diff --git a/Ontology/v2/sbol-vo.rdf b/Ontology/v2/sbol-vo.rdf index f3c78e5..355adaf 100644 --- a/Ontology/v2/sbol-vo.rdf +++ b/Ontology/v2/sbol-vo.rdf @@ -1,1471 +1,1794 @@ - - - - - - - - - Glyph - - - - isGlyphOf - - - - hasGlyph - - - - defaultGlyph - - - - glyphDirectory - - - - recommended - - - - isAlternativeOf - - - - prototypicalExample - - - - notes - - - - - - - - - - - - - - - - - - - - - - An arrow whose head is a bar, suggesting blocking: - InhibitionGlyph - inhibition-specification.png - SBOL-visual/Glyphs/Interactions/inhibition - true - Repression of pTAL14 promoter by TAL14 - *This section left intentionally blank* - - - - - - - - - - - - - - - - - - - - - - Identical to the Process glyph, but with an empty set at the sink of the arrowhead: - DegradationGlyph - degradation-specification.png - SBOL-visual/Glyphs/Interactions/degradation - true - Cellular recycling of mRNA - *This section left intentionally blank* - - - - - - - - - - - - - - - - - - - - - - An arrow with an head that is empty or of a different color than the line: - StimulationGlyph - stimulation-specification.png - SBOL-visual/Glyphs/Interactions/stimulation - true - Activation of pTAL14 promoter by Gal4VP16 activator - *This section left intentionally blank* - - - - - - - - - - - - - - - - - - - - - - An arrow with a diamond head: - ControlGlyph - control-specification.png - SBOL-visual/Glyphs/Interactions/control - true - Inversion of a sequence flanked by FRT sites by FLP recombinase - *This section left intentionally blank* - - - - - - - - - - - - - - - - - - - - - - An arrow with a filled head the same color as the line: - ProcessGlyph - process-specification.png - SBOL-visual/Glyphs/Interactions/process - true - Production of Green Fluorescent Protein (GFP) from the gfp Coding Sequence - The assocated SBO term also covers: + + + + + -- SBO:0000176 Biochemical Reaction -- SBO:0000589 Genetic Production (source is DNAcomponent, sink is usually RNA or Macromolecule) -- SBO:0000177 Non-covalent Binding (sink is a Complex) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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) - StabilityElementGlyph - stem-top-specification.png - SBOL-visual/Glyphs/stability-element - PEST tag, 3’ Hairpin - RNA Stability Element glyph was previously also associated with SO:0001957, but that SO term has been declared obsolete in Sequence Ontology. + -This glyph is not backwards compatible with SBOL Visual 1.0. + -Despite both being stem-top glyphs, Biopolymer Location is not a parent to Stability Element, since the length of a Stability Element is typically multiple bases / amino acids. - - - - - 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): - DnaStabilityElementGlyph - dna-stability-element-specification.png - SBOL-visual/Glyphs/stability-element - true - - - - - - - - - - - - - - - - - - - - - - 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): - RnaStabilityElementGlyph - rna-stability-element-specification.png - SBOL-visual/Glyphs/stability-element - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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): - ProteinStabilityElementGlyph - protein-stability-element-specification.png - SBOL-visual/Glyphs/stability-element - true - - - - - - - - - - - - - - - - - - - - - - The ribosome entry promoter glyph is a half-ovoid sitting on the backbone, suggesting an attached ribosome beginning transcription: - RibosomeEntrySiteGlyph - ribosome-entry-site-specification.png - SBOL-visual/Glyphs/ribosome-entry-site - true - T7g10 ribosome binding site - *this section deliberately blank* - - - - - - - - - - - - - - - - - - - - - - The aptamer glyph is a cartoon diagram of a prototypical nucleic acid secondary structure for an aptamer: - AptamerGlyph - aptamer-specification.png - SBOL-visual/Glyphs/aptamer - true - theophylline aptamer - *this section deliberately blank* - - - - - - - - - - - - - - - - - - - - - - -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: - ChromosomalLocusGlyph - chromosomal-locus-specification.png - SBOL-visual/Glyphs/chromosomal-locus - true - _B. subtilis_ amyE locus - Complementary "left" and "right" versions of this glyph SHOULD be used together, flanking the region whose genomic context is being described. -The Omitted Detail glyph SHOULD generally be contatenated to indicate that there is information about the chromosome not being represented. + -Examples of RECOMMENDED usage: + + defaultGlyph + + -- A functional unit consisting of promoter, ribosome entry site, CDS, and terminator, all integrated together into the chromosome: -![glyph specification](chromosomal-locus-example.png) + -- Two functional units, one integrated into the amyE locus, another integrated into the ganA locus: + + glyphDirectory + + -![glyph specification](chromosomal-locus-example2.png) - - - - - - - - - - - - - - - - - - - - - - The signature glyph is a box sitting atop the backbone with an X and line inside it, suggesting a signature on a form: - SignatureGlyph - signature-specification.png - SBOL-visual/Glyphs/signature - true - DNA Barcode - *this section deliberately blank* - - - - - - - - - - - - - - - - - - - - - - The polyA site glyph is a sequence of As sitting atop the backbone: - PolyASiteGlyph - polyA-specification.png - SBOL-visual/Glyphs/polyA - true - polyA tail on mammalian coding sequence - *This section left deliberately blank* - - - - - - - - - - - - - - - - - - - - - - A circular node: - AssociationGlyph - association-specification.png - SBOL-visual/Glyphs/InteractionNodes/association - true - Association of gRNA and Cas9 to form an active CRISPR complex. - The association glyph is based on the SBGN Process Description association glyph. - - - - - - - - - - - - - - - - - - - - - - An circular node inside another circle - DissociationGlyph - dissociation-specification.png - SBOL-visual/Glyphs/InteractionNodes/dissociation - true - Dissociation of an active CRISPR complex into gRNA and Cas9. - The dissociation glyph is based on the SBGN Process Description dissociation glyph. - - - - - - - - - - - - - - - - - - - - - - A square node: - ProcessNodeGlyph - process-specification.png - SBOL-visual/Glyphs/InteractionNodes/process - true - Association of gRNA and Cas9 to form an active CRISPR complex. - The process glyph is based on the SBGN Process Description process glyph. -The assocated SBO term also covers: + -- SBO:0000176 Biochemical Reaction -- SBO:0000177 Non-covalent Binding (sink is a Complex) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Biopolymer Location is a "stem-top" glyph for describing small sites. In this system: + + notes + + + + + + + + prototypicalExample + + + + + + + + recommended + + + + + + + + + + + + + hasGlyph + + + + + + + + isAlternativeOf + + + + + + + + isGlyphOf + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -- 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) - BiopolymerLocationGlyph - stem-top-specification.png - SBOL-visual/Glyphs/location - CRISPR-targeted insertion site, protease site, mutation site - Biopolymer Location is a general glyph for all zero- and one-length sequence features, including insertion and deletion sites and X-ase cut sites. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + aptamer-specification.png + SBOL-visual/Glyphs/aptamer + *this section deliberately blank* + theophylline aptamer + true + The aptamer glyph is a cartoon diagram of a prototypical nucleic acid secondary structure for an aptamer: + AptamerGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + assembly-scar-specification.png + SBOL-visual/Glyphs/assembly-scar + *this section deliberately blank* + Ligated sticky ends following BioBrick assembly. + true + 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: + AssemblyScarGlyph + + + + + + + + + + + + + + + assembly-scar-specification-doublestrand.png + SBOL-visual/Glyphs/assembly-scar + With a double-stranded backbone: + AssemblyScarGlyphAlternative + + + + + + + + + + + + + + + + + + + + + + + + + + association-specification.png + SBOL-visual/Glyphs/InteractionNodes/association + The association glyph is based on the SBGN Process Description association glyph. + Association of gRNA and Cas9 to form an active CRISPR complex. + true + A circular node: + AssociationGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + stem-top-specification.png + SBOL-visual/Glyphs/location + Biopolymer Location is a general glyph for all zero- and one-length sequence features, including insertion and deletion sites and X-ase cut sites. Note also that Biopolymer Location does not cover stability elements, since their length is typically multiple bases / amino acids. Describing a Restriction Enzyme Cleavage Site with a vertical line glyph on a DNA backbone (as done previously in SBOL Visual 1.0 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 RECOMMENDED top for Biopolymer Location is a circle, reminiscent of a pin stuck into a location (in order: DNA, RNA, Protein): - DnaBiopolymerLocationGlyph - location-dna-specification.png - SBOL-visual/Glyphs/location - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The RECOMMENDED top for Biopolymer Location is a circle, reminiscent of a pin stuck into a location (in order: DNA, RNA, Protein): - RnaBiopolymerLocationGlyph - location-rna-specification.png - SBOL-visual/Glyphs/location - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The RECOMMENDED top for Biopolymer Location is a circle, reminiscent of a pin stuck into a location (in order: DNA, RNA, Protein): - ProteinBiopolymerLocationGlyph - location-protein-specification.png - SBOL-visual/Glyphs/location - true - - - - - - - - - - - An alternative is to have "nothing" for the top, just an extended version of the stem itself (in order: DNA, RNA, Protein): - DnaBiopolymerLocationGlyphAlternative - location-dna-no-top-specification.png - SBOL-visual/Glyphs/location - - - - - - - - - - - An alternative is to have "nothing" for the top, just an extended version of the stem itself (in order: DNA, RNA, Protein): - RnaBiopolymerLocationGlyphAlternative - location-rna-no-top-specification.png - SBOL-visual/Glyphs/location - - - - - - - - - - - An alternative is to have "nothing" for the top, just an extended version of the stem itself (in order: DNA, RNA, Protein): - ProteinBiopolymerLocationGlyphAlternative - location-protein-no-top-specification.png - SBOL-visual/Glyphs/location - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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): - StickyEndRestrictionEnzymeCleavageSiteGlyph - EcoRI restriction site. - - - - - - - - - - - - - - - - - - - - - - - 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): - FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph - five-prime-sticky-restriction-site-specification.png - SBOL-visual/Glyphs/sticky-restriction-site - true - - - - - - - - - - - - - - - - - - - - - - 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): - ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph - three-prime-sticky-restriction-site-specification.png - SBOL-visual/Glyphs/sticky-restriction-site - true - - - - - - - - - - - and between strands of a double backbone (in order: five-prime double stranded, three-prime double stranded): - FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphAlternative - five-prime-sticky-restriction-site-specification-doublestrand.png - SBOL-visual/Glyphs/sticky-restriction-site - - - - - - - - - - - and between strands of a double backbone (in order: five-prime double stranded, three-prime double stranded): - ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphAlternative - three-prime-sticky-restriction-site-specification-doublestrand.png - SBOL-visual/Glyphs/sticky-restriction-site - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Cleavage Site is a "stem-top" glyph for describing small sites. In this system: + CRISPR-targeted insertion site, protease site, mutation site + +Biopolymer Location 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 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) - CleavageSiteGlyph - stem-top-specification.png - SBOL-visual/Glyphs/cleavage-site - RNAse E site, BamHI - SO:0000061 (which was previously associated with Restriction Enzyme Recognition Site in SBOL Visual 1.0) is no longer associated with the DNA Cleavage glyph in SBOL Visual 2, as SO:0000061 refers to the binding site and not the location of cleavage. + BiopolymerLocationGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + blunt-restriction-site-specification.png + SBOL-visual/Glyphs/blunt-restriction-site + *this section deliberately blank* + EcoRV restriction site + true + The blunt restriction site glyph is an image of two brackets facing away from one another to make a smooth-edged gap: + BluntRestrictionSiteGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + cds-specification.png + SBOL-visual/Glyphs/cds + *this section deliberately blank* + α-Hemoglobin coding sequence + true + The coding sequence glyph is a "box" with one side bent out arrow-like to show direction: + CDSGlyph + + + + + + + + + + + + + + + cds-arrow-specification.png + SBOL-visual/Glyphs/cds + Alternately, CDS may be represented as a block arrow: + CDSGlyphAlternative + + + + + + + + + + + + + + + + + + + + + + + + + + chromosomal-locus-specification.png + SBOL-visual/Glyphs/chromosomal-locus + Complementary "left" and "right" versions of this glyph SHOULD be used together, flanking the region whose genomic context is being described. -The Ribonuclease Site, Protease Site, and Restriction Enzyme Recognition Site glyphs from SBOL Visual 1.0 are now replaced by the Cleavage Site glyph with the appropriate stem. +The Omitted Detail glyph SHOULD generally be contatenated to indicate that there is information about the chromosome not being represented. -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. +Examples of RECOMMENDED usage: -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 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): - DnaCleavageSiteGlyph - nuclease-site-specification.png - SBOL-visual/Glyphs/cleavage-site - true - - - - - - - - - - - - - - - - - - - - - - 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): - RnaCleavageSiteGlyph - ribonuclease-site-specification.png - SBOL-visual/Glyphs/cleavage-site - true - - - - - - - - - - - - - - - - - - - - - - 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): - ProteinCleavageSiteGlyph - protease-site-specification.png - SBOL-visual/Glyphs/cleavage-site - true - - - - - - - - - - - - - - - - - - - - - - The origin of replication glyph is a circle suggesting the "bulge" opened in a piece of circular DNA when replication is beginning: - OriginofReplicationGlyph - origin-of-replication-specification.png - SBOL-visual/Glyphs/origin-of-replication - true - human herpesvirus-6 OOR - The label on an origin of replication glyph is RECOMMENDED as the location to label either specifically the identity of the origin of replication or the name of the entire plasmid backbone more generally. - - - - - - - - - - - - - - - - - - - - - - The primer binding site glyph is a line with a bent end suggesting a partially complementary strand of nucleic acid attaching to the backbone: - PrimerBindingSiteGlyph - primer-binding-site-specification.png - SBOL-visual/Glyphs/primer-binding-site - true - seq-F - *this section deliberately blank* - - - - - - - - - - - - - - - - - - - - - - The terminator is a T sitting atop the backbone: - TerminatorGlyph - terminator-specification.png - SBOL-visual/Glyphs/terminator - true - T1 terminator - *this section deliberately blank* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The non-coding RNA glyph is a rectangular box whose top is a single-stranded RNA "wiggle": - Non-CodingRNAGeneGlyph - ncrna-specification.png - SBOL-visual/Glyphs/non-coding-rna - true - gRNA sequence for targeting a dCas9 repressor - *This section left deliberately blank* - - - - - - - - - - - - - - - - - - - - - - -Unspecified is RECOMMENDED to be represented by the unicode "replacement character" glyph, indicating a missing or invalid symbol: - UnspecifiedGlyph - replacement-glyph-specification.png - SBOL-visual/Glyphs/unspecified - true - An anonymous sequence that is missing any information about its nature or intended purpose. - The Unspecified glyph is intended for showing where a sequence's role is missing (or, equivalently, given only the uninformative "Sequence Feature" root role). It should never appear with well-curated designs or diagrams. - - - - - - - - - - - A half-rounded rectangle, the SBGN glyph for a nucleic acid, is an alternative: - UnspecifiedGlyphAlternative - halfround-rectangle-specification.png - SBOL-visual/Glyphs/unspecified - - - - - - - - - - - - - - - - - - - - - - -The glyph to indicate embedding in a plasmid is a turn of the backbone indicating its circular structure: - CircularPlasmidGlyph - circular-plasmid-specification.png - SBOL-visual/Glyphs/circular-plasmid - true - _E. coli_ p15A plasmid - Note that for SBOL data representations, circularity SHOULD also be indicated with a type of SO:0000988. +- A functional unit consisting of promoter, ribosome entry site, CDS, and terminator, all integrated together into the chromosome: -Complementary "left" and "right" versions of this glyph SHOULD be used together, flanking the region whose genomic context is being described. +![glyph specification](chromosomal-locus-example.png) + +- Two functional units, one integrated into the amyE locus, another integrated into the ganA locus: + +![glyph specification](chromosomal-locus-example2.png) + _B. subtilis_ amyE locus + true + +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: + ChromosomalLocusGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + circular-plasmid-specification.png + SBOL-visual/Glyphs/circular-plasmid + Note that for SBOL data representations, circularity SHOULD also be indicated with a type of SO:0000988. + +Complementary "left" and "right" versions of this glyph SHOULD be used together, flanking the region whose genomic context is being described. The Omitted Detail glyph SHOULD generally be concatenated to indicate that there is information about the plasmid not being represented. Example of RECOMMENDED usage: a plasmid containing a functional unit consisting of promoter, ribosome entry site, CDS, and terminator: ![glyph specification](circular-plasmid-example.png) - + _E. coli_ p15A plasmid + true + +The glyph to indicate embedding in a plasmid is a turn of the backbone indicating its circular structure: + CircularPlasmidGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + stem-top-specification.png + SBOL-visual/Glyphs/cleavage-site + SO:0000061 (which was previously associated with Restriction Enzyme Recognition Site in SBOL Visual 1.0) is no longer associated with the DNA Cleavage glyph in SBOL Visual 2, as SO:0000061 refers to the binding site and not the location of cleavage. + +The Ribonuclease Site, Protease Site, and Restriction Enzyme Recognition Site glyphs from SBOL Visual 1.0 are now replaced by the Cleavage Site glyph with the appropriate stem. - - - -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 - composite-specification.png - SBOL-visual/Glyphs/composite - true - An "expression cassette" containing a ribosome entry site, coding sequence, and terminator. +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. -In this case, the recommended "base" glyph would be Engineered Region. - An "abbreviated" representation of composite, simply indicating that more structure is available, can be made by using short lines and placing only an Omitted Detail glyph in the secondary backbone. For example, here is an example of an abbreviated composite promoter: +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. + RNAse E site, BamHI + 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) + CleavageSiteGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + Alternate BioPAX definition: Complex: http://www.biopax.org/release/biopax-level3.owl#Complex + Arabinose bound to AraC + 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): + ComplexGlyph + + + + + + + + + + + + complex-sbgn-specification.png + SBOL-visual/Glyphs/FunctionalComponents/complex + An alternative is the SBGN "cornered rectangle" glyph for a complex: + ComplexGlyphAlternative + + + + + + + + + composite-specification.png + SBOL-visual/Glyphs/composite + An "abbreviated" representation of composite, simply indicating that more structure is available, can be made by using short lines and placing only an Omitted Detail glyph in the secondary backbone. For example, here is an example of an abbreviated composite promoter: ![glyph specification](abbreviated-composite-example.png) and a composite with an Engineered Region of otherwise unspecified content: ![glyph specification](abbreviated-composite-example2.png) - - - - - - - - - - - - - - - - - - - - - - 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: - IntronGlyph - intron-specification.png - SBOL-visual/Glyphs/intron - true - Example of a coding sequence with three domains: an N-tag (blue), C-tag (yellow), and internal region (red) interrupted by an