SBOL3 Ontology

Represents a participation of a feature that is a reactant in an interaction, with the role of SBO:reactant.

Represents an operator DNA component, with the role of SO:operator.

The subject and object, after tracing through any layers of ComponentReference, MUST NOT both refer to SubComponent objects with the same instanceOf value or both refer to ExternallyDefined objects with the same definition. Example: two fluorescent reporters must be different.

Controlled vocabulary for the types of physical entities that can be represented in SBOL. The value of a Component's type property must be an instance of a class that is a subclass of ComponentType.

• physical entity representation ^c
• sbol:SBOLValue ^c

• non-covalent complex ^c or simple chemical ^c or deoxyribonucleic acid ^c or polypeptide chain ^c or functional entity ^c or ribonucleic acid ^c
• single ^c or double ^c or circular ^c or Component Type ^c or linear ^c

Represents a functional entity component, with the type of SBO:functional_entity.

Orientation restrictions are a subset of the ConstraintRestriction class that are used to express orientation relationships between pairs of Features within a template Component. The value of an OrientationRestriction must be one of the following: sameOrientationAs or oppositeOrientationAs.

• sameOrientationAs ^c
• oppositeOrientationAs ^c

Represents a promoter DNA component, with the role of SO:promoter.

The GenericTopLevel class is a way to create a placeholder for a top-level entity that is not defined in the SBOL data model.

Controlled vocabulary for the roles that a DNA Component can play in a design. The value of a Component's role property must be an instance of a class that is a subclass of DNARole.

Represents a chemical structure using the IUPAC International Chemical Identifier (InChI) format, with the encoding of EDAM format 1197. The elements property MUST contain a valid InChI string.

A real thing, defined by its properties or the actions it performs, rather than it physico-chemical structure.

Represents a participation of a feature that is a modifier in an interaction, with the role of SBO:modifier.

Substance consumed by a chemical reaction. Reactants react with each other to form the products of a chemical reaction. In a chemical equation the Reactants are the elements or compounds on the left hand side of the reaction equation. A reactant can be consumed and produced by the same reaction, its global quantity remaining unchanged.

Represents a coding sequence DNA component, with the role of SO:CDS.

A small molecule which increases (activator) or decreases (inhibitor) the activity of an (allosteric) enzyme by binding to the enzyme at the regulatory site (which is different from the substrate-binding catalytic site).

In the context of the parent object of the Constraint, information about the subject should be used in place of all instances of the object. Example: the J23101 promoter replaces a generic promoter.

A wrapper class to enable the use of OM Prefixes in SBOL. This class allows adding custom SBOL relationships.

• TopLevel ^c
• Prefix ^c

• SBOLSIPrefix ^c
• SBOLBinaryPrefix ^c

Represents a gene DNA component, with the role of SO:gene.

Substance that decreases the probability of a chemical reaction without itself being consumed or transformed by the reaction.

Represents an RNA component, with the type of SBO:RNA, the role of RNARole. It restricts instances to have the sequences with the correct RNA encoding.

Conceptual or material entity that is the object of an inhibition process, and is acted upon by an inhibitor.

The Collection class is a class that groups together a set of TopLevel objects that have something in common.

Provides a vocabulary to choose the modeling language of a Model. Model languages are typically identified using IRIs, such as terms from the EDAM ontology.

Representation of an entity used in a systems biology knowledge reconstruction, such as a model, pathway, network.

• physical entity representation ^c
• occurring entity representation ^c
• participant role ^c
• modelling framework ^c

Represents a protein component, with the type of SBO:protein, the role of ProteinRole. It restricts instances to have the sequences with the correct protein encoding.

The purpose of the om:UnitMultiplication class is to describe a unit of measure that is the multiplication of two other units of measure.

• hasTerm2 ^op
• hasTerm1 ^op

• hasTerm1 ^op some Unit ^c
  
• hasTerm2 ^op some Unit ^c
  

Represents a genetic production interaction, with the type of SBO:genetic_production, that involves at least one template participation and at least one product participation.

