diff --git a/Ontology/README.md b/Ontology/README.md index fdb31f3..274a5c4 100644 --- a/Ontology/README.md +++ b/Ontology/README.md @@ -19,27 +19,27 @@ SBOL-VO is available as an RDF file. [Click here](http://synbiodex.github.io/SBO **An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}"}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: -* -* -* +* +* +* The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending "/svg" or "/png" to the query interface : -* -* +* +* **Mapping glyphs to terms from ontologies**: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the `http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"}` interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term's distance to the query term. URL examples below return information about AptamerGlyph. -* -* +* +* **Searching for glyphs**: The SBOL-VO-WS can be used to search for glyphs using the `http://{SBOL-VO-WS}/query/{ONTOLOGY_TERM}"}` REST interface. This query interface is the reverse of the mapping interface and returns information about glyphs using a query term and for all its child terms. Glyphs are searched for by using a term from the SBOL-Visual Ontology, the Sequence Ontology or the Systems Biology Ontology. Examples: * Returning information about the CDSGlyph and CDSAlternativeGlyph terms: - * - * + * + * * Returning information abut all glyphs that represent molecular interactions: - * + * **Retrieving metadata about glyphs**: The SBOL-VO-WS can also be used to retrieve metadata about SBOL Visual glyphs, using the for glyphs using the `http://{SBOL-VO-WS}/metadata/{SBOL-VO-TERM}"}` REST interface. Examples: -* +* diff --git a/Ontology/v2/sbol-vo.html b/Ontology/v2/sbol-vo.html index 190e9ec..3ecd769 100644 --- a/Ontology/v2/sbol-vo.html +++ b/Ontology/v2/sbol-vo.html @@ -79,9 +79,12 @@

Classes

  • HexagonSimpleChemicalGlyph
  • InhibitionGlyph
  • InsulatorGlyph
    • +
  • InteractionGlyph
    • +
  • InteractionNodeGlyph
  • IntronGlyph
  • MacromoleculeGlyph
  • MacromoleculeGlyphAlternative
    • +
  • MolecularSpeciesGlyph
  • NoGlyphAssignedGlyph
  • NoGlyphAssignedSpeciesGlyph
  • Non-CodingRNAGeneGlyph
    • @@ -110,6 +113,7 @@

    Classes

  • RnaBiopolymerLocationGlyphAlternative
  • RnaCleavageSiteGlyph
  • RnaStabilityElementGlyph
    • +
  • SequenceFeatureGlyph
  • SignatureGlyph
  • SimpleChemicalGlyph
  • SimpleChemicalGlyphAlternative
    • @@ -148,6 +152,10 @@

    AptamerGlyphc Glyph c +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -185,6 +193,10 @@

    AssemblyScarGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -260,18 +272,8 @@

    AssociationGlyphcc

    - isGlyphOf - op - some - interaction -
    -
    - isGlyphOf - op - some - type - some - s b o:0000177 + InteractionNodeGlyph + c
    default glyph @@ -300,6 +302,10 @@

    BiopolymerLocationGlyphcGlyph c +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -364,6 +370,10 @@

    BluntRestrictionSiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -401,6 +411,10 @@

    CDSGlyphc bac Glyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -475,6 +489,10 @@

    ChromosomalLocusGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -512,6 +530,10 @@

    CircularPlasmidGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -553,6 +575,10 @@

    CleavageSiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -625,6 +651,10 @@

    ComplexGlyphc Glyph c

    +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op @@ -704,6 +734,10 @@

    CompositeGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    default glyph
    @@ -728,18 +762,8 @@

    ControlGlyphc c
    - isGlyphOf - op - some - interaction -
    -
    - isGlyphOf - op - some - type - some - s b o:0000168 + InteractionGlyph + c
    default glyph @@ -765,18 +789,8 @@

    DegradationGlyphcc
    - isGlyphOf - op - some - interaction -
    -
    - isGlyphOf - op - some - type - some - s b o:0000179 + InteractionGlyph + c
    default glyph @@ -802,18 +816,8 @@

    DissociationGlyphcc
    - isGlyphOf - op - some - interaction -
    -
    - isGlyphOf - op - some - type - some - s b o:0000180 + InteractionNodeGlyph + c
    default glyph @@ -988,6 +992,10 @@

    Double-StrandedNucleicAcidGlyphcGlyph c +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op @@ -1062,6 +1070,10 @@

    EngineeredRegionGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1284,10 +1296,16 @@

    Glyphc back t c, InsulatorGlyph c, + InteractionGlyph + c, + InteractionNodeGlyph + c, IntronGlyph c, MacromoleculeGlyph c, + MolecularSpeciesGlyph + c, NoGlyphAssignedGlyph c, NoGlyphAssignedSpeciesGlyph @@ -1320,6 +1338,8 @@

    Glyphc back t c, RibosomeEntrySiteGlyph c, + SequenceFeatureGlyph + c, SignatureGlyph c, SimpleChemicalGlyph @@ -1391,18 +1411,8 @@

    InhibitionGlyphcc

    - isGlyphOf - op - some - interaction -
    -
    - isGlyphOf - op - some - type - some - s b o:0000169 + InteractionGlyph + c
    default glyph @@ -1427,6 +1437,10 @@

    InsulatorGlyphcGlyph c +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1449,6 +1463,60 @@

    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 +
    +
    +

    IntronGlyphc back to ToC or Class ToC

    @@ -1464,6 +1532,10 @@

    IntronGlyphc Glyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1501,6 +1573,10 @@

    MacromoleculeGlyphcGlyph c

    +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op @@ -1560,6 +1636,41 @@

    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 +1687,10 @@

    NoGlyphAssignedGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    default glyph
    @@ -1600,6 +1715,10 @@

    NoGlyphAssignedSpeciesGlyphcGlyph c +
    + MolecularSpeciesGlyph + c +
    default glyph
    @@ -1623,6 +1742,10 @@

    Non-CodingRNAGeneGlyphcGlyph c +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1668,6 +1791,10 @@

    OmittedDetailGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    default glyph
    @@ -1691,6 +1818,10 @@

    OperatorBindingSiteGlyphcGlyph c +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1736,6 +1867,10 @@

    OriginofReplicationGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1773,6 +1908,10 @@

    OriginofTransferGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1810,6 +1949,10 @@

    OverhangSiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1888,6 +2031,10 @@

    PolyASiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1925,6 +2072,10 @@

    PolypeptideRegionGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -1962,6 +2113,10 @@

    PrimerBindingSiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -2000,18 +2155,8 @@

    ProcessGlyphc c

    - isGlyphOf - op - some - interaction -
    -
    - isGlyphOf - op - some - type - some - s b o:0000375 + InteractionGlyph + c
    default glyph @@ -2037,18 +2182,8 @@

    ProcessNodeGlyphcc
    - isGlyphOf - op - some - interaction -
    -
    - isGlyphOf - op - some - type - some - s b o:0000375 + InteractionNodeGlyph + c
    default glyph @@ -2073,6 +2208,10 @@

    PromoterSiteGlyphcGlyph c +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -2229,6 +2368,10 @@

    ProteinGlyphc Glyph c

    +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op @@ -2401,6 +2544,10 @@

    RibosomeEntrySiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -2579,6 +2726,87 @@

    RnaStabilityElementGlyphc +

    SignatureGlyphc back to ToC or Class ToC

    @@ -2594,6 +2822,10 @@

    SignatureGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -2631,6 +2863,10 @@

    SimpleChemicalGlyphcGlyph c

    +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op @@ -2710,6 +2946,10 @@

    Single-StrandedNucleicAcidGlyphcGlyph c

    +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op @@ -2784,6 +3024,10 @@

    SpecificRecombinationSiteGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -2825,6 +3069,10 @@

    StabilityElementGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -2889,6 +3137,10 @@

    StickyEndRestrictionEnzymeCleavageSiteGlyphGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -2938,18 +3190,8 @@

    StimulationGlyphcc

    - isGlyphOf - op - some - interaction -
    -
    - isGlyphOf - op - some - type - some - s b o:0000170 + InteractionGlyph + c
    default glyph @@ -2978,6 +3220,10 @@

    StopSiteGlyphcGlyph c +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -3040,6 +3286,10 @@

    TerminatorGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -3337,6 +3587,10 @@