intron that includes a gRNA non-coding RNA sequence (green): + An "expression cassette" containing a ribosome entry site, coding sequence, and terminator. + +In this case, the recommended "base" glyph would be Engineered Region. + true + +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 + + + + + + + + + + + + + + + + + + + + + + + + + + control-specification.png + SBOL-visual/Glyphs/Interactions/control + *This section left intentionally blank* + Inversion of a sequence flanked by FRT sites by FLP recombinase + true + An arrow with a diamond head: + ControlGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + degradation-specification.png + SBOL-visual/Glyphs/Interactions/degradation + *This section left intentionally blank* + Cellular recycling of mRNA + true + Identical to the Process glyph, but with an empty set at the sink of the arrowhead: + DegradationGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + dissociation-specification.png + SBOL-visual/Glyphs/InteractionNodes/dissociation + The dissociation glyph is based on the SBGN Process Description dissociation glyph. + Dissociation of an active CRISPR complex into gRNA and Cas9. + true + An circular node inside another circle + DissociationGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + location-dna-specification.png + SBOL-visual/Glyphs/location + true + The RECOMMENDED top for Biopolymer Location is a circle, reminiscent of a pin stuck into a location (in order: DNA, RNA, Protein): + DnaBiopolymerLocationGlyph + + + + + + + + + + + + + + + location-dna-no-top-specification.png + SBOL-visual/Glyphs/location + An alternative is to have "nothing" for the top, just an extended version of the stem itself (in order: DNA, RNA, Protein): + DnaBiopolymerLocationGlyphAlternative + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nuclease-site-specification.png + SBOL-visual/Glyphs/cleavage-site + true + 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): + DnaCleavageSiteGlyph + + + + + + + + + dna-stability-element-specification.png + SBOL-visual/Glyphs/stability-element + true + 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): + DnaStabilityElementGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + dsNA-specification.png + SBOL-visual/Glyphs/FunctionalComponents/dsNA + Alternate BioPAX definition: Dna: http://www.biopax.org/release/biopax-level3.owl#Dna + DNA fragment during assembly + true + The RECOMMENDED glyph for dsNA is a double-helix: + Double-StrandedNucleicAcidGlyph + + + + + + + + + + + + + + + na-sbgn-specification.png + SBOL-visual/Glyphs/FunctionalComponents/dsNA + An alternative is the SBGN "nucleic acid" half-round rectangle: + Double-StrandedNucleicAcidGlyphAlternative + + + + + + + + + + + + + + + + + + + + + + + + + + engineered-region-specification.png + SBOL-visual/Glyphs/engineered-region + *this section deliberately blank* + An "expression cassette" containing a ribosome entry site, coding sequence, and terminator. + true + +Engineered Region is represented by a plain rectangle suggesting a blank slate to be written upon: + EngineeredRegionGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + five-prime-overhang-specification.png + SBOL-visual/Glyphs/overhang + true + 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): + FivePrimeOverhangSiteGlyph + + + + + + + + + + + + + + + five-prime-overhang-specification-doublestrand.png + SBOL-visual/Glyphs/overhang + With a double-stranded backbone (in order: five-prime double stranded, three-prime double stranded): + FivePrimeOverhangSiteGlyphAlternative + + + + + + + + + + + + + + + + + + + + + + + + + + five-prime-sticky-restriction-site-specification.png + SBOL-visual/Glyphs/sticky-restriction-site + true + 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): + FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph + + + + + + + + + + + + + + + five-prime-sticky-restriction-site-specification-doublestrand.png + SBOL-visual/Glyphs/sticky-restriction-site + and between strands of a double backbone (in order: five-prime double stranded, three-prime double stranded): + FivePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphAlternative + + + + + + + + + Glyph + + + + + + + + + simple-chemical-hexagon-specification.png + SBOL-visual/Glyphs/FunctionalComponents/simple-chemical + true + The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon): + HexagonSimpleChemicalGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + inhibition-specification.png + SBOL-visual/Glyphs/Interactions/inhibition + *This section left intentionally blank* + Repression of pTAL14 promoter by TAL14 + true + An arrow whose head is a bar, suggesting blocking: + InhibitionGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + insulator-specification.png + SBOL-visual/Glyphs/insulator + *this section deliberately blank* + RiboJ + true + The insulator glyph is a box inside another box that isolates it from its environment: + InsulatorGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intron-specification.png + SBOL-visual/Glyphs/intron + *this section deliberately blank* + Example of a coding sequence with three domains: an N-tag (blue), C-tag (yellow), and internal region (red) interrupted by an intron that includes a gRNA non-coding RNA sequence (green): ![example](intron-example.png) - *this section deliberately blank* - - - - - - - - - - - - - - - - - - - - - - The coding sequence glyph is a "box" with one side bent out arrow-like to show direction: - CDSGlyph - cds-specification.png - SBOL-visual/Glyphs/cds - true - α-Hemoglobin coding sequence - *this section deliberately blank* - - - - - - - - - - - Alternately, CDS may be represented as a block arrow: - CDSGlyphAlternative - cds-arrow-specification.png - SBOL-visual/Glyphs/cds - - - - - + true + 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: + IntronGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + macromolecule-specification.png + SBOL-visual/Glyphs/FunctionalComponents/macromolecule + *this section deliberately blank* + AraC protein, polymerized chitin + true + The macromolecule glyph is a rounded rectangle, as used in SBGN: + MacromoleculeGlyph + + + + + + + + + + + + + + + macromolecule-deprecated-specification.png + SBOL-visual/Glyphs/FunctionalComponents/macromolecule + 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: + MacromoleculeGlyphAlternative + + + + + + + + + + + + + + + + + no-glyph-assigned-specification.png + SBOL-visual/Glyphs/no-glyph-assigned + No Glyph Assigned is intended for constructs with a defined specific role that happens to not yet be covered by available approved glyphs (other than the root "Sequence Feature"). It is more likely to appear in machine-generated diagrams than in human-generated diagrams, since humans are likely to invent and use their own glyph for the purpose. + No Glyph Assigned is intended to be used for any Component that is not covered by other SBOL Visual glyphs. + +For example, at present there is no glyph recommended for representing a transposon. + true + 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: - NoGlyphAssignedGlyph - no-glyph-assigned-specification.png - SBOL-visual/Glyphs/no-glyph-assigned - true - No Glyph Assigned is intended to be used for any Component that is not covered by other SBOL Visual glyphs. + NoGlyphAssignedGlyph + + -For example, at present there is no glyph recommended for representing a transposon. - No Glyph Assigned is intended for constructs with a defined specific role that happens to not yet be covered by available approved glyphs (other than the root "Sequence Feature"). It is more likely to appear in machine-generated diagrams than in human-generated diagrams, since humans are likely to invent and use their own glyph for the purpose. - - - - - - - - - - - - - - - - - - - - - - The insulator glyph is a box inside another box that isolates it from its environment: - InsulatorGlyph - insulator-specification.png - SBOL-visual/Glyphs/insulator - true - RiboJ - *this section deliberately blank* - - - - - - - - - - - - - - - - - - - - - - The origin of transfer glyph is circular like origin of replication, but also includes an outbound arrow: - OriginofTransferGlyph - origin-of-transfer-specification.png - SBOL-visual/Glyphs/origin-of-transfer - true - oriT - *This section left deliberately blank* - - - - - - - - - - - - - - - - - - - - - - -Engineered Region is represented by a plain rectangle suggesting a blank slate to be written upon: - EngineeredRegionGlyph - engineered-region-specification.png - SBOL-visual/Glyphs/engineered-region - true - An "expression cassette" containing a ribosome entry site, coding sequence, and terminator. - *this section deliberately blank* - - - - - - - - - - - - - - - - - - - - - - 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: - PolypeptideRegionGlyph - polypeptide-region-specification.png - SBOL-visual/Glyphs/polypeptide-region - true - degradation tag on a protein coding sequence + + + + + + no-glyph-assigned-specification.png + SBOL-visual/Glyphs/FunctionalComponents/no-glyph-assigned + No Glyph Assigned is intended for molecular species with a defined specific type that happens to not yet be covered by available approved glyphs (other than the root). It is more likely to appear in machine-generated diagrams than in human-generated diagrams, since humans are likely to invent and use their own glyph for the purpose. + No Glyph Assigned is intended to be used for any chemical species whose type is not covered by other SBOL Visual glyphs. + true + 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: + NoGlyphAssignedSpeciesGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ncrna-specification.png + SBOL-visual/Glyphs/non-coding-rna + *This section left deliberately blank* + gRNA sequence for targeting a dCas9 repressor + true + The non-coding RNA glyph is a rectangular box whose top is a single-stranded RNA "wiggle": + Non-CodingRNAGeneGlyph + + + + + + + + + omitted-detail-specification.png + SBOL-visual/Glyphs/omitted-detail + This glyph actually places a "break" in the nucleic acid backbone. + A diagram in which a sequence feature is not drawn. + true + The Omitted Detail glyph is a break in the backbone with an ellipsis to indicate that material would normally be in that location: + OmittedDetailGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + operator-specification.png + SBOL-visual/Glyphs/operator + This glyph puts a "dent" in the backbone line. + Gal4 binding site in an activatable promoter. + true + The operator glyph is an open "cup" suggesting a binding location: + OperatorBindingSiteGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + origin-of-replication-specification.png + SBOL-visual/Glyphs/origin-of-replication + The label on an origin of replication glyph is RECOMMENDED as the location to label either specifically the identity of the origin of replication or the name of the entire plasmid backbone more generally. + human herpesvirus-6 OOR + true + The origin of replication glyph is a circle suggesting the "bulge" opened in a piece of circular DNA when replication is beginning: + OriginofReplicationGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + origin-of-transfer-specification.png + SBOL-visual/Glyphs/origin-of-transfer + *This section left deliberately blank* + oriT + true + The origin of transfer glyph is circular like origin of replication, but also includes an outbound arrow: + OriginofTransferGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + EcoRI site after cleavage. + 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): + OverhangSiteGlyph + + + + + + + + + simple-chemical-pentagon-specification.png + SBOL-visual/Glyphs/FunctionalComponents/simple-chemical + true + The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon): + PentagonSimpleChemicalGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + polyA-specification.png + SBOL-visual/Glyphs/polyA + *This section left deliberately blank* + polyA tail on mammalian coding sequence + true + The polyA site glyph is a sequence of As sitting atop the backbone: + PolyASiteGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + polypeptide-region-specification.png + SBOL-visual/Glyphs/polypeptide-region + *This section left deliberately blank* + degradation tag on a protein coding sequence nuclear localization tag on a protein coding sequence @@ -1474,761 +1797,1256 @@ 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* - - - - - - - - - - - - - - - - - - - - - - The blunt restriction site glyph is an image of two brackets facing away from one another to make a smooth-edged gap: - BluntRestrictionSiteGlyph - blunt-restriction-site-specification.png - SBOL-visual/Glyphs/blunt-restriction-site - true - EcoRV restriction site - *this section deliberately blank* - - - - - 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 - SBOL-visual/Glyphs/omitted-detail - true - A diagram in which a sequence feature is not drawn. - This glyph actually places a "break" in the nucleic acid backbone. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Transcription/Translation End Point is a "stem-top" glyph for describing small sites. In this system: + true + 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: + PolypeptideRegionGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + primer-binding-site-specification.png + SBOL-visual/Glyphs/primer-binding-site + *this section deliberately blank* + seq-F + true + The primer binding site glyph is a line with a bent end suggesting a partially complementary strand of nucleic acid attaching to the backbone: + PrimerBindingSiteGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + process-specification.png + SBOL-visual/Glyphs/Interactions/process + The assocated SBO term also covers: -- 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) - StopSiteGlyph - stem-top-specification.png - SBOL-visual/Glyphs/stop-site - Location where a terminator causes transcription to stop, stop codon - Note that the number of points in the asterisk is not specified, accomodating font differences. - - - - - - - - - - - - - - - - - - - - - - The Transcription/Translation