The LocalSubComponent class is a subclass of Feature. This class serves as a way to create a placeholder in more complex Components, such as a variable to be filled in later or a composite that exists only within the context of the parent Component.

Represents an effector simple chemical component, with the role of CHEBI:effector.

Synonym: new synonym

• Component Type ^c
• functional entity ^c
• ribonucleic acid ^c
• polypeptide chain ^c
• simple chemical ^c
• non-covalent complex ^c
• deoxyribonucleic acid ^c

All SBOL-defined classes are directly or indirectly derived from the Identified abstract class.

• wasGeneratedBy ^op
• displayId ^dp
• wasDerivedFrom ^op
• hasMeasure ^op
• description ^dp
• name ^dp

• Constraint ^c
• Interface ^c
• Interaction ^c
• Location ^c
• Metadata ^c
• Participation ^c
• SBOL Association ^c
• Feature ^c
• SBOL Usage ^c
• TopLevel ^c
• SBOL Measure ^c
• VariableFeature ^c

Controlled vocabulary for the types of restrictions that can be expressed in a Constraint. The value of a Constraint's restriction property must be an instance of a class that is a subclass of ConstraintRestriction. Subclasses of ConstraintRestriction include IdentityRestriction, TopologyRestriction, SequentialRestriction, and OrientationRestriction.

• differentFrom ^c
• OrientationRestriction ^c
• replaces ^c
• strictlyPrecedes ^c
• overlaps ^c
• IdentityRestriction ^c
• strictlyContains ^c
• isDisjointFrom ^c
• equals ^c
• meets ^c
• finishes ^c
• contains ^c
• SequentialRestriction ^c
• starts ^c
• precedes ^c
• verifyIdentical ^c
• covers ^c
• TopologyRestriction ^c

Positive modulation of the execution of a process.

An event involving physical entities that results in modification of structure, location, or free energy.

A wrapper class to enable the use of OM UnitDivisions in SBOL. This class allows adding custom SBOL relationships.

• SBOLUnit ^c
• UnitDivision ^c

An Activity is used to represent the execution of a process or set of processes. An Activity is linked through prov:qualifiedAssociation to one or more Associations, and is linked through prov:used to one or more Entities.

• qualifiedAssociation ^op
• wasInformedBy ^op
• endedAtTime ^dp
• qualifiedUsage ^op
• startedAtTime ^dp

Represents an engineered region DNA component, with the role of SO:engineered_region.

Substance that is produced in a reaction. In a chemical equation the Products are the elements or compounds on the right hand side of the reaction equation. A product can be produced and consumed by the same reaction, its global quantity remaining unchanged.

The purpose of the CombinatorialDerivation class is to specify combinatorial biological designs without having to specify every possible design variant.

• strategy ^op
• template ^op
• hasVariableFeature ^op

Representation of an entity that manifests, unfolds or develops through time, such as a discrete event, or a mutual or reciprocal action or influence that happens between participating physical entities, and/or other occurring entities.

• biochemical or transport reaction ^c
• control ^c
• genetic production ^c

Controlled vocabulary for the roles that a Protein Component can play in a design. The value of a Component's role property must be an instance of a class that is a subclass of ProteinRole.

The EntireSequence class does not have any additional properties. Use of this class indicates that the linked Sequence describes the entirety of the Component or Feature parent of this Location object.

The purpose of the om:SIPrefix class is to describe standard SI prefixes such as "milli", "centi", "kilo", etc.

A wrapper for the PROV-O Agent class. The purpose of this class is to allow for the inclusion of SBOL-specific properties on PROV Agents, such as the association of an Agent with a particular Component or Interaction.

• TopLevel ^c
• Agent ^c

The Constraint class can be used to assert restrictions on the relationships of pairs of Feature objects contained by the same parent Component. Uses of this class include expressing containment (e.g., a plasmid transformed into a chassis strain), identity mappings (e.g., replacing a placeholder value with a complete definition), and expressing relative, sequence-based positions (e.g., the ordering of features within a template).

• subject ^op
• object ^op
• restriction ^op

• restriction ^op some Thing ^c
  
• subject ^op some Feature ^c
  
• object ^op some Feature ^c
  

A wrapper class to enable the use of OM SIPrefixes in SBOL. This class allows adding custom SBOL relationships.

• SBOLPrefix ^c
• SIPrefix ^c

Represents a non-covalent binding interaction, with the type of SBO:non_covalent_binding, that involves at least one reactant participation and at least one product participation.

The end of the location for subject is less than the start of the location for object.

Represents a participation of a feature that is inhibited in an interaction, with the role of SBO:inhibited.

Represents a participation of a feature that stimulates an interaction, with the role of SBO:stimulator.

Controlled vocabulary for the roles that an RNA Component can play in a design. The value of a Component's role property must be an instance of a class that is a subclass of RNARole.

The subject and object overlap in space, but portions of each are outside of the other.

Synonym: regulation

• stimulation ^c
• inhibition ^c

Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation.

Represents an inhibition interaction, with the type of SBO:inhibition, that involves at least one inhibitor participation and at least one inhibited participation.

The purpose of the Model class is to serve as a placeholder for an external computational model and provide additional meta-data to enable better reasoning about the contents of this model.

• language ^op
• framework ^op

• source ^op some Thing ^c
  
• language ^op some Thing ^c
  
• framework ^op some Thing ^c
  

Identity restrictions are a subset of the ConstraintRestriction class that are used to express identity relationships between pairs of Features within a template Component. The value of an IdentityRestriction must be one of the following: verifyIdentical, differentFrom, or replaces.

Use the union of the two sets: both the set of zero or more role properties given for this SubComponent as well as the set of zero or more role properties given for the included Component.

A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.

A wrapper for the PROV-O Plan class. The purpose of this class is to allow for the inclusion of SBOL-specific properties on PROV Plans, such as the association of a Plan with a particular Component or Interaction.

• TopLevel ^c
• Plan ^c

Represents a degradation interaction, with the type of SBO:degradation, that involves at least one reactant participation.

Type for DNA or RNA components. The value of a Component's type property must be an instance of a class that is a subclass of DNARNAComponentType if the Component has a role that is a subclass of DNARole or RNARole.

The purpose of the om:Measure class is to link a numerical value to a om:Unit.

• hasMeasure ^op
• variantMeasure ^op

• hasNumericalValue ^dp some xsd:decimal ^c
  
• hasUnit ^op some Unit ^c
  

om:Unit is an abstract class that is extended by other classes to describe units of measure using a shared set of properties.

• hasUnit ^op
• hasTerm2 ^op
• hasDenominator ^op
• hasBase ^op
• hasTerm1 ^op
• hasNumerator ^op

• label ^ap some xsd:string ^c
  
• symbol ^dp some xsd:string ^c
  

• UnitMultiplication ^c
• UnitExponentiation ^c
• SBOLUnit ^c
• PrefixedUnit ^c
• SingularUnit ^c
• UnitDivision ^c
• CompoundUnit ^c

Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters.

The Interface class is a way of explicitly specifying the interface of a Component.

• output ^op
• nondirectional ^op
• input ^op

Represents a non-covalent complex Component, with the type SBO:non-covalent complex.

A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.

The subject entirely contains the object: they do not share a boundary.

The ComponentReference class is a subclass of Feature that can be used to reference Features within SubComponents.

• refersTo ^op
• inChildOf ^op

• refersTo ^op some Feature ^c
  
• inChildOf ^op some SubComponent ^c
  

The subject and object do not overlap in space.

The Cut class has been introduced to enable the specification of a region between two discrete positions. This specification is accomplished using the at property, which specifies a discrete position that corresponds to the index of a character in the elements String of a Sequence (except in the case when at is equal to zero.)

Complete disappearance of a physical entity.

A wrapper class to enable the use of OM UnitExponentiations in SBOL. This class allows adding custom SBOL relationships.

• SBOLUnit ^c
• UnitExponentiation ^c

A Range object specifies a region via discrete, inclusive start and end positions that correspond to indices for characters in the elements String of a Sequence.

• end ^dp
• start ^dp

• start ^dp some Na8ed0eb40e354e61b5e379e2d2c1afc4 ^c
  
• end ^dp some Nd1d4f78caa484ba3ac1e5f0ef2d81b87 ^c
  

A region of DNA to which various transcription factors and RNA polymerase must bind in order to initiate transcription for a gene.

Controlled vocabulary for the orientation of a Feature or Location. The value of a Feature or Location's orientation property must be an instance of a class that is a subclass of Orientation.

• inline ^c
• reverseComplement ^c

Represents a ribosome binding site DNA component, with the role of SO:RBS.

The purpose of the Sequence class is to represent the primary structure of a Component object and the manner in which it is encoded.

• encoding ^op
• elements ^dp

The SubComponent class is a subclass of the Feature class that can be used to specify structural hierarchy.

• sourceLocation ^op
• instanceOf ^op
• roleIntegration ^op

Synonym: RNA

The Interaction class provides more detailed description of how the Feature objects of a Component are intended to work together. For example, this class can be used to represent different forms of genetic regulation (e.g., transcriptional activation or repression), processes from the central dogma of biology (e.g. transcription and translation), and other basic molecular interactions (e.g., non-covalent binding or enzymatic phosphorylation).

• higherOrderParticipant ^op
• hasInteraction ^op

• GeneticProductionInteraction ^c
• NonCovalentBindingInteraction ^c
• InhibitionInteraction ^c
• DegradationInteraction ^c
• StimulationInteraction ^c
• ControlInteraction ^c
• BiochemicalReactionInteraction ^c

A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.

• SBML ^c
• nucleotide ^c
• SMILES ^c
• protein ^c
• InChI ^c
• CellML ^c
• BioPAX ^c

A roleIntegration specifies the relationship between a SubComponent instance's own set of role properties and the set of role properties on the included Component.

• mergeRoles ^c
• overrideRoles ^c

An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.

Attributes added to describe the different kinds of replicon. SO workshop, September 2006. A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.

Modelling approach where the quantities of participants are considered continuous, and represented by real values. The associated simulation methods make use of differential equations.

The function of a physical or conceptual entity, that is its role, in the execution of an event or process.

• reactant ^c
• inhibited ^c
• product ^c
• promoter ^c
• stimulated ^c
• template ^c
• functional compartment ^c
• modified ^c
• modifier ^c

The purpose of the Experiment class is to aggregate ExperimentalData objects for subsequent analysis, usually in accordance with an experimental design.

The Location class is used to represent the location of Features within Sequences. This class is extended by the Range, Cut, and EntireSequence classes. Location is an abstract class; only its child classes are actually instantiated.

• hasLocation ^op
• sourceLocation ^op

• hasSequence ^op some Sequence ^c
  
• hasSequence ^op max 1 Sequence ^c
  

• EntireSequence ^c
• Cut ^c
• Range ^c

A Usage is used to describe the involvement of an Entity in an Activity, specifying how the Entity was used during the execution of the Activity.

Represents a stimulation interaction, with the type of SBO:stimulation, that involves at least one stimulator participation and at least one stimulated participation.

A region that is engineered.

Any extent of continuous biological sequence.

• CDS ^c
• mRNA ^c
• engineered_region ^c
• operator ^c
• terminator ^c
• gene ^c
• promoter ^c
• ribosome_entry_site ^c

The purpose of the om:UnitExponentiation class is to describe a unit of measure that is raised to an integer power.

• hasExponent ^dp
• hasBase ^op

• hasBase ^op some Unit ^c
  
• hasExponent ^dp some xsd:integer ^c
  

The purpose of the ExperimentalData class is to aggregate links to experimental data files. An ExperimentalData is typically associated with a single sample, lab instrument, or experimental condition and can be used to describe the output of the test phase of a design-build-test-learn workflow.

Naturally occurring macromolecule formed by the repetition of amino-acid residues linked by peptidic bonds. A polypeptide chain is synthesized by the ribosome.

Inline is an attribute of the feature, where the feature is in the 5' to 3' direction.

The purpose of the om:BinaryPrefix class is to describe standard binary prefixes such as "kibi", "mebi", "gibi", etc.

The subject and object occupy the same location in space.

A wrapper class to enable the use of OM BinaryPrefixes in SBOL. This class allows adding custom SBOL relationships.

• SBOLPrefix ^c
• BinaryPrefix ^c

Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529. A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.

Custom data in the form of independent objects can participate in the SBOL data model if they are assigned one of the SBOL types Identified or TopLevel. An example is an RDF object that is annotated such that it represents a data sheet that describes the performance of a Component in a particular context.

Represents a DNA component, with the type of SBO:DNA, the role of DNARole. It restricts instances to have the sequences with the correct DNA encoding.

• Operator DNA Component ^c
• Promoter DNA Component ^c
• CDS DNA Component ^c
• Gene DNA Component ^c
• Engineered Region DNA Component ^c
• RBS DNA Component ^c
• Generic DNA Component ^c
• Terminator DNA Component ^c

The subject and object are connected at a shared boundary.

Exactly one Feature in the derived Component SHOULD have a prov:wasDerivedFrom property that refers to the template Feature.

The Component class represents the structural and/or functional entities of a biological design. The primary usage of this class is to represent entities with designed sequences, such as DNA, RNA, and proteins, but it can also be used to represent any other entity that is part of a design, such as simple chemicals, molecular complexes, strains, media, light, and abstract functional groupings of other entities.

• hasInterface ^op
• hasModel ^op
• hasFeature ^op
• hasConstraint ^op
• hasInteraction ^op

• built ^op
• instanceOf ^op
• template ^op
• variant ^op

• type ^op some Thing ^c
  
• type ^op some Component Type ^c
  
• type ^op max 1 Component Type ^c
  

• Functional Entity Component ^c
• RNA Component ^c
• Protein Component ^c
• Non-Covalent Complex Component ^c
• DNA Component ^c
• Simple Chemical Component ^c

A wrapper class to enable the use of OM Units in SBOL. This class allows adding custom SBOL relationships.

• TopLevel ^c
• Unit ^c

• SBOLUnitDivision ^c
• SBOLUnitExponentiation ^c
• SBOLUnitMultiplication ^c
• SBOLPrefixedUnit ^c
• SBOLSingularUnit ^c
• SBOLCompoundUnit ^c

Each Participation represents how a particular Feature behaves in its parent Interaction.

• participant ^op
• higherOrderParticipant ^op

• ReactantParticipation ^c
• ModifierParticipation ^c
• InhibitedParticipation ^c
• StimulatorParticipation ^c
• StimulatedParticipation ^c
• ProductParticipation ^c
• TemplateParticipation ^c
• InhibitorParticipant ^c
• ModifiedParticipation ^c
• PromoterParticipation ^c

Specifies the topology of a nucleic acid Component. Values are linear, circular, single, and double. For DNA Components with a fully specified sequence, topology information is recommended and should be provided using a term from the Topology Attribute branch of the Sequence Ontology.

An attribute describes a quality of sequence.

• linear ^c
• circular ^c
• single ^c
• forward ^c
• double ^c
• reverse ^c

Controlled vocabulary for the types of encoding that can be used to represent the primary structure of a Component. The value of a Sequence's encoding property must be an instance of a class that is a subclass of Encoding.

An Agent is something that bears some form of responsibility for an Activity taking place, such as a person, organization, or software agent.

Represents a generic DNA component, with the role of SO:sequence_feature.

Represents a participation of a feature that is stimulated in an interaction, with the role of SBO:stimulated.

Simple, non-repetitive chemical entity.

Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.

In the context of this SubComponent, ignore any role given for the included Component. Instead use only the set of zero or more role properties given for this SubComponent.

The start of the location for subject is after the start of the location for object and the end of the location for subject is equal to the end of the location for object.

A wrapper class to enable the use of OM UnitMultiplications in SBOL. This class allows adding custom SBOL relationships.

• SBOLUnit ^c
• UnitMultiplication ^c

Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation.

Entity composed of several independant components that are not linked by covalent bonds.

A wrapper for the PROV-O Association class. The purpose of this class is to allow for the inclusion of SBOL-specific properties on PROV Associations, such as the association of an Association with a particular Component or Interaction.

• Identified ^c
• Association ^c

Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters.

Represents a participation of a feature that is a product in an interaction, with the role of SBO:product.

The Feature class, is used to compose Component objects into a structural or functional hierarchy. Feature is an abstract class; only its child classes are actually instantiated.

• output ^op
• refersTo ^op
• nondirectional ^op
• participant ^op
• hasFeature ^op
• subject ^op
• variable ^op
• input ^op
• object ^op

• LocalSubComponent ^c
• ComponentReference ^c
• SubComponent ^c
• SequenceFeature ^c
• ExternallyDefined ^c

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.

A wrapper for the PROV-O Usage class. The purpose of this class is to allow for the inclusion of SBOL-specific properties on PROV Usages, such as the association of a Usage with a particular Component or Interaction.

• Identified ^c
• Usage ^c

Conceptual or material entity that is the object of a stimulation process, and is acted upon by a stimulator.

TopLevel is an abstract class that is extended by any Identified class that can be found at the top level of an SBOL document or file.

• hasNamespace ^op
• hasAttachment ^op

• GenericTopLevel ^c
• SBOLPrefix ^c
• Collection ^c
• CombinatorialDerivation ^c
• SBOL Agent ^c
• Model ^c
• SBOL Plan ^c
• Sequence ^c
• ExperimentalData ^c
• Component ^c
• SBOLUnit ^c
• Implementation ^c
• Attachment ^c
• SBOL Activity ^c

The subject contains the object and they might or might not share a boundary.

The subject and object Component objects MUST have the same orientation.

A wrapper class to enable the use of OM PrefixedUnits in SBOL. This class allows adding custom SBOL relationships.

• SBOLUnit ^c
• PrefixedUnit ^c

This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. Moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. Merged with RNA_polymerase_promoter (SO:0001203) Aug 2020. Moved up one level from is_a CRM (SO:0000727) to is_a transcriptional_cis_regulatory_region (SO:0001055) as part of the GREEKC work January 2021. Pascale Gaudet from Gene Ontology pointed out that CRM can be located upstream of the promoter and therefore cannot include the promoter. A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription.

Sequential restrictions are a subset of the ConstraintRestriction class that are used to express relative, sequence-based positions of pairs of Features within a template Component. The value of a SequentialRestriction must be one of the following: precedes, strictlyPrecedes, meets, overlaps, contains, strictlyContains, equals, starts, or finishes.

Synonym: activator

Represents a simple chemical component, with the type of SBO:simple_chemical, the role of SmallMoleculeRole. It restricts instances to have the sequences with the correct chemical encoding.

A wrapper for the OM Measure class. The purpose of this class is to allow for the inclusion of SBOL-specific properties on OM Measures, such as the association of a Measure with a particular Component or Interaction.

• Identified ^c
• Measure ^c

Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation.

An Implementation represents a realized instance of a Component, such a sample of DNA resulting from fabricating a genetic design or an aliquot of a specified reagent.

CellML, the format for mathematical models of biological and other networks.

Represents a participation of a feature that is a template in an interaction, with the role of SBO:template.

A role is particular behaviour which a material entity may exhibit.

Synonym: association

Modelling approach, pioneered by Rene Thomas and Stuart Kaufman, where the evolution of a system is described by the transitions between discrete activity states of 'genes' that control each other.

The start of the location for subject is equal to the start of the location for object and the end of the location for subject is before the end of the location for object.

Controlled vocabulary for the roles that a Component can play in a design. The value of a Component's role property must be an instance of a class that is a subclass of ComponentRole.

• DNA Role ^c
• Protein Role ^c
• RNA role ^c
• Small Molecule Role ^c

VariableFeature class specifies a variable and set of values that will replace one of the Feature objects in the template of a CombinatorialDerivation. The variable is specified by the variable property, and the set of values is defined by the union of Component objects referred to by the variant, variantCollection, and variantDerivation properties.

• cardinality ^op
• variant ^op
• variantMeasure ^op
• variantDerivation ^op
• variable ^op
• variantCollection ^op

• cardinality ^op some Cardinality ^c
  
• variable ^op some Feature ^c
  

Controlled vocabulary for the strategies that can be used to derive new Components from a template Component.

• sample ^c
• enumerate ^c

An entity that acts as the starting material for genetic production (http://identifiers.org/biomodels.sbo/SBO:0000589).

Modelling approach where the quantities of participants are considered discrete, and represented by integer values. The associated simulation methods can be deterministic or stochastic.

Any number of Feature objects in the derived Component MAY have prov:wasDerivedFrom properties that refer to the template Feature.

The purpose of the om:PrefixedUnit class is to describe a unit of measure that is the multiplication of another unit of measure and a factor represented by a standard prefix such as "milli", "centi", "kilo", etc.

• hasUnit ^op some Unit ^c
  
• hasPrefix ^op some Prefix ^c
  

Represents an RNA sequence, with the encoding of EDAM format 1207. The elements property MUST contain only characters from the IUPAC RNA character set: A, C, G, U, M, R, W, S, Y, K, V, H, D, B, N and -.

Sample is a strategy for deriving new Components from a template Component. The sample strategy specifies that a new Component should be derived for a random sample of the possible combinations of values for the variable specified by the VariableFeature objects in the template Component.

The purpose of the om:SingularUnit class is to describe a unit of measure that is not explicitly represented as a combination of multiple units, but could be equivalent to such a representation.

An Association is used to link an Activity to one or more Agents, and to describe the role of each Agent in the execution of the Activity. An Association is linked through prov:qualifiedAssociation to an Activity, and is linked through prov:agent to one or more Agents.

• hadPlan ^op
• agent ^op

Attributes added to describe the different kinds of replicon. SO workshop, September 2006. A quality of a nucleotide polymer that has no terminal nucleotide residues.

Provides a controlled vocabulary for describing restrictions between pairs of Feature objects, including identity, topology, sequence order, and orientation relationships.

• one ^c
• zeroOrMore ^c
• OneOrMore ^c
• zeroOrOne ^c

Logical or physical subset of the event space that contains pools, that is sets of participants considered identical when it comes to the event they are involved into. A compartment can have any number of dimensions, including 0, and be of any size including null.

The purpose of the om:UnitDivision class is to describe a unit of measure that is the division of one unit of measure by another.

• hasDenominator ^op
• hasNumerator ^op

• hasNumerator ^op some Unit ^c
  
• hasDenominator ^op some Unit ^c
  

The start of the location for subject is less than the start of the location for object.

Represents a DNA sequence, with the encoding of EDAM format 1207. The elements property MUST contain only characters from the IUPAC DNA character set: A, C, G, T, U, M, R, W, S, Y, K, V, H, D, B, N and -.

Conceptual or material entity that is the object of a modification process, and is acted upon by a modifier.

Enumerate is a strategy for deriving new Components from a template Component. The enumerate strategy specifies that a new Component should be derived for every possible combination of values for the variable specified by the VariableFeature objects in the template Component.

Provides a vocabulary to choose the interaction type of behavior represented by an Interaction. Interaction types are typically identified using IRIs, such as terms from the Systems Biology Ontology.

A composite biochemical process through which a gene sequence is fully converted into mature gene products. These gene products may include RNA species as well as proteins, and the process encompasses all intermediate steps required to generate the active form of the gene product.

A Plan is used to describe a set of actions or steps intended to achieve a specific goal or outcome.

Represents a participation of a feature that inhibits an interaction, with the role of SBO:inhibitor.

The purpose of the Attachment class is to serve as a general container for data files, especially experimental data files. It provides a means for linking files and metadata to SBOL designs.

• hash ^dp
• size ^dp
• format ^op
• hashAlgorithm ^dp

A wrapper class to enable the use of OM SingularUnits in SBOL. This class allows adding custom SBOL relationships.

• SBOLUnit ^c
• SingularUnit ^c

Represents a control interaction, with the type of SBO:control, that involves at least one modifier participation and at least one modified participation.

A SequenceWithElements is a Sequence that contains elements and an encoding.

• InChI Sequence ^c
• RNA Sequence ^c
• DNA Sequence ^c
• SMILES Sequence ^c
• Protein Sequence ^c

The subject and object, after tracing through any layers of ComponentReference, MUST both refer to SubComponent objects with the same instanceOf value or both refer to ExternallyDefined objects with the same definition. Example: a promoter included via two different subsystems must be the identical.

Provides a vocabulary to choose the modeling framework of a Model. Model frameworks are typically identified using IRIs, such as terms from the Systems Biology Ontology.

Attributes added to describe the different kinds of replicon. SO workshop, September 2006. When a nucleotide polymer has only one strand.

A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.

Controlled vocabulary for the roles that a Small Molecule Component can play in a design. The value of a Component's role property must be an instance of a class that is a subclass of SmallMoleculeRole.

A wrapper for the PROV Activity class. The purpose of this class is to allow for the inclusion of SBOL-specific properties on PROV Activities, such as the association of an Activity with a particular Component or Interaction.

• TopLevel ^c
• Activity ^c

Represents a transcription factor protein component, with the role of GO:DNA-binding transcription factor activity.

Forward is an attribute of the feature, where the feature is in the 5' to 3' direction.

Represents a chemical structure using the Simplified Molecular-Input Line-Entry System (SMILES) format, with the encoding of EDAM format 1196. The elements property MUST contain a valid SMILES string.

Represents a participation of a feature that is modified in an interaction, with the role of SBO:modified.

The SequenceFeature class describes one or more regions of interest on the Sequence objects referred to by its parent Component.

At least one Feature in the derived Component SHOULD have a prov:wasDerivedFrom property that refers to the template Feature.

Represents a protein sequence, with the encoding of EDAM format 1208. The elements property MUST contain only characters from the IUPAC Protein character set: A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y and -.

Modelling approach which captures bounds on the possible behavior of a system, which may be further reduced using an objective function.

An event involving one or more chemical entities that modifies the electrochemical structure of at least one of the participants.

• degradation ^c
• non-covalent binding ^c

Represents a participation of a feature that is a promoter in an interaction, with the role of SBO:promoter.

Synonym: DNA

The subject contains the object but also shares a boundary.

Provides a vocabulary to choose the role of a Participation in an Interaction. Participation roles are typically identified using IRIs, such as terms from the Systems Biology Ontology.

Attributes added to describe the different kinds of replicon. SO workshop, September 2006. When a nucleotide polymer has two strands that are reverse-complement to one another and pair together.

Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer.

Region in mRNA where ribosome assembles.

The ExternallyDefined class has been introduced so that external definitions in databases like ChEBI or UniProt can be referenced.

• type ^op some Thing ^c
  
• definition ^op some Thing ^c
  

Set of assumptions that underlay a mathematical description.

• continuous framework ^c
• logical framework ^c
• discrete framework ^c
• constraint-based framework ^c
• hybrid framework ^c

Represents a terminator DNA component, with the role of SO:terminator.