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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://raw.githubusercontent.com/SynBioDex/sbol-owl3/main/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="#SignatureGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001978"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The signature glyph is a box sitting atop the backbone with an X and line inside it, suggesting a signature on a form:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SignatureGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">signature-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/signature</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA Barcode</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#CompositeGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
The glyph for Composite is dashed "expanding lines" connecting any "base" glyph representing the more abstract composite (e.g., Omitted Detail, or Terminator, or Promoter) to a backbone diagramming the contents of the composite. Note the bounding box is indicating the location of the base glyph, and would scale with that glyph.</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CompositeGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">composite-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/composite</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An "expression cassette" containing a ribosome entry site, coding sequence, and terminator.
In this case, the recommended "base" glyph would be Engineered Region.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An "abbreviated" representation of composite, simply indicating that more structure is available, can be made by using short lines and placing only an Omitted Detail glyph in the secondary backbone. For example, here is an example of an abbreviated composite promoter:
and a composite with an Engineered Region of otherwise unspecified content:
</notes>
</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 part 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 is brackets, 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/SequenceFeatures/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 Component that is not covered by other SBOL Visual glyphs.
For example, at present there is no glyph recommended for representing a transposon.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">No Glyph Assigned is intended for constructs with a defined specific role that happens to not yet be covered by available approved glyphs (other than the root "Sequence Feature"). 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="#AptamerGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000031"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The aptamer glyph is a cartoon diagram of a prototypical nucleic acid secondary structure for an aptamer:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AptamerGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">aptamer-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/aptamer</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">theophylline aptamer</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#ChromosomalLocusGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000830"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
The glyph to indicate integration into a chromosome is an S-shaped curve of the backbone, suggesting something that might be part of a larger looping structure:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ChromosomalLocusGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">chromosomal-locus-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/chromosomal-locus</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">_B. subtilis_ amyE locus</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Complementary "left" and "right" versions of this glyph SHOULD be used together, flanking the region whose genomic context is being described.
The Omitted Detail glyph SHOULD generally be contatenated to indicate that there is information about the chromosome not being represented.
Examples of RECOMMENDED usage:
- A functional unit consisting of promoter, ribosome entry site, CDS, and terminator, all integrated together into the chromosome:
- Two functional units, one integrated into the amyE locus, another integrated into the ganA locus:
</notes>
</owl:Class>
<owl:Class rdf:about="#OriginofTransferGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000724"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The origin of transfer glyph is circular like origin of replication, but also includes an outbound arrow:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OriginofTransferGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">origin-of-transfer-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/origin-of-transfer</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">oriT</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*This section left deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#PolypeptideRegionGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000839"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A polypeptide region inside a coding sequence is indicated by insertion of triangular boundaries inside of the CDS, parallel to the 3' side of the CDS. This will produce chevron segments on the 3' side and a CDS shape on the 5' side:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PolypeptideRegionGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">polypeptide-region-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/polypeptide-region</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">degradation tag on a protein coding sequence
nuclear localization tag on a protein coding sequence
coding sequence for the membrane-crossing region of a protein
This glyph is intended to be used in composition or superposition with the glyph for the coding sequence of which the polypeptide regions are fragments: Example of a coding sequence with three designated domains, an N-tag (blue), C-tag (yellow), and internal region (red):
</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Polypeptide region can also be used to represent regions that involve cleavage, such as a 2A self-cleaving polypeptide region (SO:0002224, a child term of SO:0000839). It is RECOMMENDED that cleavage-inducing polypeptide regions be visually distinguished from intact, e.g., through the use of dashed lines.
</notes>
</owl:Class>
<owl:Class rdf:about="#StabilityElementGlyph">
<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#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>
<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">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">ProteinStabilityElementGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">protein-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="#OmittedDetailGlyph">
<rdfs:subClassOf rdf:resource="#Glyph"/>
<rdfs:subClassOf rdf:resource="#MolecularSpeciesGlyph"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Omitted Detail glyph is a break in the backbone with an ellipsis to indicate that material would normally be in that location:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OmittedDetailGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">omitted-detail-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/omitted-detail</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A diagram in which a sequence feature is not drawn.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This glyph actually places a "break" in the nucleic acid backbone.</notes>
</owl:Class>
<owl:Class rdf:about="#EngineeredRegionGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000804"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
Engineered Region is represented by a plain rectangle suggesting a blank slate to be written upon:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EngineeredRegionGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">engineered-region-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/engineered-region</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An "expression cassette" containing a ribosome entry site, coding sequence, and terminator.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#CleavageSiteGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001688"/>
</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:0001687"/>
</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:0001977"/>
</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:0001956"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cleavage Site is a "stem-top" glyph for describing small sites. In this system:
- the top glyph indicates the type of site (e.g., Cleavage Site)
- 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">CleavageSiteGlyph</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/cleavage-site</glyphDirectory>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RNAse E site, BamHI</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SO:0000061 (which was previously associated with Restriction Enzyme Recognition Site in SBOL Visual 1) is no longer associated with the DNA Cleavage glyph in SBOL Visual 2 or 3, as SO:0000061 refers to the binding site and not the location of cleavage.
The Ribonuclease Site, Protease Site, and Restriction Enzyme Recognition Site glyphs from SBOL Visual 1.0 are now replaced by the Cleavage Site glyph with the appropriate stem.
Describing a Restriction Enzyme Cleavage Site with a vertical line glyph on a DNA backbone (as done previously in SBOL Visual 1.0 via the Restriction Enzyme Recognition Site glyph) can persist in a SBOL Visual 2 or 3 diagram and still be considered compliant with SBOL Visual 2 or 3, where it is now classified as a Biopolymer Location (which is a superclass of cleavage sites). Thus, the Biopolymer Location glyph from SBOL Visual 2 or 3 is backwards compatible with the Restriction Enzyme Recognition Site glyph from SBOL Visual 1.
The 5' Sticky Restriction Site, 3' Sticky Restriction Site, and Blunt Restriction Site glyphs remain unchanged, and are more specific children/derivatives of the DNA-Stem Cleavage-Top glyph.
A 2A self-cleaving polypeptide region (SO:0002224) SHOULD NOT be represented by a protease site, as its cleavage mechanism is different. Instead, 2A sequences should be represented using the Polypeptide Region glyph (see example in its specification).</notes>
</owl:Class>
<owl:Class rdf:about="#DnaCleavageSiteGlyph">
<rdfs:subClassOf rdf:resource="#CleavageSiteGlyph"/>
<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:0001688"/>
</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:0001687"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Cleavage Site top is an "X" suggesting slicing on top of a stem connecting to the backbone at the point where cleavage will occur (in order: DNA, RNA, Protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DnaCleavageSiteGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nuclease-site-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/cleavage-site</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#RnaCleavageSiteGlyph">
<rdfs:subClassOf rdf:resource="#CleavageSiteGlyph"/>
<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:0001977"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Cleavage Site top is an "X" suggesting slicing on top of a stem connecting to the backbone at the point where cleavage will occur (in order: DNA, RNA, Protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RnaCleavageSiteGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ribonuclease-site-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/cleavage-site</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#ProteinCleavageSiteGlyph">
<rdfs:subClassOf rdf:resource="#CleavageSiteGlyph"/>
<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:0001956"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Cleavage Site top is an "X" suggesting slicing on top of a stem connecting to the backbone at the point where cleavage will occur (in order: DNA, RNA, Protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ProteinCleavageSiteGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">protease-site-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/cleavage-site</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>
<owl:Class rdf:about="#OperatorBindingSiteGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000057"/>
</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:0000409"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The operator glyph is an open "cup" suggesting a binding location:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OperatorBindingSiteGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">operator-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/operator</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gal4 binding site in an activatable promoter.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This glyph puts a "dent" in the backbone line.</notes>
</owl:Class>
<owl:Class rdf:about="#OriginofReplicationGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000296"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The origin of replication glyph is a circle suggesting the "bulge" opened in a piece of circular DNA when replication is beginning:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OriginofReplicationGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">origin-of-replication-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/origin-of-replication</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">human herpesvirus-6 OOR</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The label on an origin of replication glyph is RECOMMENDED as the location to label either specifically the identity of the origin of replication or the name of the entire plasmid backbone more generally.</notes>
</owl:Class>
<owl:Class rdf:about="#TerminatorGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000141"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The terminator is a T sitting atop the backbone:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TerminatorGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">terminator-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/terminator</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">T1 terminator</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#CDSGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000316"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The coding sequence glyph is a "box" with one side bent out arrow-like to show direction:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDSGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cds-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/cds</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">α-Hemoglobin coding sequence</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#CDSGlyphAlternative">
<rdfs:subClassOf rdf:resource="#CDSGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isAlternativeOf"/>
<owl:someValuesFrom rdf:resource="#CDSGlyph"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alternately, CDS may be represented as a block arrow:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDSGlyphAlternative</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cds-arrow-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/cds</glyphDirectory>
</owl:Class>
<owl:Class rdf:about="#AssemblyScarGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001953"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The assembly scar glyph is an "equal sign" image, the pattern produced by the union of a 5' sticky end and 3' sticky end glyph. The scar will cover the backbone, creating a visual break suggesting the potential disruption associated with a scar:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AssemblyScarGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">assembly-scar-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/assembly-scar</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Ligated sticky ends following BioBrick assembly.</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#AssemblyScarGlyphAlternative">
<rdfs:subClassOf rdf:resource="#AssemblyScarGlyph"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="#isAlternativeOf"/>
<owl:someValuesFrom rdf:resource="#AssemblyScarGlyph"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">With a double-stranded backbone:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AssemblyScarGlyphAlternative</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">assembly-scar-specification-doublestrand.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/assembly-scar</glyphDirectory>
</owl:Class>
<owl:Class rdf:about="#SpecificRecombinationSiteGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000299"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The specific recombination site glyph is a triangle, centered on the backbone, as has appeared in a number of recombinase circuit papers:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SpecificRecombinationSiteGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">specific-recombination-site-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/specific-recombination-site</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">flippase recognition target (FRT) site</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*This section left deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#PrimerBindingSiteGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0005850"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The primer binding site glyph is a line with a bent end suggesting a partially complementary strand of nucleic acid attaching to the backbone:</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PrimerBindingSiteGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">primer-binding-site-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/primer-binding-site</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">seq-F</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*this section deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#Non-CodingRNAGeneGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0001263"/>
</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:0000834"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The non-coding RNA glyph is a rectangular box whose top is a single-stranded RNA "wiggle":</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Non-CodingRNAGeneGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ncrna-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/non-coding-rna</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">gRNA sequence for targeting a dCas9 repressor</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">*This section left deliberately blank*</notes>
</owl:Class>
<owl:Class rdf:about="#BiopolymerLocationGlyph">
<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#role"/>
<owl:someValuesFrom rdf:resource="http://identifiers.org/so/SO:0000699"/>
</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:0001236"/>
</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:0001237"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
Biopolymer Location is a "stem-top" glyph for describing small sites. In this system:
- the top glyph indicates the type of site (e.g., Biopolymer Location)
- 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">BiopolymerLocationGlyph</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/location</glyphDirectory>
<prototypicalExample rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CRISPR-targeted insertion site, protease site, mutation site</prototypicalExample>
<notes rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Biopolymer Location is a general glyph for all zero- and one-length sequence features, including insertion and deletion sites and X-ase cut sites.
Note also that Biopolymer Location does not cover stability elements, since their length is typically multiple bases / amino acids.
Describing a Restriction Enzyme Cleavage Site with a vertical line glyph on a DNA backbone (as done previously in SBOL Visual 1 via the Restriction Enzyme Recognition Site glyph) can persist in a SBOL Visual 2 or 3 diagram and still be considered compliant with SBOL Visual 2 or 3, where it is now classified as a Biopolymer Location (which is a superclass of cleavage sites). Thus, the Biopolymer Location glyph from SBOL Visual 2 or 3 is backwards compatible with the Restriction Enzyme Recognition Site glyph from SBOL Visual 1.</notes>
</owl:Class>
<owl:Class rdf:about="#DnaBiopolymerLocationGlyph">
<rdfs:subClassOf rdf:resource="#BiopolymerLocationGlyph"/>
<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:0000699"/>
</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:0001236"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The RECOMMENDED top for Biopolymer Location is a circle, reminiscent of a pin stuck into a location (in order: DNA, RNA, Protein):</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DnaBiopolymerLocationGlyph</rdfs:label>
<defaultGlyph rdf:datatype="http://www.w3.org/2001/XMLSchema#string">location-dna-specification.png</defaultGlyph>
<glyphDirectory rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glyphs/SequenceFeatures/location</glyphDirectory>
<recommended rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</recommended>
</owl:Class>