End Point top is an asterisk in a circle (in order: transcription, translation): - TranscriptionStopSiteGlyph - transcription-end-specification.png - SBOL-visual/Glyphs/stop-site - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The Transcription/Translation End Point top is an asterisk in a circle (in order: transcription, translation): - TranslationStopSiteGlyph - translation-end-specification.png - SBOL-visual/Glyphs/stop-site - true - - - - - - - - - - - - - - - - - - - - - - The specific recombination site glyph is a triangle, centered on the backbone, as has appeared in a number of recombinase circuit papers: - SpecificRecombinationSiteGlyph - specific-recombination-site-specification.png - SBOL-visual/Glyphs/specific-recombination-site - true - flippase recognition target (FRT) site - *This section left deliberately blank* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The operator glyph is an open "cup" suggesting a binding location: - OperatorBindingSiteGlyph - operator-specification.png - SBOL-visual/Glyphs/operator - true - Gal4 binding site in an activatable promoter. - This glyph puts a "dent" in the backbone line. - - - - - - - - - - - - - - - - - - - - - - The macromolecule glyph is a rounded rectangle, as used in SBGN: - MacromoleculeGlyph - macromolecule-specification.png - SBOL-visual/Glyphs/FunctionalComponents/macromolecule - true - AraC protein, polymerized chitin - *this section deliberately blank* - - - - - - - - - - - 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: - MacromoleculeGlyphAlternative - macromolecule-deprecated-specification.png - SBOL-visual/Glyphs/FunctionalComponents/macromolecule - - - - - - - - - - - - - - - - - - - - - - The RECOMMENDED glyph for dsNA is a double-helix: - Double-StrandedNucleicAcidGlyph - dsNA-specification.png - SBOL-visual/Glyphs/FunctionalComponents/dsNA - true - DNA fragment during assembly - Alternate BioPAX definition: Dna: http://www.biopax.org/release/biopax-level3.owl#Dna - - - - - - - - - - - An alternative is the SBGN "nucleic acid" half-round rectangle: - Double-StrandedNucleicAcidGlyphAlternative - na-sbgn-specification.png - SBOL-visual/Glyphs/FunctionalComponents/dsNA - - - - - - - - - - - - - - - - - - - - - - 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): - ComplexGlyph - Arabinose bound to AraC - Alternate BioPAX definition: Complex: http://www.biopax.org/release/biopax-level3.owl#Complex - - - - - 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): - ProteinSmallMoleculeComplexGlyph - complex-ps-specification.png - SBOL-visual/Glyphs/FunctionalComponents/complex - true - - - - - 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): - ProteinGuideRnaComplexGlyph - complex-pr-specification.png - SBOL-visual/Glyphs/FunctionalComponents/complex - true - - - - - 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): - ProteinProteinComplexGlyph - complex-pp-specification.png - SBOL-visual/Glyphs/FunctionalComponents/complex - true - - - - - - - - An alternative is the SBGN "cornered rectangle" glyph for a complex: - ComplexGlyphAlternative - complex-sbgn-specification.png - SBOL-visual/Glyphs/FunctionalComponents/complex - - - - - - - - - - - - - - - - - - - - - - The RECOMMENDED glyph for ssNA is a wiggly line: - Single-StrandedNucleicAcidGlyph - ssNA-specification.png - SBOL-visual/Glyphs/FunctionalComponents/ssNA - true - mRNA, gRNA, siRNA - Alternate BioPAX definition: Rna: http://www.biopax.org/release/biopax-level3.owl#Rna - - - - - - - - - - - An alternative is the SBGN "nucleic acid" half-round rectangle: - Single-StrandedNucleicAcidGlyphAlternative - na-sbgn-specification.png - SBOL-visual/Glyphs/FunctionalComponents/ssNA - - - - - - - - - - - - - - - - - - - - - - The protein glyph is a "pill" shape with a rectangular body and rounded ends, representing the compact space-filling mass of many proteins: - ProteinGlyph - protein-specification.png - SBOL-visual/Glyphs/FunctionalComponents/protein - true - AraC protein - To avoid confusion with circles or ellipses, the "pill" shape SHOULD be significantly longer than it is tall, emphasizing its straight sides. +- SBO:0000176 Biochemical Reaction +- SBO:0000589 Genetic Production (source is DNAcomponent, sink is usually RNA or Macromolecule) +- SBO:0000177 Non-covalent Binding (sink is a Complex) + Production of Green Fluorescent Protein (GFP) from the gfp Coding Sequence + true + An arrow with a filled head the same color as the line: + ProcessGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + process-specification.png + SBOL-visual/Glyphs/InteractionNodes/process + The process glyph is based on the SBGN Process Description process glyph. -Alternate BioPAX definition: Protein: http://www.biopax.org/release/biopax-level3.owl#Protein - - - - - - - - - - - - - - - - - - - - - - Unspecified is RECOMMENDED to be represented by the unicode "replacement character" glyph, indicating a missing or invalid symbol: - UnspecifiedSpeciesGlyph - replacement-glyph-specification.png - SBOL-visual/Glyphs/FunctionalComponents/unspecified - true - An anonymous chemical species that is missing any information about its nature or intended purpose. - The Unspecified glyph is intended for showing where a chemical species' type is missing (or, equivalently, given only the uninformative root role). It should never appear with well-curated designs or diagrams. +The assocated SBO term also covers: -Alternate BioPAX definition: PhysicalEntity: http://www.biopax.org/release/biopax-level3.owl#PhysicalEntity - - - - - - - - - - - An alternative is the SBGN "generic species" glyph, which is an ellipse: - UnspecifiedSpeciesGlyphAlternative - generic-sbgn-specification.png - SBOL-visual/Glyphs/FunctionalComponents/unspecified - - - - - 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. +- SBO:0000176 Biochemical Reaction +- SBO:0000177 Non-covalent Binding (sink is a Complex) + Association of gRNA and Cas9 to form an active CRISPR complex. + true + A square node: + ProcessNodeGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + promoter-specification.png + SBOL-visual/Glyphs/promoter + *this section deliberately blank* + The lacYZA promoter + true + The promoter glyph is a bent arrow pointing forward, suggesting the action of transcription from its transcription start site: + PromoterSiteGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + location-protein-specification.png + SBOL-visual/Glyphs/location + true + The RECOMMENDED top for Biopolymer Location is a circle, reminiscent of a pin stuck into a location (in order: DNA, RNA, Protein): + ProteinBiopolymerLocationGlyph + + + + + + + + + + + + + + + location-protein-no-top-specification.png + SBOL-visual/Glyphs/location + An alternative is to have "nothing" for the top, just an extended version of the stem itself (in order: DNA, RNA, Protein): + ProteinBiopolymerLocationGlyphAlternative + + + + + + + + + + + + + + + + + + + + + + + + + + protease-site-specification.png + SBOL-visual/Glyphs/cleavage-site + true + 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): + ProteinCleavageSiteGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + protein-specification.png + SBOL-visual/Glyphs/FunctionalComponents/protein + To avoid confusion with circles or ellipses, the "pill" shape SHOULD be significantly longer than it is tall, emphasizing its straight sides. -An alternative option is to have a bracket, suggesting information that needs to be filled in: - NoGlyphAssignedSpeciesGlyph - no-glyph-assigned-specification.png - SBOL-visual/Glyphs/FunctionalComponents/no-glyph-assigned - true - No Glyph Assigned is intended to be used for any chemical species whose type is not covered by other SBOL Visual glyphs. - No Glyph Assigned is intended for molecular species with a defined specific type that happens to not yet be covered by available approved glyphs (other than the root). It is more likely to appear in machine-generated diagrams than in human-generated diagrams, since humans are likely to invent and use their own glyph for the purpose. - - - - - - - - - - - - - - - - - - - - - - The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon): - SimpleChemicalGlyph - Arabinose - It is RECOMMENDED that visual differentiation be maximized by associating each distinct species in a diagram with a different small geometric shape. Rotations may also be used (e.g., pentagon pointing up vs. pentagon pointing down). +Alternate BioPAX definition: Protein: http://www.biopax.org/release/biopax-level3.owl#Protein + AraC protein + true + The protein glyph is a "pill" shape with a rectangular body and rounded ends, representing the compact space-filling mass of many proteins: + ProteinGlyph + + + + + + + + + complex-pr-specification.png + SBOL-visual/Glyphs/FunctionalComponents/complex + true + 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): + ProteinGuideRnaComplexGlyph + + + + + + + + + complex-pp-specification.png + SBOL-visual/Glyphs/FunctionalComponents/complex + true + 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): + ProteinProteinComplexGlyph + + + + + + + + + complex-ps-specification.png + SBOL-visual/Glyphs/FunctionalComponents/complex + true + 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): + ProteinSmallMoleculeComplexGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + protein-stability-element-specification.png + SBOL-visual/Glyphs/stability-element + true + 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): + ProteinStabilityElementGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + ribosome-entry-site-specification.png + SBOL-visual/Glyphs/ribosome-entry-site + *this section deliberately blank* + T7g10 ribosome binding site + true + The ribosome entry promoter glyph is a half-ovoid sitting on the backbone, suggesting an attached ribosome beginning transcription: + RibosomeEntrySiteGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + location-rna-specification.png + SBOL-visual/Glyphs/location + true + The RECOMMENDED top for Biopolymer Location is a circle, reminiscent of a pin stuck into a location (in order: DNA, RNA, Protein): + RnaBiopolymerLocationGlyph + + + + + + + + + + + + + + + location-rna-no-top-specification.png + SBOL-visual/Glyphs/location + An alternative is to have "nothing" for the top, just an extended version of the stem itself (in order: DNA, RNA, Protein): + RnaBiopolymerLocationGlyphAlternative + + + + + + + + + + + + + + + + + + + + + + + + + + ribonuclease-site-specification.png + SBOL-visual/Glyphs/cleavage-site + true + 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): + RnaCleavageSiteGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + rna-stability-element-specification.png + SBOL-visual/Glyphs/stability-element + true + 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): + RnaStabilityElementGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + signature-specification.png + SBOL-visual/Glyphs/signature + *this section deliberately blank* + DNA Barcode + true + The signature glyph is a box sitting atop the backbone with an X and line inside it, suggesting a signature on a form: + SignatureGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + It is RECOMMENDED that visual differentiation be maximized by associating each distinct species in a diagram with a different small geometric shape. Rotations may also be used (e.g., pentagon pointing up vs. pentagon pointing down). It is RECOMMENDED that labels should be placed outside of the shapes rather than inside, to avoid squeezing the labels. To avoid confusion with pills or ellipses, when the small circle alternative glyph is used, it SHOULD be significantly smaller than other types of molecular species glyphs, as indicated by the recommended scale of the glyph. Alternate BioPAX definition: Small Molecule: http://www.biopax.org/release/biopax-level3.owl#SmallMolecule - - - - - The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon): - TriangleSimpleChemicalGlyph - simple-chemical-triangle-specification.png - SBOL-visual/Glyphs/FunctionalComponents/simple-chemical - true - - - - - The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon): - PentagonSimpleChemicalGlyph - simple-chemical-pentagon-specification.png - SBOL-visual/Glyphs/FunctionalComponents/simple-chemical - true - - - - - The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon): - HexagonSimpleChemicalGlyph - simple-chemical-hexagon-specification.png - SBOL-visual/Glyphs/FunctionalComponents/simple-chemical - true - - - - - - - - Alternately, a simple chemical may also be represented a small circle: - SimpleChemicalGlyphAlternative - simple-chemical-circle-specification.png - SBOL-visual/Glyphs/FunctionalComponents/simple-chemical - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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): - OverhangSiteGlyph - EcoRI site after cleavage. - - - - - - - - - - - - - - - - - - - - - - - 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): - FivePrimeOverhangSiteGlyph - five-prime-overhang-specification.png - SBOL-visual/Glyphs/overhang - true - - - - - - - - - - - - - - - - - - - - - - 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): - ThreePrimeOverhangSiteGlyph - three-prime-overhang-specification.png - SBOL-visual/Glyphs/overhang - true - - - - - - - - - - - With a double-stranded backbone (in order: five-prime double stranded, three-prime double stranded): - FivePrimeOverhangSiteGlyphAlternative - five-prime-overhang-specification-doublestrand.png - SBOL-visual/Glyphs/overhang - - - - - - - - - - - With a double-stranded backbone (in order: five-prime double stranded, three-prime double stranded): - ThreePrimeOverhangSiteGlyphAlternative - three-prime-overhang-specification-doublestrand.png - SBOL-visual/Glyphs/overhang - - - - - - - - - - - - - - - - - - - - - - The promoter glyph is a bent arrow pointing forward, suggesting the action of transcription from its transcription start site: - PromoterSiteGlyph - promoter-specification.png - SBOL-visual/Glyphs/promoter - true - The lacYZA promoter - *this section deliberately blank* - - - - - - - - - - - - - - - - - - - - - - 