Classes
- AptamerGlyph
- AssemblyScarGlyph
- AssemblyScarGlyphAlternative
- AssociationGlyph
- BiopolymerLocationGlyph
- BluntRestrictionSiteGlyph
- CDSGlyph
- CDSGlyphAlternative
- ChromosomalLocusGlyph
- CircularPlasmidGlyph
- CleavageSiteGlyph
- ComplexGlyph
- ComplexGlyphAlternative
- CompositeGlyph
- ControlGlyph
- DegradationGlyph
- DissociationGlyph
- DnaBiopolymerLocationGlyph
- DnaBiopolymerLocationGlyphAlternative
- DnaCleavageSiteGlyph
- DnaStabilityElementGlyph
- Double-StrandedNucleicAcidGlyph
- Double-StrandedNucleicAcidGlyphAlternative
- EngineeredRegionGlyph
- FivePrimeOverhangSiteGlyph
- FivePrimeOverhangSiteGlyphAlternative
- FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph
- FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphAlternative
- Glyph
- HexagonSimpleChemicalGlyph
- InertDNASpacerGlyph
- InhibitionGlyph
- InteractionGlyph
- InteractionNodeGlyph
- IntronGlyph
- MacromoleculeGlyph
- MolecularSpeciesGlyph
- NoGlyphAssignedGlyph
- NoGlyphAssignedSpeciesGlyph
- Non-CodingRNAGeneGlyph
- OmittedDetailGlyph
- OperatorBindingSiteGlyph
- OriginofReplicationGlyph
- OriginofTransferGlyph
- OverhangSiteGlyph
- PentagonSimpleChemicalGlyph
- PolyASiteGlyph
- PolypeptideRegionGlyph
- PrimerBindingSiteGlyph
- ProcessGlyph
- ProcessInteractionGlyph
- PromoterSiteGlyph
- ProteinBiopolymerLocationGlyph
- ProteinBiopolymerLocationGlyphAlternative
- ProteinCleavageSiteGlyph
- ProteinGlyph
- ProteinGuideRnaComplexGlyph
- ProteinProteinComplexGlyph
- ProteinSmallMoleculeComplexGlyph
- ProteinStabilityElementGlyph
- RibosomeEntrySiteGlyph
- RnaBiopolymerLocationGlyph
- RnaBiopolymerLocationGlyphAlternative
- RnaCleavageSiteGlyph
- RnaStabilityElementGlyph
- SequenceFeatureGlyph
- SignatureGlyph
- SimpleChemicalGlyph
- SimpleChemicalGlyphAlternative
- Single-StrandedNucleicAcidGlyph
- Single-StrandedNucleicAcidGlyphAlternative
- SpecificRecombinationSiteGlyph
- StabilityElementGlyph
- StickyEndRestrictionEnzymeCleavageSiteGlyph
- StimulationGlyph
- StopSiteGlyph
- TerminatorGlyph
- ThreePrimeOverhangSiteGlyph
- ThreePrimeOverhangSiteGlyphAlternative
- ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph
- ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphAlternative
- TranscriptionStopSiteGlyph
- TranslationStopSiteGlyph
- TriangleSimpleChemicalGlyph
- UnspecifiedGlyph
- UnspecifiedGlyphAlternative
- UnspecifiedNodeGlyph
- UnspecifiedSpeciesGlyph
- UnspecifiedSpeciesGlyphAlternative
AptamerGlyphc back to ToC or Class ToC
IRI: #AptamerGlyph
The aptamer glyph is a cartoon diagram of a prototypical nucleic acid secondary structure for an aptamer:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000031
- default glyph
-
AssemblyScarGlyphc back to ToC or Class ToC
IRI: #AssemblyScarGlyph
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:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001953
- has sub-classes
- AssemblyScarGlyphAlternative c
- default glyph
-
AssemblyScarGlyphAlternativec back to ToC or Class ToC
IRI: #AssemblyScarGlyphAlternative
With a double-stranded backbone:
- has super-classes
- AssemblyScarGlyph c
- isAlternativeOf op some AssemblyScarGlyph c
