Expand Down
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