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: - AssemblyScarGlyph - assembly-scar-specification.png - SBOL-visual/Glyphs/assembly-scar - true - Ligated sticky ends following BioBrick assembly. - *this section deliberately blank* - - - - - - - - - - - With a double-stranded backbone: - AssemblyScarGlyphAlternative - assembly-scar-specification-doublestrand.png - SBOL-visual/Glyphs/assembly-scar - + Arabinose + The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon): + SimpleChemicalGlyph + + + + + + + + + + + + simple-chemical-circle-specification.png + SBOL-visual/Glyphs/FunctionalComponents/simple-chemical + Alternately, a simple chemical may also be represented a small circle: + SimpleChemicalGlyphAlternative + + + + + + + + + + + + + + + + + + + + + + + + + + ssNA-specification.png + SBOL-visual/Glyphs/FunctionalComponents/ssNA + Alternate BioPAX definition: Rna: http://www.biopax.org/release/biopax-level3.owl#Rna + mRNA, gRNA, siRNA + true + The RECOMMENDED glyph for ssNA is a wiggly line: + Single-StrandedNucleicAcidGlyph + + + + + + + + + + + + + + + na-sbgn-specification.png + SBOL-visual/Glyphs/FunctionalComponents/ssNA + An alternative is the SBGN "nucleic acid" half-round rectangle: + Single-StrandedNucleicAcidGlyphAlternative + + + + + + + + + + + + + + + + + + + + + + + + + + specific-recombination-site-specification.png + SBOL-visual/Glyphs/specific-recombination-site + *This section left deliberately blank* + flippase recognition target (FRT) site + true + The specific recombination site glyph is a triangle, centered on the backbone, as has appeared in a number of recombinase circuit papers: + SpecificRecombinationSiteGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + stem-top-specification.png + SBOL-visual/Glyphs/stability-element + RNA Stability Element glyph was previously also associated with SO:0001957, but that SO term has been declared obsolete in Sequence Ontology. + +This glyph is not backwards compatible with SBOL Visual 1.0. + +Despite both being stem-top glyphs, Biopolymer Location is not a parent to Stability Element, since the length of a Stability Element is typically multiple bases / amino acids. + PEST tag, 3’ Hairpin + 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) + StabilityElementGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + EcoRI restriction site. + 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): + StickyEndRestrictionEnzymeCleavageSiteGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + stimulation-specification.png + SBOL-visual/Glyphs/Interactions/stimulation + *This section left intentionally blank* + Activation of pTAL14 promoter by Gal4VP16 activator + true + An arrow with an head that is empty or of a different color than the line: + StimulationGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + stem-top-specification.png + SBOL-visual/Glyphs/stop-site + Note that the number of points in the asterisk is not specified, accomodating font differences. + Location where a terminator causes transcription to stop, stop codon + +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) + StopSiteGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + terminator-specification.png + SBOL-visual/Glyphs/terminator + *this section deliberately blank* + T1 terminator + true + The terminator is a T sitting atop the backbone: + TerminatorGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + three-prime-overhang-specification.png + SBOL-visual/Glyphs/overhang + true + 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): + ThreePrimeOverhangSiteGlyph + + + + + + + + + + + + + + + three-prime-overhang-specification-doublestrand.png + SBOL-visual/Glyphs/overhang + With a double-stranded backbone (in order: five-prime double stranded, three-prime double stranded): + ThreePrimeOverhangSiteGlyphAlternative + + + + + + + + + + + + + + + + + + + + + + + + + + three-prime-sticky-restriction-site-specification.png + SBOL-visual/Glyphs/sticky-restriction-site + true + 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): + ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyph + + + + + + + + + + + + + + + three-prime-sticky-restriction-site-specification-doublestrand.png + SBOL-visual/Glyphs/sticky-restriction-site + and between strands of a double backbone (in order: five-prime double stranded, three-prime double stranded): + ThreePrimeStickyEndRestrictionEnzymeCleavageSiteGlyphAlternative + + + + + + + + + + + + + + + + + + + + + + + + + + transcription-end-specification.png + SBOL-visual/Glyphs/stop-site + true + The Transcription/Translation End Point top is an asterisk in a circle (in order: transcription, translation): + TranscriptionStopSiteGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + translation-end-specification.png + SBOL-visual/Glyphs/stop-site + true + The Transcription/Translation End Point top is an asterisk in a circle (in order: transcription, translation): + TranslationStopSiteGlyph + + + + + + + + + simple-chemical-triangle-specification.png + SBOL-visual/Glyphs/FunctionalComponents/simple-chemical + true + The simple chemical glyph is any one of three small polygonal shapes, triangle, pentagon, or hexagon (in order: triangle, pentagon, hexagon): + TriangleSimpleChemicalGlyph + + + + + + + + + + + + + + + + + + + + + + + + + + replacement-glyph-specification.png + SBOL-visual/Glyphs/unspecified + The Unspecified glyph is intended for showing where a sequence's role is missing (or, equivalently, given only the uninformative "Sequence Feature" root role). It should never appear with well-curated designs or diagrams. + An anonymous sequence that is missing any information about its nature or intended purpose. + true + +Unspecified is RECOMMENDED to be represented by the unicode "replacement character" glyph, indicating a missing or invalid symbol: + UnspecifiedGlyph + + + + + + + + + + + + + + + halfround-rectangle-specification.png + SBOL-visual/Glyphs/unspecified + A half-rounded rectangle, the SBGN glyph for a nucleic acid, is an alternative: + UnspecifiedGlyphAlternative + + + + + + + + + + + + + + + + + + + + + + + + + + replacement-glyph-specification.png + SBOL-visual/Glyphs/FunctionalComponents/unspecified + The Unspecified glyph is intended for showing where a chemical species' type is missing (or, equivalently, given only the uninformative root role). It should never appear with well-curated designs or diagrams. + +Alternate BioPAX definition: PhysicalEntity: http://www.biopax.org/release/biopax-level3.owl#PhysicalEntity + An anonymous chemical species that is missing any information about its nature or intended purpose. + true + Unspecified is RECOMMENDED to be represented by the unicode "replacement character" glyph, indicating a missing or invalid symbol: + UnspecifiedSpeciesGlyph + + + + + + + + + + + + + + + generic-sbgn-specification.png + SBOL-visual/Glyphs/FunctionalComponents/unspecified + An alternative is the SBGN "generic species" glyph, which is an ellipse: + UnspecifiedSpeciesGlyphAlternative + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +