IRI:
http://sbols.org/visual/v2

Table of Content

  1. Classes
  2. Object Properties
  3. Annotation Properties
  4. Namespace Declarations

Classes

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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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

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
default glyph

ControlGlyphc back to ToC or Class ToC

IRI: #ControlGlyph

An arrow with a diamond head:

has super-classes
Glyph c
isGlyphOf op some interaction
isGlyphOf op some type some s b o:0000168
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
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
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 definition
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 definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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 definition
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 definition
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, InhibitionGlyph c, InsulatorGlyph 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, ProcessGlyph c, ProcessNodeGlyph c, PromoterSiteGlyph c, ProteinGlyph c, RibosomeEntrySiteGlyph c, SignatureGlyph c, SimpleChemicalGlyph c, Single-StrandedNucleicAcidGlyph c, SpecificRecombinationSiteGlyph c, StabilityElementGlyph c, StickyEndRestrictionEnzymeCleavageSiteGlyph c, StimulationGlyph c, StopSiteGlyph c, TerminatorGlyph c, UnspecifiedGlyph 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

InhibitionGlyphc back to ToC or Class ToC

IRI: #InhibitionGlyph

An arrow whose head is a bar, suggesting blocking:

has super-classes
Glyph c
isGlyphOf op some interaction
isGlyphOf op some type some s b o:0000169
default glyph

InsulatorGlyphc back to ToC or Class ToC

IRI: #InsulatorGlyph

The insulator glyph is a box inside another box that isolates it from its environment:

has super-classes
Glyph c
isGlyphOf op some component definition
isGlyphOf op some role some s o:0000627
default glyph

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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
isGlyphOf op some type some s b o:0000245
has sub-classes
MacromoleculeGlyphAlternative c
default glyph

MacromoleculeGlyphAlternativec back to ToC or Class ToC

IRI: #MacromoleculeGlyphAlternative

A deprecated alternative is a diagonally offset union of a large and small circle, intended to invoke the complex shapes of protein. It is now deprecated for being too similar to a yeast cell "shmoo" symbol:

has super-classes
MacromoleculeGlyph c
isAlternativeOf op some MacromoleculeGlyph c
default glyph

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
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
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
isGlyphOf op some component definition
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
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
isGlyphOf op some role some s o:0005850
default glyph

ProcessGlyphc back to ToC or Class ToC

IRI: #ProcessGlyph

An arrow with a filled head the same color as the line:

has super-classes
Glyph c
isGlyphOf op some interaction
isGlyphOf op some type some s b o:0000375
default glyph

ProcessNodeGlyphc back to ToC or Class ToC

IRI: #ProcessNodeGlyph

A square node:

has super-classes
Glyph c
isGlyphOf op some interaction
isGlyphOf op some type some s b o:0000375
default glyph

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
isGlyphOf op some component definition
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 definition
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 definition
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
isGlyphOf op some component definition
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 definition
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
isGlyphOf op some component definition
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 definition
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 definition
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 definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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:

has super-classes
Glyph c
isGlyphOf op some interaction
isGlyphOf op some type some s b o:0000170
default glyph

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
isGlyphOf op some component definition
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
isGlyphOf op some component definition
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 definition
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 definition
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 definition
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 definition
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
isGlyphOf op some component definition
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

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
isGlyphOf op some component definition
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

Object Properties

hasGlyphop back to ToC or Object Property ToC

IRI: #hasGlyph

isAlternativeOfop back to ToC or Object Property ToC

IRI: #isAlternativeOf

isGlyphOfop back to ToC or Object Property ToC

IRI: #isGlyphOf

Annotation Properties

defaultGlyphap back to ToC or Annotation Property ToC

IRI: #defaultGlyph

glyphDirectoryap back to ToC or Annotation Property ToC

IRI: #glyphDirectory

notesap back to ToC or Annotation Property ToC

IRI: #notes

prototypicalExampleap back to ToC or Annotation Property ToC

IRI: #prototypicalExample

Namespace Declarations back to ToC

default namespace
http://sbols.org/visual/v2#
owl
http://www.w3.org/2002/07/owl#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
sbo
http://identifiers.org/sbo/
sbol-owl
https://dissys.github.io/sbol-owl/
so
http://identifiers.org/so/
v2
http://sbols.org/v2#
visual
http://sbols.org/visual/
xsd
http://www.w3.org/2001/XMLSchema#

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni.