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sbol-vo.rdf
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sbol-vo.rdf
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<?xml version="1.0"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xml:base="http://sbols.org/visual/v3"
xmlns="http://sbols.org/visual/v3#">
<owl:Ontology rdf:about="http://sbols.org/visual/v3">
<owl:imports rdf:resource="https://synbiodex.github.io/sbol-owl3/sbolowl3.rdf"/>
</owl:Ontology>
<owl:ObjectProperty rdf:about="#isGlyphOf">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">isGlyphOf</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#hasGlyph">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hasGlyph</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#hasHead">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hasHead</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#hasTail">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hasTail</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#hasIncoming">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hasIncoming</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#hasOutgoing">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hasOutgoing</rdfs:label>
</owl:ObjectProperty>
<owl:ObjectProperty rdf:about="#isAlternativeOf">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">isAlternativeOf</rdfs:label>
</owl:ObjectProperty>
<owl:AnnotationProperty rdf:about="#defaultGlyph">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">defaultGlyph</rdfs:label>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="#glyphDirectory">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">glyphDirectory</rdfs:label>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="#recommended">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">recommended</rdfs:label>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="#prototypicalExample">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">prototypicalExample</rdfs:label>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="#notes">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">notes</rdfs:label>
</owl:AnnotationProperty>
<owl:Class rdf:about="#Glyph">
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyph</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#InteractionGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">InteractionGlyph</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#InteractionNodeGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">InteractionNodeGlyph</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#MolecularSpeciesGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MolecularSpeciesGlyph</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#SequenceFeatureGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SequenceFeatureGlyph</rdfs:label>
</owl:Class>
<owl:Class rdf:about="#InhibitionGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasHead"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000642"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasTail"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000020"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf rdf:resource="#InteractionGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Interaction"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000169"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An arrow whose head is a bar, suggesting blocking:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">InhibitionGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">inhibition-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/Interactions/inhibition</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Repression of pTAL14 promoter by TAL14</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*This section left intentionally blank*</notes>
</owl:Class>
<owl:Class rdf:about="#DegradationGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasTail"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000010"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf rdf:resource="#InteractionGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Interaction"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000179"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Identical to the Process glyph, but with an empty set at the sink of the arrowhead:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DegradationGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">degradation-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/Interactions/degradation</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cellular recycling of mRNA</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*This section left intentionally blank*</notes>
</owl:Class>
<owl:Class rdf:about="#StimulationGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasHead"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000643"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasTail"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000459"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf rdf:resource="#InteractionGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Interaction"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000170"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An arrow with an head that is empty or of a different color than the line:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">StimulationGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">stimulation-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/Interactions/stimulation</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Activation of pTAL14 promoter by Gal4VP16 activator</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*This section left intentionally blank*</notes>
</owl:Class>
<owl:Class rdf:about="#ControlGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasHead"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000644"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasTail"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000019"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf rdf:resource="#InteractionGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Interaction"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000168"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An arrow with a diamond head:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ControlGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">control-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/Interactions/control</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Inversion of a sequence flanked by FRT sites by FLP recombinase</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*This section left intentionally blank*</notes>
</owl:Class>
<owl:Class rdf:about="#ProcessGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasHead"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000011"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasTail"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000010"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasTail"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000645"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf rdf:resource="#InteractionGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Interaction"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000375"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An arrow with a filled head the same color as the line:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ProcessGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">process-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/Interactions/process</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Production of Green Fluorescent Protein (GFP) from the gfp Coding Sequence</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The assocated SBO term also covers:
- SBO:0000176 Biochemical Reaction
- SBO:0000589 Genetic Production (source is DNA, sink is usually RNA or Macromolecule)
- SBO:0000177 Non-covalent Binding (sink is a Complex)</notes>
</owl:Class>
<owl:Class rdf:about="#AssociationGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasIncoming"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000010"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasOutgoing"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000011"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf rdf:resource="#InteractionNodeGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Interaction"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000177"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A circular node:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AssociationGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">association-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/InteractionNodes/association</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Association of gRNA and Cas9 to form an active CRISPR complex.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The association glyph is based on the SBGN Process Description association glyph.</notes>
</owl:Class>
<owl:Class rdf:about="#UnspecifiedGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasIncoming"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000003"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf rdf:resource="#InteractionNodeGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Interaction"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000231"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Unspecified is represented by the unicode "replacement character" glyph, indicating a missing or invalid symbol:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UnspecifiedGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">unspecified-glyph-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/InteractionNodes/unspecified</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An interaction that is missing any information about its nature or intended purpose.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note that there are no outgoing edges for the Unspecified interaction, because there is no difference in roles to indicate.
The Unspecified glyph is intended for showing where information about an interaction is missing. It should not generally appear with well-curated designs or diagrams.</notes>
</owl:Class>
<owl:Class rdf:about="#DissociationGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasIncoming"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000010"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasOutgoing"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000011"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf rdf:resource="#InteractionNodeGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Interaction"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000180"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An circular node inside another circle</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DissociationGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dissociation-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/InteractionNodes/dissociation</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dissociation of an active CRISPR complex into gRNA and Cas9.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The dissociation glyph is based on the SBGN Process Description dissociation glyph.</notes>
</owl:Class>
<owl:Class rdf:about="#ProcessNodeGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasIncoming"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000010"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#hasOutgoing"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000011"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf rdf:resource="#InteractionNodeGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Interaction"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000375"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A square node:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ProcessNodeGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">process-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/InteractionNodes/process</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Reaction process of citrate and aconitase to produce cis-aconitate.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The process glyph is based on the SBGN Process Description process glyph.
The assocated SBO term also covers:
- SBO:0000176 Biochemical Reaction
- SBO:0000177 Non-covalent Binding (sink is a Complex)
Examples of RECOMMENDED usage:
- Biochemical reaction process of the reactant citrate and the catalyst aconitase to produce the product cis-aconitate:
</notes>
</owl:Class>
<owl:Class rdf:about="#MacromoleculeGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000245"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The macromolecule glyph is a rounded rectangle, as used in SBGN:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MacromoleculeGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">macromolecule-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/macromolecule</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AraC protein, polymerized chitin</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The alternative "shmoo" shape from SBOL Visual 2 is no longer valid, having been deprecated for looking too similar to a typical representation of a yeast cell.</notes>
</owl:Class>
<owl:Class rdf:about="#Double-StrandedNucleicAcidGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000251"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The RECOMMENDED glyph for dsNA is a double-helix:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Double-StrandedNucleicAcidGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dsNA-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/dsNA</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA fragment during assembly</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#Double-StrandedNucleicAcidGlyphAlternative">
<rdfs:subClassOf rdf:resource="#Double-StrandedNucleicAcidGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isAlternativeOf"/>
<owl:someValuesFrom rdf:resource="#Double-StrandedNucleicAcidGlyph"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An alternative is the SBGN "nucleic acid" half-round rectangle:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Double-StrandedNucleicAcidGlyphAlternative</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">na-sbgn-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/dsNA</glyphDirectory>
</owl:Class>
<owl:Class rdf:about="#ComplexGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000253"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The RECOMMENDED glyph for a complex is a composite of the glyphs for the molecules comprising the complex. For example, a protein bound to a simple chemical, a guide RNA, or another protein (in order:protein-small molecule, protein-guide RNA, protein-protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ComplexGlyph</rdfs:label>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Arabinose bound to AraC</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#ProteinSmallMoleculeComplexGlyph">
<rdfs:subClassOf rdf:resource="#ComplexGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The RECOMMENDED glyph for a complex is a composite of the glyphs for the molecules comprising the complex. For example, a protein bound to a simple chemical, a guide RNA, or another protein (in order:protein-small molecule, protein-guide RNA, protein-protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ProteinSmallMoleculeComplexGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">complex-ps-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/complex</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#ProteinGuideRnaComplexGlyph">
<rdfs:subClassOf rdf:resource="#ComplexGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The RECOMMENDED glyph for a complex is a composite of the glyphs for the molecules comprising the complex. For example, a protein bound to a simple chemical, a guide RNA, or another protein (in order:protein-small molecule, protein-guide RNA, protein-protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ProteinGuideRnaComplexGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">complex-pr-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/complex</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#ProteinProteinComplexGlyph">
<rdfs:subClassOf rdf:resource="#ComplexGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The RECOMMENDED glyph for a complex is a composite of the glyphs for the molecules comprising the complex. For example, a protein bound to a simple chemical, a guide RNA, or another protein (in order:protein-small molecule, protein-guide RNA, protein-protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ProteinProteinComplexGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">complex-pp-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/complex</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#ComplexGlyphAlternative">
<rdfs:subClassOf rdf:resource="#ComplexGlyph"/>
<rdfs:subClassOf rdf:resource="#ProteinSmallMoleculeComplexGlyph"/>
<rdfs:subClassOf rdf:resource="#ProteinGuideRnaComplexGlyph"/>
<rdfs:subClassOf rdf:resource="#ProteinProteinComplexGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This may also be applied to show complex formation (binding) of a molecule to a nucleic acid construct by compositing the molecule glyph with the appropriate portion of the nucleic acid construct. For example, a protein binding to the promoter of a transcriptional unit:
An alternative is the SBGN "cornered rectangle" glyph for a complex:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ComplexGlyphAlternative</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">complex-sbgn-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/complex</glyphDirectory>
</owl:Class>
<owl:Class rdf:about="#Single-StrandedNucleicAcidGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000250"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The RECOMMENDED glyph for ssNA is a wiggly line:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Single-StrandedNucleicAcidGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ssNA-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/ssNA</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mRNA, gRNA, siRNA</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#Single-StrandedNucleicAcidGlyphAlternative">
<rdfs:subClassOf rdf:resource="#Single-StrandedNucleicAcidGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isAlternativeOf"/>
<owl:someValuesFrom rdf:resource="#Single-StrandedNucleicAcidGlyph"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An alternative is the SBGN "nucleic acid" half-round rectangle:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Single-StrandedNucleicAcidGlyphAlternative</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">na-sbgn-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/ssNA</glyphDirectory>
</owl:Class>
<owl:Class rdf:about="#ProteinGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000252"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The protein glyph is a "pill" shape with a rectangular body and rounded ends, representing the compact space-filling mass of many proteins:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ProteinGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">protein-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/protein</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AraC protein</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">To avoid confusion with circles or ellipses, the "pill" shape SHOULD be significantly longer than it is tall, emphasizing its straight sides.</notes>
</owl:Class>
<owl:Class rdf:about="#UnspecifiedSpeciesGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000285"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Unspecified is RECOMMENDED to be represented by the unicode "replacement character" glyph, indicating a missing or invalid symbol:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UnspecifiedSpeciesGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">replacement-glyph-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/unspecified</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An anonymous chemical species that is missing any information about its nature or intended purpose.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Unspecified glyph is intended for showing where a chemical species' type is missing (or, equivalently, given only the uninformative root role). It should never appear with well-curated designs or diagrams.</notes>
</owl:Class>
<owl:Class rdf:about="#UnspecifiedSpeciesGlyphAlternative">
<rdfs:subClassOf rdf:resource="#UnspecifiedSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isAlternativeOf"/>
<owl:someValuesFrom rdf:resource="#UnspecifiedSpeciesGlyph"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An alternative is the SBGN "generic species" glyph, which is an ellipse:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UnspecifiedSpeciesGlyphAlternative</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">generic-sbgn-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/unspecified</glyphDirectory>
</owl:Class>
<owl:Class rdf:about="#NoGlyphAssignedGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">When a species has no assigned glyph it is RECOMMENDED that a user provide their own glyph. The user is also encouraged to submit the new glyph for possible adoption into the SBOLv standard.
An alternative option is to have a bracket, suggesting information that needs to be filled in:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NoGlyphAssignedGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">no-glyph-assigned-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/no-glyph-assigned</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">No Glyph Assigned is intended to be used for any chemical species whose type is not covered by other SBOL Visual glyphs.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">No Glyph Assigned is intended for molecular species with a defined specific type that happens to not yet be covered by available approved glyphs (other than the root). It is more likely to appear in machine-generated diagrams than in human-generated diagrams, since humans are likely to invent and use their own glyph for the purpose.</notes>
</owl:Class>
<owl:Class rdf:about="#SimpleChemicalGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#type"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/sbo/SBO:0000247"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SimpleChemicalGlyph</rdfs:label>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Arabinose</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">It is RECOMMENDED that visual differentiation be maximized by associating each distinct species in a diagram with a different small geometric shape. Rotations may also be used (e.g., pentagon pointing up vs. pentagon pointing down).
It is RECOMMENDED that labels should be placed outside of the shapes rather than inside, to avoid squeezing the labels.
To avoid confusion with pills or ellipses, when the small circle alternative glyph is used, it SHOULD be significantly smaller than other types of molecular species glyphs, as indicated by the recommended scale of the glyph.</notes>
</owl:Class>
<owl:Class rdf:about="#TriangleSimpleChemicalGlyph">
<rdfs:subClassOf rdf:resource="#SimpleChemicalGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TriangleSimpleChemicalGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">simple-chemical-triangle-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/simple-chemical</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#PentagonSimpleChemicalGlyph">
<rdfs:subClassOf rdf:resource="#SimpleChemicalGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PentagonSimpleChemicalGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">simple-chemical-pentagon-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/simple-chemical</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#HexagonSimpleChemicalGlyph">
<rdfs:subClassOf rdf:resource="#SimpleChemicalGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HexagonSimpleChemicalGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">simple-chemical-hexagon-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/simple-chemical</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#SimpleChemicalGlyphAlternative">
<rdfs:subClassOf rdf:resource="#SimpleChemicalGlyph"/>
<rdfs:subClassOf rdf:resource="#TriangleSimpleChemicalGlyph"/>
<rdfs:subClassOf rdf:resource="#PentagonSimpleChemicalGlyph"/>
<rdfs:subClassOf rdf:resource="#HexagonSimpleChemicalGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alternately, a simple chemical may also be represented a small circle:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SimpleChemicalGlyphAlternative</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">simple-chemical-circle-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/MolecularSpecies/simple-chemical</glyphDirectory>
</owl:Class>
<owl:Class rdf:about="#StabilityElementGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#SequenceFeatureGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001979"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001955"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001546"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stability Element is a "stem-top" glyph for describing small sites. In this system:
- the top glyph indicates the type of site (e.g., Stability Element)
- the stem glyph indicates whether the site affects DNA, RNA, or protein (respectively: straight, wavy, or looped)</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">StabilityElementGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">stem-top-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/stability-element</glyphDirectory>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PEST tag, 3’ Hairpin</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RNA Stability Element glyph was previously also associated with SO:0001957, but that SO term has been declared obsolete in Sequence Ontology.
This glyph is not backwards compatible with SBOL Visual 1.
Despite both being stem-top glyphs, Biopolymer Location is not a parent to Stability Element, since the length of a Stability Element is typically multiple bases / amino acids.</notes>
</owl:Class>
<owl:Class rdf:about="#DnaStabilityElementGlyph">
<rdfs:subClassOf rdf:resource="#StabilityElementGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The top for a Stability Element is a pentagon suggesting the shape of a shield, on top of a stem connecting to the backbone at the point where the stability element is located (in order: DNA, RNA, Protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DnaStabilityElementGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dna-stability-element-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/stability-element</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#RnaStabilityElementGlyph">
<rdfs:subClassOf rdf:resource="#StabilityElementGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001979"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The top for a Stability Element is a pentagon suggesting the shape of a shield, on top of a stem connecting to the backbone at the point where the stability element is located (in order: DNA, RNA, Protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RnaStabilityElementGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">rna-stability-element-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/stability-element</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#ProteinStabilityElementGlyph">
<rdfs:subClassOf rdf:resource="#StabilityElementGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom rdf:resource="http://sbols.org/v3#Component"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isGlyphOf"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://sbols.org/v3#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001955"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>