diff --git a/Glyphs/FunctionalComponents/complex/README.md b/Glyphs/FunctionalComponents/complex/README.md index 7078f1f..39c111e 100644 --- a/Glyphs/FunctionalComponents/complex/README.md +++ b/Glyphs/FunctionalComponents/complex/README.md @@ -6,9 +6,9 @@ SBO:0000253 Non-covalent complex ## Recommended Glyph and Alternates 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): -![glyph example](complex-ps-specification.png) -![glyph example](complex-pr-specification.png) -![glyph example](complex-pp-specification.png) +![glyph specification](complex-ps-specification.png) +![glyph specification](complex-pr-specification.png) +![glyph specification](complex-pp-specification.png) 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: diff --git a/Ontology/v2/sbol-vo.html b/Ontology/v2/sbol-vo.html index 190e9ec..da44b25 100644 --- a/Ontology/v2/sbol-vo.html +++ b/Ontology/v2/sbol-vo.html @@ -77,11 +77,15 @@

Classes

  • FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphAlternative
  • Glyph
  • HexagonSimpleChemicalGlyph
    • +
  • InertDNASpacerGlyph
  • InhibitionGlyph
  • InsulatorGlyph
    • +
  • InteractionGlyph
    • +
  • InteractionNodeGlyph
  • IntronGlyph
  • MacromoleculeGlyph
  • MacromoleculeGlyphAlternative
    • +
  • MolecularSpeciesGlyph
  • NoGlyphAssignedGlyph
  • NoGlyphAssignedSpeciesGlyph
  • Non-CodingRNAGeneGlyph
    • @@ -110,6 +114,7 @@

    Classes

  • RnaBiopolymerLocationGlyphAlternative
  • RnaCleavageSiteGlyph
  • RnaStabilityElementGlyph
    • +
  • SequenceFeatureGlyph
  • SignatureGlyph
  • SimpleChemicalGlyph
  • SimpleChemicalGlyphAlternative
    • @@ -130,6 +135,7 @@

    Classes

  • TriangleSimpleChemicalGlyph
  • UnspecifiedGlyph
  • UnspecifiedGlyphAlternative
    • +
  • UnspecifiedNodeGlyph
  • UnspecifiedSpeciesGlyph
  • UnspecifiedSpeciesGlyphAlternative
    • @@ -148,6 +154,10 @@

    AptamerGlyphc Glyph c +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -185,6 +195,10 @@

    AssemblyScarGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -259,6 +273,26 @@

    AssociationGlyphcGlyph c

    +
    + hasIncoming + op + some + role + some + s b o:0000010 +
    +
    + hasOutgoing + op + some + role + some + s b o:0000011 +
    +
    + InteractionNodeGlyph + c +
    isGlyphOf op @@ -300,6 +334,10 @@

    BiopolymerLocationGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -364,6 +402,10 @@

    BluntRestrictionSiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -401,6 +443,10 @@

    CDSGlyphc bac Glyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -475,6 +521,10 @@

    ChromosomalLocusGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -512,6 +562,10 @@

    CircularPlasmidGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -553,6 +607,10 @@

    CleavageSiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -625,6 +683,10 @@

    ComplexGlyphc Glyph c

    +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op @@ -659,6 +721,8 @@

    ComplexGlyphc

    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:

    +

    glyph example

    An alternative is the SBGN "cornered rectangle" glyph for a complex:

    @@ -704,6 +768,10 @@

    CompositeGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    default glyph
    @@ -727,6 +795,26 @@

    ControlGlyphc Glyph c +
    + hasHead + op + some + role + some + s b o:0000644 +
    +
    + hasTail + op + some + role + some + s b o:0000019 +
    +
    + InteractionGlyph + c +
    isGlyphOf op @@ -764,6 +852,18 @@

    DegradationGlyphcGlyph c

    +
    + hasTail + op + some + role + some + s b o:0000010 +
    +
    + InteractionGlyph + c +
    isGlyphOf op @@ -801,6 +901,26 @@

    DissociationGlyphcGlyph c

    +
    + hasIncoming + op + some + role + some + s b o:0000010 +
    +
    + hasOutgoing + op + some + role + some + s b o:0000011 +
    +
    + InteractionNodeGlyph + c +
    isGlyphOf op @@ -988,6 +1108,10 @@

    Double-StrandedNucleicAcidGlyphcGlyph c

    +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op @@ -1062,6 +1186,10 @@

    EngineeredRegionGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1280,14 +1408,22 @@

    Glyphc back t c, EngineeredRegionGlyph c, + InertDNASpacerGlyph + c, InhibitionGlyph c, InsulatorGlyph c, + InteractionGlyph + c, + InteractionNodeGlyph + c, IntronGlyph c, MacromoleculeGlyph c, + MolecularSpeciesGlyph + c, NoGlyphAssignedGlyph c, NoGlyphAssignedSpeciesGlyph @@ -1320,6 +1456,8 @@

    Glyphc back t c, RibosomeEntrySiteGlyph c, + SequenceFeatureGlyph + c, SignatureGlyph c, SimpleChemicalGlyph @@ -1340,6 +1478,8 @@

    Glyphc back t c, UnspecifiedGlyph c, + UnspecifiedNodeGlyph + c, UnspecifiedSpeciesGlyph c

    @@ -1375,6 +1515,47 @@

    HexagonSimpleChemicalGlyphc +
    + +

    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 +
    +
    + SequenceFeatureGlyph + c +
    +
    + isGlyphOf + op + some + component definition +
    +
    + isGlyphOf + op + some + role + some + s o:0002223 +
    +
    + default glyph +
    +
    + +
    +
    +

    InhibitionGlyphc back to ToC or Class ToC

    @@ -1390,6 +1571,26 @@

    InhibitionGlyphcGlyph c +
    + hasHead + op + some + role + some + s b o:0000642 +
    +
    + hasTail + op + some + role + some + s b o:0000020 +
    +
    + InteractionGlyph + c +
    isGlyphOf op @@ -1427,6 +1628,10 @@

    InsulatorGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1449,6 +1654,62 @@

    InsulatorGlyphc + +

    InteractionGlyphc back to ToC or Class ToC

    +

    IRI: #InteractionGlyph

    +
    +
    + has super-classes +
    +
    + Glyph + c +
    +
    + has sub-classes +
    +
    + ControlGlyph + c, + DegradationGlyph + c, + InhibitionGlyph + c, + ProcessGlyph + c, + StimulationGlyph + c +
    +
    +

    +
    + +

    InteractionNodeGlyphc back to ToC or Class ToC

    +

    IRI: #InteractionNodeGlyph

    +
    +
    + has super-classes +
    +
    + Glyph + c +
    +
    + has sub-classes +
    +
    + AssociationGlyph + c, + DissociationGlyph + c, + ProcessNodeGlyph + c, + UnspecifiedNodeGlyph + c +
    +
    +

    IntronGlyphc back to ToC or Class ToC

    @@ -1464,6 +1725,10 @@

    IntronGlyphc Glyph c +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1501,6 +1766,10 @@

    MacromoleculeGlyphcGlyph c

    +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op @@ -1560,6 +1829,41 @@

    MacromoleculeGlyphAlternativec

    +
    + +

    MolecularSpeciesGlyphc back to ToC or Class ToC

    +

    IRI: #MolecularSpeciesGlyph

    +
    +
    + has super-classes +
    +
    + Glyph + c +
    +
    + has sub-classes +
    +
    + ComplexGlyph + c, + Double-StrandedNucleicAcidGlyph + c, + MacromoleculeGlyph + c, + NoGlyphAssignedSpeciesGlyph + c, + ProteinGlyph + c, + SimpleChemicalGlyph + c, + Single-StrandedNucleicAcidGlyph + c, + UnspecifiedSpeciesGlyph + c +
    +
    +