- default glyph
-
AssociationGlyphc back to ToC or Class ToC
IRI: #AssociationGlyph
A circular node:
- has super-classes
- Glyph c
- hasIncoming op some role some s b o:0000010
- hasOutgoing op some role some s b o:0000011
- InteractionNodeGlyph c
- isGlyphOf op some interaction
- isGlyphOf op some type some s b o:0000177
- default glyph
-
BiopolymerLocationGlyphc back to ToC or Class ToC
IRI: #BiopolymerLocationGlyph
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)
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000699
- isGlyphOf op some role some s o:0001236
- isGlyphOf op some role some s o:0001237
- has sub-classes
- DnaBiopolymerLocationGlyph c, ProteinBiopolymerLocationGlyph c, RnaBiopolymerLocationGlyph c
- default glyph
-
BluntRestrictionSiteGlyphc back to ToC or Class ToC
IRI: #BluntRestrictionSiteGlyph
The blunt restriction site glyph is an image of two brackets facing away from one another to make a smooth-edged gap:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001691
- default glyph
-
CDSGlyphc back to ToC or Class ToC
IRI: #CDSGlyph
The coding sequence glyph is a "box" with one side bent out arrow-like to show direction:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000316
- has sub-classes
- CDSGlyphAlternative c
- default glyph
-
CDSGlyphAlternativec back to ToC or Class ToC
IRI: #CDSGlyphAlternative
Alternately, CDS may be represented as a block arrow:
- has super-classes
- CDSGlyph c
- isAlternativeOf op some CDSGlyph c
- default glyph
-
ChromosomalLocusGlyphc back to ToC or Class ToC
IRI: #ChromosomalLocusGlyph
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:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000830
- default glyph
-
CircularPlasmidGlyphc back to ToC or Class ToC
IRI: #CircularPlasmidGlyph
The glyph to indicate embedding in a plasmid is a turn of the backbone indicating its circular structure:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0002211
- default glyph
-
CleavageSiteGlyphc back to ToC or Class ToC
IRI: #CleavageSiteGlyph
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)
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001688
- isGlyphOf op some role some s o:0001687
- isGlyphOf op some role some s o:0001977
- isGlyphOf op some role some s o:0001956
- has sub-classes
- DnaCleavageSiteGlyph c, ProteinCleavageSiteGlyph c, RnaCleavageSiteGlyph c
- default glyph
-
ComplexGlyphc back to ToC or Class ToC
IRI: #ComplexGlyph
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):
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some type some s b o:0000253
- has sub-classes
- ComplexGlyphAlternative c, ProteinGuideRnaComplexGlyph c, ProteinProteinComplexGlyph c, ProteinSmallMoleculeComplexGlyph c
ComplexGlyphAlternativec back to ToC or Class ToC
IRI: #ComplexGlyphAlternative
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:
- has super-classes
- ComplexGlyph c
- ProteinSmallMoleculeComplexGlyph c
- ProteinGuideRnaComplexGlyph c
- ProteinProteinComplexGlyph c
- default glyph
-
CompositeGlyphc back to ToC or Class ToC
IRI: #CompositeGlyph
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.
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- default glyph
-
DegradationGlyphc back to ToC or Class ToC
IRI: #DegradationGlyph
Identical to the Process glyph, but with an empty set at the sink of the arrowhead:
- has super-classes
- Glyph c
- hasTail op some role some s b o:0000010
- InteractionGlyph c
- isGlyphOf op some interaction
- isGlyphOf op some type some s b o:0000179
- default glyph
-
DissociationGlyphc back to ToC or Class ToC
IRI: #DissociationGlyph
An circular node inside another circle
- has super-classes
- Glyph c
- hasIncoming op some role some s b o:0000010
- hasOutgoing op some role some s b o:0000011
- InteractionNodeGlyph c
- isGlyphOf op some interaction
- isGlyphOf op some type some s b o:0000180
- default glyph
-
DnaBiopolymerLocationGlyphc back to ToC or Class ToC
IRI: #DnaBiopolymerLocationGlyph
The RECOMMENDED top for Biopolymer Location is a circle, reminiscent of a pin stuck into a location (in order: DNA, RNA, Protein):
- has super-classes
- BiopolymerLocationGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000699
- isGlyphOf op some role some s o:0001236
- has sub-classes
- DnaBiopolymerLocationGlyphAlternative c
- default glyph
-
DnaBiopolymerLocationGlyphAlternativec back to ToC or Class ToC
IRI: #DnaBiopolymerLocationGlyphAlternative
An alternative is to have "nothing" for the top, just an extended version of the stem itself (in order: DNA, RNA, Protein):
- has super-classes
- DnaBiopolymerLocationGlyph c
- isAlternativeOf op some DnaBiopolymerLocationGlyph c
- default glyph
-
DnaCleavageSiteGlyphc back to ToC or Class ToC
IRI: #DnaCleavageSiteGlyph
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):
- has super-classes
- CleavageSiteGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001688
- isGlyphOf op some role some s o:0001687
- default glyph
-
DnaStabilityElementGlyphc back to ToC or Class ToC
IRI: #DnaStabilityElementGlyph
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):
- has super-classes
- StabilityElementGlyph c
- default glyph
-
Double-StrandedNucleicAcidGlyphc back to ToC or Class ToC
IRI: #Double-StrandedNucleicAcidGlyph
The RECOMMENDED glyph for dsNA is a double-helix:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some type some s b o:0000251
- has sub-classes
- Double-StrandedNucleicAcidGlyphAlternative c
- default glyph
-
Double-StrandedNucleicAcidGlyphAlternativec back to ToC or Class ToC
IRI: #Double-StrandedNucleicAcidGlyphAlternative
An alternative is the SBGN "nucleic acid" half-round rectangle:
- has super-classes
- Double-StrandedNucleicAcidGlyph c
- isAlternativeOf op some Double-StrandedNucleicAcidGlyph c
- default glyph
-
EngineeredRegionGlyphc back to ToC or Class ToC
IRI: #EngineeredRegionGlyph
Engineered Region is represented by a plain rectangle suggesting a blank slate to be written upon:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000804
- default glyph
-
FivePrimeOverhangSiteGlyphc back to ToC or Class ToC
IRI: #FivePrimeOverhangSiteGlyph
The 5' overhang site glyph is an image of a strand of DNA extended on the 5' edge of its forward strand, and the complementary 3' Overhang Site glyph is a reflection of the 5' Overhang Site (in order: five-prime, three-prime):
- has super-classes
- OverhangSiteGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001932
- has sub-classes
- FivePrimeOverhangSiteGlyphAlternative c
- default glyph
-
FivePrimeOverhangSiteGlyphAlternativec back to ToC or Class ToC
IRI: #FivePrimeOverhangSiteGlyphAlternative
With a double-stranded backbone (in order: five-prime double stranded, three-prime double stranded):
- has super-classes
- FivePrimeOverhangSiteGlyph c
- isAlternativeOf op some FivePrimeOverhangSiteGlyph c
- default glyph
-
FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphc back to ToC or Class ToC
IRI: #FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph
The 5' sticky restriction site glyph is an image of the lines along which two strands of DNA will be cut into 5' sticky ends, and the complementary 3' Sticky Restriction Site glyph is a reflection of the 5' Sticky Restriction Site. Vertical position with respect to the backbone is in a break in a single backbone (in order: five-prime, three-prime):
- has super-classes
- StickyEndRestrictionEnzymeCleavageSiteGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001975
- has sub-classes
- FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphAlternative c
- default glyph
-
FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphAlternativec back to ToC or Class ToC
IRI: #FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphAlternative
and between strands of a double backbone (in order: five-prime double stranded, three-prime double stranded):
- has super-classes
- FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph c
- isAlternativeOf op some FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph c
- default glyph
-
Glyphc back to ToC or Class ToC
IRI: #Glyph
- has super-classes
- thing c
- has sub-classes
- AptamerGlyph c, AssemblyScarGlyph c, AssociationGlyph c, BiopolymerLocationGlyph c, BluntRestrictionSiteGlyph c, CDSGlyph c, ChromosomalLocusGlyph c, CircularPlasmidGlyph c, CleavageSiteGlyph c, ComplexGlyph c, CompositeGlyph c, ControlGlyph c, DegradationGlyph c, DissociationGlyph c, Double-StrandedNucleicAcidGlyph c, EngineeredRegionGlyph c, InertDNASpacerGlyph c, InhibitionGlyph c, InteractionGlyph c, InteractionNodeGlyph c, IntronGlyph c, MacromoleculeGlyph c, MolecularSpeciesGlyph c, NoGlyphAssignedGlyph c, NoGlyphAssignedSpeciesGlyph c, Non-CodingRNAGeneGlyph c, OmittedDetailGlyph c, OperatorBindingSiteGlyph c, OriginofReplicationGlyph c, OriginofTransferGlyph c, OverhangSiteGlyph c, PolyASiteGlyph c, PolypeptideRegionGlyph c, PrimerBindingSiteGlyph c, ProcessGlyph c, ProcessInteractionGlyph c, PromoterSiteGlyph c, ProteinGlyph c, RibosomeEntrySiteGlyph c, SequenceFeatureGlyph c, SignatureGlyph c, SimpleChemicalGlyph c, Single-StrandedNucleicAcidGlyph c, SpecificRecombinationSiteGlyph c, StabilityElementGlyph c, StickyEndRestrictionEnzymeCleavageSiteGlyph c, StimulationGlyph c, StopSiteGlyph c, TerminatorGlyph c, UnspecifiedGlyph c, UnspecifiedNodeGlyph c, UnspecifiedSpeciesGlyph c
HexagonSimpleChemicalGlyphc back to ToC or Class ToC
IRI: #HexagonSimpleChemicalGlyph
The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon):
- has super-classes
- SimpleChemicalGlyph c
- has sub-classes
- SimpleChemicalGlyphAlternative c
- default glyph
-
InertDNASpacerGlyphc back to ToC or Class ToC
IRI: #InertDNASpacerGlyph
The inert DNA spacer glyph is a circle with an X in its middle, suggesting the intent to cancel possible interactions:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0002223
- default glyph
-
InhibitionGlyphc back to ToC or Class ToC
IRI: #InhibitionGlyph
An arrow whose head is a bar, suggesting blocking:
InteractionGlyphc back to ToC or Class ToC
IRI: #InteractionGlyph
- has super-classes
- Glyph c
- has sub-classes
- ControlGlyph c, DegradationGlyph c, InhibitionGlyph c, ProcessInteractionGlyph c, StimulationGlyph c
InteractionNodeGlyphc back to ToC or Class ToC
IRI: #InteractionNodeGlyph
- has super-classes
- Glyph c
- has sub-classes
- AssociationGlyph c, DissociationGlyph c, ProcessGlyph c, UnspecifiedNodeGlyph c
IntronGlyphc back to ToC or Class ToC
IRI: #IntronGlyph
An intron is designated by a boundaries interrupting CDS, each side having a two-triangle "torn out" edges, suggesting removal from an enclosing coding sequence:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000188
- default glyph
-
MacromoleculeGlyphc back to ToC or Class ToC
IRI: #MacromoleculeGlyph
The macromolecule glyph is a rounded rectangle, as used in SBGN:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some type some s b o:0000245
- default glyph
-
MolecularSpeciesGlyphc back to ToC or Class ToC
IRI: #MolecularSpeciesGlyph
- has super-classes
- Glyph c
- has sub-classes
- AptamerGlyph c, AssemblyScarGlyph c, BiopolymerLocationGlyph c, BluntRestrictionSiteGlyph c, CDSGlyph c, ChromosomalLocusGlyph c, CircularPlasmidGlyph c, CleavageSiteGlyph c, ComplexGlyph c, CompositeGlyph c, Double-StrandedNucleicAcidGlyph c, EngineeredRegionGlyph c, InertDNASpacerGlyph c, IntronGlyph c, MacromoleculeGlyph c, NoGlyphAssignedGlyph c, NoGlyphAssignedSpeciesGlyph c, Non-CodingRNAGeneGlyph c, OmittedDetailGlyph c, OperatorBindingSiteGlyph c, OriginofReplicationGlyph c, OriginofTransferGlyph c, OverhangSiteGlyph c, PolyASiteGlyph c, PolypeptideRegionGlyph c, PrimerBindingSiteGlyph c, PromoterSiteGlyph c, ProteinGlyph c, RibosomeEntrySiteGlyph c, SignatureGlyph c, SimpleChemicalGlyph c, Single-StrandedNucleicAcidGlyph c, SpecificRecombinationSiteGlyph c, StabilityElementGlyph c, StickyEndRestrictionEnzymeCleavageSiteGlyph c, StopSiteGlyph c, TerminatorGlyph c, UnspecifiedGlyph c, UnspecifiedSpeciesGlyph c
NoGlyphAssignedGlyphc back to ToC or Class ToC
IRI: #NoGlyphAssignedGlyph
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:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- default glyph
-
NoGlyphAssignedSpeciesGlyphc back to ToC or Class ToC
IRI: #NoGlyphAssignedSpeciesGlyph
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:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- default glyph
-
Non-CodingRNAGeneGlyphc back to ToC or Class ToC
IRI: #Non-CodingRNAGeneGlyph
The non-coding RNA glyph is a rectangular box whose top is a single-stranded RNA "wiggle":
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001263
- isGlyphOf op some role some s o:0000834
- default glyph
-
OmittedDetailGlyphc back to ToC or Class ToC
IRI: #OmittedDetailGlyph
The Omitted Detail glyph is a break in the backbone with an ellipsis to indicate that material would normally be in that location:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- default glyph
-
OperatorBindingSiteGlyphc back to ToC or Class ToC
IRI: #OperatorBindingSiteGlyph
The operator glyph is an open "cup" suggesting a binding location:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000057
- isGlyphOf op some role some s o:0000409
- default glyph
-
OriginofReplicationGlyphc back to ToC or Class ToC
IRI: #OriginofReplicationGlyph
The origin of replication glyph is a circle suggesting the "bulge" opened in a piece of circular DNA when replication is beginning:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000296
- default glyph
-
OriginofTransferGlyphc back to ToC or Class ToC
IRI: #OriginofTransferGlyph
The origin of transfer glyph is circular like origin of replication, but also includes an outbound arrow:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000724
- default glyph
-
OverhangSiteGlyphc back to ToC or Class ToC
IRI: #OverhangSiteGlyph
The 5' overhang site glyph is an image of a strand of DNA extended on the 5' edge of its forward strand, and the complementary 3' Overhang Site glyph is a reflection of the 5' Overhang Site (in order: five-prime, three-prime):
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001932
- isGlyphOf op some role some s o:0001933
- has sub-classes
- FivePrimeOverhangSiteGlyph c, ThreePrimeOverhangSiteGlyph c
PentagonSimpleChemicalGlyphc back to ToC or Class ToC
IRI: #PentagonSimpleChemicalGlyph
The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon):
- has super-classes
- SimpleChemicalGlyph c
- has sub-classes
- SimpleChemicalGlyphAlternative c
- default glyph
-
PolyASiteGlyphc back to ToC or Class ToC
IRI: #PolyASiteGlyph
The polyA site glyph is a sequence of As sitting atop the backbone:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000553
- default glyph
-
PolypeptideRegionGlyphc back to ToC or Class ToC
IRI: #PolypeptideRegionGlyph
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:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000839
- default glyph
-
PrimerBindingSiteGlyphc back to ToC or Class ToC
IRI: #PrimerBindingSiteGlyph
The primer binding site glyph is a line with a bent end suggesting a partially complementary strand of nucleic acid attaching to the backbone:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0005850
- default glyph
-
ProcessGlyphc back to ToC or Class ToC
IRI: #ProcessGlyph
A square node:
- has super-classes
- Glyph c
- hasIncoming op some role some s b o:0000010
- hasOutgoing op some role some s b o:0000011
- InteractionNodeGlyph c
- isGlyphOf op some interaction
- isGlyphOf op some type some s b o:0000375
- default glyph
-
ProcessInteractionGlyphc back to ToC or Class ToC
IRI: #ProcessInteractionGlyph
An arrow with a filled head the same color as the line:
