If true, indicates that the term corresponds to a domain entity. Software automation tools should create a specific entity.
If specified, create the entity name according to the value of this property. E.g. for sbol3:SBOLActivity otol:replacementOf prov:Activity, create the entities using the Activity name only.
If true, an object should be created for the container class.
The built property is OPTIONAL and MAY contain a IRI that MUST refer to a Component. This Component is intended to describe the actual physical structure and/or functional behavior of the Implementation.
The cardinality property is REQUIRED and has type of IRI. This property specifies how many Feature objects SHOULD be derived from the template Feature during the derivation of a new Component.
The comprises property can be used to express parent-child compositional relationships as a custom approach if needed.
The definition property is REQUIRED and is of type IRI that links to a canonical definition external to SBOL.
Subclass of comprises that is used to express direct parent-child compositional relationships.
The encoding property has a data type of IRI, and is OPTIONAL unless elements is set, in which case it is REQUIRED.
The format property is OPTIONAL and MAY contain a IRI that specifies the format of the attached file. It is RECOMMENDED that this IRI refer to a term from the EMBRACE Data and Methods (EDAM) ontology
The framework property is REQUIRED and MUST contain a IRI that specifies the framework in which the model is implemented. It is RECOMMENDED this IRI refer to a term from the modeling framework branch of the SBO when possible.
A TopLevel object can have zero or more hasAttachment properties, each of type IRI specifying an Attachment object.
A Component MAY have any number of hasConstraint properties, each of type IRI, that MUST reference a Constraint object.
A Component MAY have any number of hasFeature properties, each of type IRI that MUST reference a Feature object
A Component MAY have any number of hasInteraction properties, each of type IRI, that MUST reference an Interaction object.
A Component MAY have zero or one hasInterface property of type IRI that MUST reference an Interface object.
A SubComponent MAY have any number of hasLocation properties, each of type IRI, that MUST refer to Location objects that indicates the location of the Sequence from the instanceOf Component in a Sequence of the parent Component. A LocalSubComponent MAY have any number of hasLocation properties, each of type IRI, that MUST refer to Location objects. In SequenceFeature, the hasLocation is REQUIRED and contains one or more IRIs, which MUST refer to Location objects.
A Component MAY have any number of hasModel properties, each of type IRI, that MUST reference a Model object.
A TopLevel object MUST have precisely one hasNamespace property, which contains a URL that defines the namespace portion of URLs for this object and any child objects.
An Interaction MAY have any number of hasParticipation properties, each of type IRI, that MUST reference a Participation object, each of which identifies the role that its referenced Feature plays in the Interaction.
This property can be used in a Component or Location. A Component MAY have any number of hasSequence properties, each of type IRI, that MUST reference a Sequence object. In a Location, the hasSequence property is REQUIRED and MUST contain the IRI of a Sequence object.
A CombinatorialDerivation object can have zero or more hasVariableFeature properties, each of type IRI, specifying a VariableFeature. The set of hasVariableFeature properties MUST NOT contain two or more VariableFeature objects that refer to the same template.
The higherOrderParticipant property indicates an Interaction object that plays the designated role in its parent Interaction object. Precisely one value MUST be specified for precisely one of participant or higherOrderParticipant.
An Interface MAY have any number of input properties, each of type IRI, that MUST reference a Feature object in the same Component.
The instanceOf property is a REQUIRED IRI that refers to the Component providing the definition for this SubComponent.
The language property is REQUIRED and MUST contain a IRI that specifies the language in which the model is implemented. It is RECOMMENDED that this IRI refer to a term from the EMBRACE Data and Methods (EDAM) ontology.
A Collection object can have zero or more member properties, each of type IRI specifying a TopLevel object.
An Interface MAY have any number of nondirectional properties, each of type IRI, that MUST reference a Feature object in the same Component.
The object property is REQUIRED and MUST contain a IRI that refers to a Feature contained by the same parent Component that contains the Constraint. This Feature MUST NOT be the same Feature that the Constraint refers to via its subject property.
The orientation property is OPTIONAL and has a data type of IRI.
An Interface MAY have any number of output properties, each of type IRI, that MUST reference a Feature object in the same Component.
The participant property indicates a Feature object that plays the designated role in its parent Interaction object. Precisely one value MUST be specified for precisely one of participant or higherOrderParticipant.
The refersTo property is a REQUIRED IRI that refers to a Feature.
The restriction property is REQUIRED and has a data type of IRI. This property MUST indicate the type of restriction on the locations, orientations, or identities of the subject and object Feature objects in relation to each other.
This property can be used in a Component, Feature or Participation. A Component MAY have any number of role properties, each of type IRI, that MUST identify terms from ontologies that are consistent with the type property of the Component. Each Feature can have zero or more role property IRIs describing the purpose or potential function of this Feature in the context of its parent Component. A Participation is REQUIRED to have one or more role properties, each of type IRI, that describes the behavior of a Participation (and by extension its referenced Feature) in the context of its parent Interaction.
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.
The source property is REQUIRED and MUST contain a IRI reference to the source file.
The sourceLocation property allows for only a portion of a Component's Sequence to be included, rather than its entirety.
The strategy property is OPTIONAL and has a data type of IRI.
The subject property is REQUIRED and MUST contain a IRI that refers to a Feature contained by the same parent Component that contains the Constraint.
The template property is REQUIRED and MUST contain a IRI that refers to a Component.
A Component MUST have one or more type properties, each of type IRI specifying the category of biochemical or physical entity (for example DNA, protein, or simple chemical) that a Component object abstracts for the purpose of engineering design
The variable property is REQUIRED and MUST contain a IRI that refers to a template Feature in the template Component referred to by this VariableFeature's parent CombinatorialDerivation
A VariableFeature object can have zero or more variant properties, each of type IRI, specifying a Component object. This property specifies individual Component objects to serve as options when deriving a new Feature for the variable Feature from the template.
A VariableFeature object can have zero or more variantCollection properties, each of type IRI, specifying a Collection object. Such a Collection MUST NOT contain any objects besides Component objects or Collection objects that themselves contain only Component or Collection objects. This property enables the specification of existing groups of Component objects to serve as options.
A VariableFeature object can have zero or more variantDerivation properties, each of type IRI, specifying a CombinatorialDerivation object. This property enables the specification of Component objects derived in accordance with another CombinatorialDerivation to serve as options when deriving a new Feature for the variable Feature from the template.
A VariableFeature object can have zero or more variantMeasure properties, each of type IRI, specifying a om:Measure object. This property specifies numerical values that are options to be applied to the variable Feature from the template when deriving a new Component.
The om:hasBase property is REQUIRED and MUST contain a IRI that refers to another om:Unit.
The om:hasDenominator property is REQUIRED and MUST contain a IRI that refers to another om:Unit.
The om:hasNumerator property is REQUIRED and MUST contain a IRI that refers to another om:Unit.
The om:hasPrefix property is REQUIRED and MUST contain a IRI that refers to a om:Prefix.
The om:hasTerm1 property is REQUIRED and MUST contain a IRI that refers to another om:Unit. This om:Unit is the first multiplication term.
The om:hasTerm2 property is REQUIRED and MUST contain a IRI that refers to another om:Unit. This om:Unit is the second multiplication term. It is okay if the om:Unit referred to by om:hasTerm1 is the same as that referred to by om:hasTerm2.
This property can be used in a Measure, SingularUnit or PrefixedUnit. For Measure and PrefixedUnit, the om:hasUnit property is REQUIRED and MUST contain a IRI that refers to a om:Unit. For SingularUnit, the om:hasUnit is OPTIONAL and MAY contain a IRI.
The prov:agent property is REQUIRED and MUST contain a IRI that refers to an prov:Agent object.
The prov:entity property is REQUIRED and MUST contain a IRI which MAY refer to an Identified object.
The prov:hadPlan property is OPTIONAL and contains a IRI that refers to a prov:Plan.