    UnspecifiedGlyphcGlyph c

    +
    + SequenceFeatureGlyph + c +
    isGlyphOf op @@ -3411,6 +3665,10 @@

    UnspecifiedSpeciesGlyphcGlyph c

    +
    + MolecularSpeciesGlyph + c +
    isGlyphOf op diff --git a/Ontology/v2/sbol-vo.rdf b/Ontology/v2/sbol-vo.rdf index f3c78e5..16aeea4 100644 --- a/Ontology/v2/sbol-vo.rdf +++ b/Ontology/v2/sbol-vo.rdf @@ -10,11 +10,6 @@ - - - Glyph - - isGlyphOf @@ -23,6 +18,10 @@ hasGlyph + + isAlternativeOf + + defaultGlyph @@ -35,10 +34,6 @@ recommended - - isAlternativeOf - - prototypicalExample @@ -47,25 +42,34 @@ notes + + + Glyph + + + + + InteractionGlyph + + + + + InteractionNodeGlyph + + + + + MolecularSpeciesGlyph + + + + + SequenceFeatureGlyph + + - - - - - - - - - - - - - - - - - + An arrow whose head is a bar, suggesting blocking: InhibitionGlyph inhibition-specification.png @@ -77,23 +81,7 @@ - - - - - - - - - - - - - - - - - + Identical to the Process glyph, but with an empty set at the sink of the arrowhead: DegradationGlyph degradation-specification.png @@ -105,23 +93,7 @@ - - - - - - - - - - - - - - - - - + An arrow with an head that is empty or of a different color than the line: StimulationGlyph stimulation-specification.png @@ -133,23 +105,7 @@ - - - - - - - - - - - - - - - - - + An arrow with a diamond head: ControlGlyph control-specification.png @@ -161,23 +117,7 @@ - - - - - - - - - - - - - - - - - + An arrow with a filled head the same color as the line: ProcessGlyph process-specification.png @@ -193,6 +133,7 @@ + @@ -321,6 +262,7 @@ Despite both being stem-top glyphs, Biopolymer Location is not a parent to Stabi + @@ -349,6 +291,7 @@ Despite both being stem-top glyphs, Biopolymer Location is not a parent to Stabi + @@ -377,6 +320,7 @@ Despite both being stem-top glyphs, Biopolymer Location is not a parent to Stabi + @@ -418,6 +362,7 @@ Examples of RECOMMENDED usage: + @@ -446,6 +391,7 @@ Examples of RECOMMENDED usage: + @@ -474,23 +420,7 @@ Examples of RECOMMENDED usage: - - - - - - - - - - - - - - - - - + A circular node: AssociationGlyph association-specification.png @@ -502,23 +432,7 @@ Examples of RECOMMENDED usage: - - - - - - - - - - - - - - - - - + An circular node inside another circle DissociationGlyph dissociation-specification.png @@ -530,23 +444,7 @@ Examples of RECOMMENDED usage: - - - - - - - - - - - - - - - - - + A square node: ProcessNodeGlyph process-specification.png @@ -563,6 +461,7 @@ The assocated SBO term also covers: + @@ -773,6 +672,7 @@ Describing a Restriction Enzyme Cleavage Site with a vertical line glyph on a DN + @@ -889,6 +789,7 @@ Describing a Restriction Enzyme Cleavage Site with a vertical line glyph on a DN + @@ -1047,6 +948,7 @@ The 5' Sticky Restriction Site, 3' Sticky Restriction Site, and Blunt Restrictio + @@ -1075,6 +977,7 @@ The 5' Sticky Restriction Site, 3' Sticky Restriction Site, and Blunt Restrictio + @@ -1103,6 +1006,7 @@ The 5' Sticky Restriction Site, 3' Sticky Restriction Site, and Blunt Restrictio + @@ -1131,6 +1035,7 @@ The 5' Sticky Restriction Site, 3' Sticky Restriction Site, and Blunt Restrictio + @@ -1170,6 +1075,7 @@ The 5' Sticky Restriction Site, 3' Sticky Restriction Site, and Blunt Restrictio + @@ -1213,6 +1119,7 @@ Unspecified is RECOMMENDED to be represented by the unicode "replacement charact + @@ -1250,6 +1157,7 @@ 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 +1178,7 @@ and a composite with an Engineered Region of otherwise unspecified content: + @@ -1300,6 +1209,7 @@ and a composite with an Engineered Region of otherwise unspecified content: + @@ -1342,6 +1252,7 @@ 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 +1269,7 @@ For example, at present there is no glyph recommended for representing a transpo + @@ -1386,6 +1298,7 @@ For example, at present there is no glyph recommended for representing a transpo + @@ -1414,6 +1327,7 @@ For example, at present there is no glyph recommended for representing a transpo + @@ -1443,6 +1357,7 @@ Engineered Region is represented by a plain rectangle suggesting a blank slate t + @@ -1479,6 +1394,7 @@ This glyph is intended to be used in composition or superposition with the glyph + @@ -1507,6 +1423,7 @@ 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 +1435,7 @@ This glyph is intended to be used in composition or superposition with the glyph + @@ -1634,6 +1552,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1662,6 +1581,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1701,6 +1621,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1743,6 +1664,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1785,6 +1707,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1848,6 +1771,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1890,6 +1814,7 @@ Transcription/Translation End Point is a "stem-top" glyph for describing small s + @@ -1920,6 +1845,7 @@ Alternate BioPAX definition: Protein: http://www.biopax.org/release/biopax-level + @@ -1964,6 +1890,7 @@ 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 +1904,7 @@ An alternative option is to have a bracket, suggesting information that needs to + @@ -2046,6 +1974,7 @@ Alternate BioPAX definition: Small Molecule: http://www.biopax.org/release/biopa + @@ -2162,6 +2091,7 @@ Alternate BioPAX definition: Small Molecule: http://www.biopax.org/release/biopa + @@ -2190,6 +2120,7 @@ Alternate BioPAX definition: Small Molecule: http://www.biopax.org/release/biopa + @@ -2230,5 +2161,14 @@ Alternate BioPAX definition: Small Molecule: http://www.biopax.org/release/biopa SBOL-visual/Glyphs/assembly-scar + + + + + + + + +