    NoGlyphAssignedGlyphc back to ToC or Class ToC

    @@ -1576,6 +1880,10 @@

    NoGlyphAssignedGlyphcGlyph c +
    + SequenceFeatureGlyph + c +
    default glyph
    @@ -1600,6 +1908,10 @@

    NoGlyphAssignedSpeciesGlyphcGlyph c +
    + MolecularSpeciesGlyph + c +
    default glyph
    @@ -1623,6 +1935,10 @@

    Non-CodingRNAGeneGlyphcGlyph c +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1668,6 +1984,10 @@

    OmittedDetailGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    default glyph
    @@ -1691,6 +2011,10 @@

    OperatorBindingSiteGlyphcGlyph c +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1736,6 +2060,10 @@

    OriginofReplicationGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1773,6 +2101,10 @@

    OriginofTransferGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1810,6 +2142,10 @@

    OverhangSiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1888,6 +2224,10 @@

    PolyASiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1925,6 +2265,10 @@

    PolypeptideRegionGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1962,6 +2306,10 @@

    PrimerBindingSiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1999,6 +2347,34 @@

    ProcessGlyphc Glyph c

    +
    + hasHead + op + some + role + some + s b o:0000011 +
    +
    + hasTail + op + some + role + some + s b o:0000010 +
    +
    + hasTail + op + some + role + some + s b o:0000645 +
    +
    + InteractionGlyph + c +
    isGlyphOf op @@ -2036,6 +2412,26 @@

    ProcessNodeGlyphcGlyph c

    +
    + hasIncoming + op + some + role + some + s b o:0000010 +
    +
    + hasOutgoing + op + some + role + some + s b o:0000011 +
    +
    + InteractionNodeGlyph + c +
    isGlyphOf op @@ -2073,6 +2469,10 @@

    PromoterSiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -2229,6 +2629,10 @@

    ProteinGlyphc Glyph c

    +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op @@ -2401,6 +2805,10 @@

    RibosomeEntrySiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -2579,6 +2987,89 @@

    RnaStabilityElementGlyphc

    +

    SignatureGlyphc back to ToC or Class ToC

    @@ -2594,6 +3085,10 @@

    SignatureGlyphcGlyph c +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -2631,6 +3126,10 @@

    SimpleChemicalGlyphcGlyph c

    +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op @@ -2710,6 +3209,10 @@

    Single-StrandedNucleicAcidGlyphcGlyph c

    +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op @@ -2784,6 +3287,10 @@

    SpecificRecombinationSiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -2825,6 +3332,10 @@

    StabilityElementGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -2889,6 +3400,10 @@

    StickyEndRestrictionEnzymeCleavageSiteGlyphGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -2937,6 +3452,26 @@

    StimulationGlyphcGlyph c

    +
    + hasHead + op + some + role + some + s b o:0000643 +
    +
    + hasTail + op + some + role + some + s b o:0000459 +
    +
    + InteractionGlyph + c +
    isGlyphOf op @@ -2978,6 +3513,10 @@

    StopSiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -3040,6 +3579,10 @@

    TerminatorGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -3337,6 +3880,10 @@

    UnspecifiedGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -3396,6 +3943,55 @@

    UnspecifiedGlyphAlternativec

    +
    + +

    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

    @@ -3411,6 +4007,10 @@

    UnspecifiedSpeciesGlyphcGlyph c +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op @@ -3475,6 +4075,10 @@

    UnspecifiedSpeciesGlyphAlternativec<

    Object Properties

    @@ -3483,6 +4087,26 @@

    Object Properties

    hasGlyphop back to ToC or Object Property ToC

    IRI: #hasGlyph

    +
    + +

    hasHeadop back to ToC or Object Property ToC

    +

    IRI: #hasHead

    +
    +
    + +

    hasIncomingop back to ToC or Object Property ToC

    +

    IRI: #hasIncoming

    +
    +
    + +

    hasOutgoingop back to ToC or Object Property ToC

    +

    IRI: #hasOutgoing

    +
    +
    + +

    hasTailop back to ToC or Object Property ToC

    +

    IRI: #hasTail

    +

    isAlternativeOfop back to ToC or Object Property ToC

    diff --git a/Ontology/v2/sbol-vo.rdf b/Ontology/v2/sbol-vo.rdf index f3c78e5..05f1ab6 100644 --- a/Ontology/v2/sbol-vo.rdf +++ b/Ontology/v2/sbol-vo.rdf @@ -10,11 +10,6 @@ - - - Glyph - - isGlyphOf @@ -23,6 +18,26 @@ hasGlyph + + hasHead + + + + hasTail + + + + hasIncoming + + + + hasOutgoing + + + + isAlternativeOf + + defaultGlyph @@ -35,10 +50,6 @@ recommended - - isAlternativeOf - - prototypicalExample @@ -47,8 +58,56 @@ notes + + + Glyph + + + + + InteractionGlyph + + + + + InteractionNodeGlyph + + + + + MolecularSpeciesGlyph + + + + + SequenceFeatureGlyph + + + + + + + + + + + + + + + + + + + + + + + + + @@ -77,6 +136,18 @@ + + + + + + + + + + + + @@ -105,6 +176,29 @@ + + + + + + + + + + + + + + + + + + + + + + + @@ -133,6 +227,29 @@ + + + + + + + + + + + + + + + + + + + + + + + @@ -161,6 +278,40 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -193,6 +344,7 @@ + @@ -321,6 +473,7 @@ Despite both being stem-top glyphs, Biopolymer Location is not a parent to Stabi + @@ -349,6 +502,7 @@ Despite both being stem-top glyphs, Biopolymer Location is not a parent to Stabi + @@ -377,6 +531,7 @@ Despite both being stem-top glyphs, Biopolymer Location is not a parent to Stabi + @@ -418,6 +573,7 @@ Examples of RECOMMENDED usage: + @@ -446,6 +602,7 @@ Examples of RECOMMENDED usage: + @@ -474,6 +631,29 @@ Examples of RECOMMENDED usage: + + + + + + + + + + + + + + + + + + + + + + + @@ -500,8 +680,73 @@ Examples of RECOMMENDED usage: The association glyph is based on the SBGN Process Description association glyph. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Unspecified is represented by the unicode "replacement character" glyph, indicating a missing or invalid symbol: + UnspecifiedNodeGlyph + unspecified-glyph-specification.png + SBOL-visual/Glyphs/InteractionNodes/unspecified + true + An interaction that is missing any information about its nature or intended purpose. + Note that there are no outgoing edges for the Unspecified interaction, because there is no difference in roles to indicate. + +The Unspecified glyph is intended for showing where information about an interaction is missing. It should not generally appear with well-curated designs or diagrams. + + + + + + + + + + + + + + + + + + + + + + + + + @@ -530,6 +775,29 @@ Examples of RECOMMENDED usage: + + + + + + + + + + + + + + + + + + + + + + + @@ -563,6 +831,7 @@ The assocated SBO term also covers: + @@ -773,6 +1042,7 @@ Describing a Restriction Enzyme Cleavage Site with a vertical line glyph on a DN + @@ -889,6 +1159,7 @@ Describing a Restriction Enzyme Cleavage Site with a vertical line glyph on a DN + @@ -953,7 +1224,9 @@ The Ribonuclease Site, Protease Site, and Restriction Enzyme Recognition Site gl 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 diagram and still be considered compliant with SBOL Visual 2, where it is now classified as a Biopolymer Location (which is a superclass of cleavage sites). Thus, the Biopolymer Location glyph from SBOL Visual 2.0 is backwards compatible with the Restriction Enzyme Recognition Site glyph from SBOL Visual 1.0. -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. +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). @@ -1047,6 +1320,7 @@ The 5' Sticky Restriction Site, 3' Sticky Restriction Site, and Blunt Restrictio + @@ -1075,6 +1349,7 @@ The 5' Sticky Restriction Site, 3' Sticky Restriction Site, and Blunt Restrictio + @@ -1103,6 +1378,7 @@ The 5' Sticky Restriction Site, 3' Sticky Restriction Site, and Blunt Restrictio + @@ -1131,6 +1407,7 @@ The 5' Sticky Restriction Site, 3' Sticky Restriction Site, and Blunt Restrictio + @@ -1170,6 +1447,7 @@ The 5' Sticky Restriction Site, 3' Sticky Restriction Site, and Blunt Restrictio + @@ -1213,6 +1491,7 @@ Unspecified is RECOMMENDED to be represented by the unicode "replacement charact + @@ -1250,6 +1529,7 @@ Example of RECOMMENDED usage: a plasmid containing a functional unit consisting + 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. CompositeGlyph @@ -1270,6 +1550,7 @@ and a composite with an Engineered Region of otherwise unspecified content: + @@ -1300,6 +1581,7 @@ and a composite with an Engineered Region of otherwise unspecified content: + @@ -1342,6 +1624,7 @@ and a composite with an Engineered Region of otherwise unspecified content: + 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. @@ -1358,6 +1641,7 @@ For example, at present there is no glyph recommended for representing a transpo + @@ -1381,11 +1665,12 @@ For example, at present there is no glyph recommended for representing a transpo SBOL-visual/Glyphs/insulator true RiboJ - *this section deliberately blank* + This glyph is deprecated in favor of inert DNA spacer. + @@ -1414,6 +1699,7 @@ For example, at present there is no glyph recommended for representing a transpo + @@ -1443,6 +1729,7 @@ Engineered Region is represented by a plain rectangle suggesting a blank slate t + @@ -1474,11 +1761,43 @@ 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): ![example of usage](polypeptide-region-example.png) - *This section left deliberately blank* + 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. + +![example of usage](polypeptide-2a-example.png) + + + + + + + + + + + + + + + + + + + + + + + The inert DNA spacer glyph is a circle with an X in its middle, suggesting the intent to cancel possible interactions: + InertDNASpacerGlyph + inert-dna-spacer-specification.png + SBOL-visual/Glyphs/inert-dna-spacer + true + Inserted 5' sequence intended to reduce effect of upstream genetic context on promoter behavior. + *this section deliberately blank* + @@ -1507,6 +1826,7 @@ This glyph is intended to be used in composition or superposition with the glyph + The Omitted Detail glyph is a break in the backbone with an ellipsis to indicate that material would normally be in that location: OmittedDetailGlyph omitted-detail-specification.png @@ -1518,6 +1838,7 @@ This glyph is intended to be used in composition or superposition with the glyph + @@ -1634,6 +1955,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1662,6 +1984,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1701,6 +2024,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1743,6 +2067,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1785,6 +2110,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1840,7 +2166,11 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s - An alternative is the SBGN "cornered rectangle" glyph for a complex: + 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: + +![glyph example](complex-pdna-specification.png) + +An alternative is the SBGN "cornered rectangle" glyph for a complex: ComplexGlyphAlternative complex-sbgn-specification.png SBOL-visual/Glyphs/FunctionalComponents/complex @@ -1848,6 +2178,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1890,6 +2221,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1920,6 +2252,7 @@ Alternate BioPAX definition: Protein: http://www.biopax.org/release/biopax-level + @@ -1964,6 +2297,7 @@ Alternate BioPAX definition: PhysicalEntity: http://www.biopax.org/release/biopa + 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: @@ -1977,6 +2311,7 @@ An alternative option is to have a bracket, suggesting information that needs to + @@ -2046,6 +2381,7 @@ Alternate BioPAX definition: Small Molecule: http://www.biopax.org/release/biopa + @@ -2162,6 +2498,7 @@ Alternate BioPAX definition: Small Molecule: http://www.biopax.org/release/biopa + @@ -2190,6 +2527,7 @@ Alternate BioPAX definition: Small Molecule: http://www.biopax.org/release/biopa + @@ -2230,5 +2568,14 @@ Alternate BioPAX definition: Small Molecule: http://www.biopax.org/release/biopa SBOL-visual/Glyphs/assembly-scar + + + + + + + + +