PromoterSiteGlyphc back to ToC or Class ToC
IRI: #PromoterSiteGlyph
The promoter glyph is a bent arrow pointing forward, suggesting the action of transcription from its transcription start site:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000167
- default glyph
-
ProteinBiopolymerLocationGlyphc back to ToC or Class ToC
IRI: #ProteinBiopolymerLocationGlyph
The RECOMMENDED top for Biopolymer Location is a circle, reminiscent of a pin stuck into a location (in order: DNA, RNA, Protein):
- has super-classes
- BiopolymerLocationGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000699
- isGlyphOf op some role some s o:0001237
- has sub-classes
- ProteinBiopolymerLocationGlyphAlternative c
- default glyph
-
ProteinBiopolymerLocationGlyphAlternativec back to ToC or Class ToC
IRI: #ProteinBiopolymerLocationGlyphAlternative
An alternative is to have "nothing" for the top, just an extended version of the stem itself (in order: DNA, RNA, Protein):
- has super-classes
- ProteinBiopolymerLocationGlyph c
- isAlternativeOf op some ProteinBiopolymerLocationGlyph c
- default glyph
-
ProteinCleavageSiteGlyphc back to ToC or Class ToC
IRI: #ProteinCleavageSiteGlyph
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):
- has super-classes
- CleavageSiteGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001956
- default glyph
-
ProteinGlyphc back to ToC or Class ToC
IRI: #ProteinGlyph
The protein glyph is a "pill" shape with a rectangular body and rounded ends, representing the compact space-filling mass of many proteins:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some type some s b o:0000252
- default glyph
-
ProteinGuideRnaComplexGlyphc back to ToC or Class ToC
IRI: #ProteinGuideRnaComplexGlyph
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):
- has super-classes
- ComplexGlyph c
- has sub-classes
- ComplexGlyphAlternative c
- default glyph
-
ProteinProteinComplexGlyphc back to ToC or Class ToC
IRI: #ProteinProteinComplexGlyph
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):
- has super-classes
- ComplexGlyph c
- has sub-classes
- ComplexGlyphAlternative c
- default glyph
-
ProteinSmallMoleculeComplexGlyphc back to ToC or Class ToC
IRI: #ProteinSmallMoleculeComplexGlyph
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):
- has super-classes
- ComplexGlyph c
- has sub-classes
- ComplexGlyphAlternative c
- default glyph
-
ProteinStabilityElementGlyphc back to ToC or Class ToC
IRI: #ProteinStabilityElementGlyph
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):
- has super-classes
- StabilityElementGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001955
- isGlyphOf op some role some s o:0001546
- default glyph
-
RibosomeEntrySiteGlyphc back to ToC or Class ToC
IRI: #RibosomeEntrySiteGlyph
The ribosome entry promoter glyph is a half-ovoid sitting on the backbone, suggesting an attached ribosome beginning transcription:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000139
- default glyph
-
RnaBiopolymerLocationGlyphc back to ToC or Class ToC
IRI: #RnaBiopolymerLocationGlyph
The RECOMMENDED top for Biopolymer Location is a circle, reminiscent of a pin stuck into a location (in order: DNA, RNA, Protein):
- has super-classes
- BiopolymerLocationGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000699
- isGlyphOf op some role some s o:0001236
- has sub-classes
- RnaBiopolymerLocationGlyphAlternative c
- default glyph
-
RnaBiopolymerLocationGlyphAlternativec back to ToC or Class ToC
IRI: #RnaBiopolymerLocationGlyphAlternative
An alternative is to have "nothing" for the top, just an extended version of the stem itself (in order: DNA, RNA, Protein):
- has super-classes
- RnaBiopolymerLocationGlyph c
- isAlternativeOf op some RnaBiopolymerLocationGlyph c
- default glyph
-
RnaCleavageSiteGlyphc back to ToC or Class ToC
IRI: #RnaCleavageSiteGlyph
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):
- has super-classes
- CleavageSiteGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001977
- default glyph
-
RnaStabilityElementGlyphc back to ToC or Class ToC
IRI: #RnaStabilityElementGlyph
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):
- has super-classes
- StabilityElementGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001979
- default glyph
-
SignatureGlyphc back to ToC or Class ToC
IRI: #SignatureGlyph
The signature glyph is a box sitting atop the backbone with an X and line inside it, suggesting a signature on a form:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001978
- default glyph
-
SimpleChemicalGlyphc back to ToC or Class ToC
IRI: #SimpleChemicalGlyph
The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon):
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some type some s b o:0000247
- has sub-classes
- HexagonSimpleChemicalGlyph c, PentagonSimpleChemicalGlyph c, SimpleChemicalGlyphAlternative c, TriangleSimpleChemicalGlyph c
SimpleChemicalGlyphAlternativec back to ToC or Class ToC
IRI: #SimpleChemicalGlyphAlternative
Alternately, a simple chemical may also be represented a small circle:
- has super-classes
- SimpleChemicalGlyph c
- TriangleSimpleChemicalGlyph c
- PentagonSimpleChemicalGlyph c
- HexagonSimpleChemicalGlyph c
- default glyph
-
Single-StrandedNucleicAcidGlyphc back to ToC or Class ToC
IRI: #Single-StrandedNucleicAcidGlyph
The RECOMMENDED glyph for ssNA is a wiggly line:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some type some s b o:0000250
- has sub-classes
- Single-StrandedNucleicAcidGlyphAlternative c
- default glyph
-
Single-StrandedNucleicAcidGlyphAlternativec back to ToC or Class ToC
IRI: #Single-StrandedNucleicAcidGlyphAlternative
An alternative is the SBGN "nucleic acid" half-round rectangle:
- has super-classes
- Single-StrandedNucleicAcidGlyph c
- isAlternativeOf op some Single-StrandedNucleicAcidGlyph c
- default glyph
-
SpecificRecombinationSiteGlyphc back to ToC or Class ToC
IRI: #SpecificRecombinationSiteGlyph
The specific recombination site glyph is a triangle, centered on the backbone, as has appeared in a number of recombinase circuit papers:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000299
- default glyph
-
StabilityElementGlyphc back to ToC or Class ToC
IRI: #StabilityElementGlyph
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)
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001979
- isGlyphOf op some role some s o:0001955
- isGlyphOf op some role some s o:0001546
- has sub-classes
- DnaStabilityElementGlyph c, ProteinStabilityElementGlyph c, RnaStabilityElementGlyph c
- default glyph
-
StickyEndRestrictionEnzymeCleavageSiteGlyphc back to ToC or Class ToC
IRI: #StickyEndRestrictionEnzymeCleavageSiteGlyph
The 5' sticky restriction site glyph is an image of the lines along which two strands of DNA will be cut into 5' sticky ends, and the complementary 3' Sticky Restriction Site glyph is a reflection of the 5' Sticky Restriction Site. Vertical position with respect to the backbone is in a break in a single backbone (in order: five-prime, three-prime):
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001975
- isGlyphOf op some role some s o:0001976
- has sub-classes
- FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph c, ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph c
StimulationGlyphc back to ToC or Class ToC
IRI: #StimulationGlyph
An arrow with an head that is empty or of a different color than the line:
StopSiteGlyphc back to ToC or Class ToC
IRI: #StopSiteGlyph
Transcription/Translation End Point 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)
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000616
- isGlyphOf op some role some s o:0000319
- isGlyphOf op some role some s o:0000327
- has sub-classes
- TranscriptionStopSiteGlyph c, TranslationStopSiteGlyph c
- default glyph
-
TerminatorGlyphc back to ToC or Class ToC
IRI: #TerminatorGlyph
The terminator is a T sitting atop the backbone:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000141
- default glyph
-
ThreePrimeOverhangSiteGlyphc back to ToC or Class ToC
IRI: #ThreePrimeOverhangSiteGlyph
The 5' overhang site glyph is an image of a strand of DNA extended on the 5' edge of its forward strand, and the complementary 3' Overhang Site glyph is a reflection of the 5' Overhang Site (in order: five-prime, three-prime):
- has super-classes
- OverhangSiteGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001933
- has sub-classes
- ThreePrimeOverhangSiteGlyphAlternative c
- default glyph
-
ThreePrimeOverhangSiteGlyphAlternativec back to ToC or Class ToC
IRI: #ThreePrimeOverhangSiteGlyphAlternative
With a double-stranded backbone (in order: five-prime double stranded, three-prime double stranded):
- has super-classes
- ThreePrimeOverhangSiteGlyph c
- isAlternativeOf op some ThreePrimeOverhangSiteGlyph c
- default glyph
-
ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphc back to ToC or Class ToC
IRI: #ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph
The 5' sticky restriction site glyph is an image of the lines along which two strands of DNA will be cut into 5' sticky ends, and the complementary 3' Sticky Restriction Site glyph is a reflection of the 5' Sticky Restriction Site. Vertical position with respect to the backbone is in a break in a single backbone (in order: five-prime, three-prime):
- has super-classes
- StickyEndRestrictionEnzymeCleavageSiteGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0001976
- has sub-classes
- ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphAlternative c
- default glyph
-
ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphAlternativec back to ToC or Class ToC
IRI: #ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphAlternative
and between strands of a double backbone (in order: five-prime double stranded, three-prime double stranded):
- has super-classes
- ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph c
- isAlternativeOf op some ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph c
- default glyph
-
TranscriptionStopSiteGlyphc back to ToC or Class ToC
IRI: #TranscriptionStopSiteGlyph
The Transcription/Translation End Point top is an asterisk in a circle (in order: transcription, translation):
- has super-classes
- StopSiteGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000616
- default glyph
-
TranslationStopSiteGlyphc back to ToC or Class ToC
IRI: #TranslationStopSiteGlyph
The Transcription/Translation End Point top is an asterisk in a circle (in order: transcription, translation):
- has super-classes
- StopSiteGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000319
- isGlyphOf op some role some s o:0000327
- default glyph
-
TriangleSimpleChemicalGlyphc back to ToC or Class ToC
IRI: #TriangleSimpleChemicalGlyph
The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon):
- has super-classes
- SimpleChemicalGlyph c
- has sub-classes
- SimpleChemicalGlyphAlternative c
- default glyph
-
UnspecifiedGlyphc back to ToC or Class ToC
IRI: #UnspecifiedGlyph
Unspecified is RECOMMENDED to be represented by the unicode "replacement character" glyph, indicating a missing or invalid symbol:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some role some s o:0000110
- has sub-classes
- UnspecifiedGlyphAlternative c
- default glyph
-
UnspecifiedGlyphAlternativec back to ToC or Class ToC
IRI: #UnspecifiedGlyphAlternative
A half-rounded rectangle, the SBGN glyph for a nucleic acid, is an alternative:
- has super-classes
- UnspecifiedGlyph c
- isAlternativeOf op some UnspecifiedGlyph c
- default glyph
-
UnspecifiedNodeGlyphc back to ToC or Class ToC
IRI: #UnspecifiedNodeGlyph
Unspecified is represented by the unicode "replacement character" glyph, indicating a missing or invalid symbol:
- has super-classes
- Glyph c
- hasIncoming op some role some s b o:0000003
- InteractionNodeGlyph c
- isGlyphOf op some interaction
- isGlyphOf op some type some s b o:0000231
- default glyph
-
UnspecifiedSpeciesGlyphc back to ToC or Class ToC
IRI: #UnspecifiedSpeciesGlyph
Unspecified is RECOMMENDED to be represented by the unicode "replacement character" glyph, indicating a missing or invalid symbol:
- has super-classes
- Glyph c
- MolecularSpeciesGlyph c
- isGlyphOf op some component
- isGlyphOf op some type some s b o:0000285
- has sub-classes
- UnspecifiedSpeciesGlyphAlternative c
- default glyph
-
UnspecifiedSpeciesGlyphAlternativec back to ToC or Class ToC
IRI: #UnspecifiedSpeciesGlyphAlternative
An alternative is the SBGN "generic species" glyph, which is an ellipse:
- has super-classes
- UnspecifiedSpeciesGlyph c
- isAlternativeOf op some UnspecifiedSpeciesGlyph c
- default glyph
-