An prov:Usage MAY have one or more prov:hadRole properties, each of type IRI that refers to particular term(s) describing the usage of an prov:Entity referenced by the prov:entity property.
An prov:Activity MAY have one or more prov:qualifiedAssociation properties, each of type IRI that refers to an prov:Association object.
An prov:Activity MAY have one or more prov:qualifiedUsage properties, each of type IRI that refers to an prov:Usage object.
An Identified object MAY have zero or more prov:wasDerivedFrom properties, each of type IRI. This property is defined by the PROV-O ontology and is located in the https://www.w3.org/ns/prov# namespace
An Identified object MAY have zero or more prov:wasGeneratedBy properties, each of type IRI.
An prov:Activity MAY have one or more prov:wasInformedBy properties, each of type IRI that refers to another prov:Activity object.
The at property is REQUIRED and MUST contain an Integer value greater than or equal to zero. The region specified by the Cut is between the position specified by this property and the position that immediately follows it. When the at property is equal to zero, the specified region is immediately before the first discrete position or character in the elements String of a Sequence.
The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.
The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between a IRI and the name property that is machine-readable, but more human-readable than the full IRI of an object
The elements property is an OPTIONAL String of characters that represents the constituents of a biological or chemical molecule.
The end property specifies the inclusive ending position of the Range. This property is REQUIRED and MUST contain an Integer value greater than zero. In addition, this Integer value MUST be greater than or equal to that of the start property.
The hash property is OPTIONAL and MAY contain a hash value for the file contents represented as a hexadecimal digest.
The hashAlgorithm property is OPTIONAL and MAY contain the name of the hash algorithm used to generate the value of the hash property. The value of this property SHOULD be a hash name string from the IANA Named Information Hash Algorithm Registry, of which sha3-256 is currently RECOMMENDED. If the hash property is set, then hashAlgorithm MUST be set as well.
The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object.
The order property is OPTIONAL and has a data type of Integer. If there are multiple Location objects associated with a Feature, the order property is used to specify the order (in increasing value) in which the specified Locations are to be joined to form the sequence of the Feature.
The size property is OPTIONAL and MAY contain a long indicating the file size in bytes.
The start property specifies the inclusive starting position of the Range. This property is REQUIRED and MUST contain an Integer value greater than zero.
This property can be used in a Unit or Prefix. The om:alternativeLabel property is OPTIONAL and MAY contain a set of Strings. This property can be used to specify alternative common names other than that specified using om:label property.
This property can be used in a Unit or Prefix. The om:alternativeSymbol property is OPTIONAL and MAY contain a set of Strings. This property can be used to specify alternative abbreviations other than that specified using the om:symbol property
The om:hasExponent property is REQUIRED and MUST contain an xsd:integer.
This property can be used in a SingularUnit or Prefix. For SingularUnit, the om:hasFactor property is OPTIONAL and MAY contain a xsd:float. If the om:hasFactor property of a om:SingularUnit is non-empty, then its om:hasUnit property SHOULD also be non-empty. For Prefix, The om:hasFactor property is REQUIRED and MUST contain an xsd:float.
The om:hasNumericalValue property is REQUIRED and MUST contain a single xsd:float.
This property can be used in a Unit or Prefix. The om:longcomment property is OPTIONAL and MAY contain a String. This String is a long description of the unit of measure and SHOULD be longer than any String contained by the om:comment property.
This property can be used in a Unit or Prefix. The om:symbol property is REQUIRED and MUST contain a String. This String is commonly used to abbreviate the name of the unit of measure or prefix.
The prov:endedAtTime property is OPTIONAL and contains a DateTime value, indicating when the activity ended.
The prov:startedAtTime property is OPTIONAL and contains a DateTime value, indicating when the activity started. If this property is present, then the prov:endedAtTime property is REQUIRED.
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.
Represents a biochemical reaction interaction, with the type of SBO:biochemical_reaction, that involves zero or more modifier, modified, product, and reactant participations.
Represents a coding sequence DNA component, with the role of SO:CDS.
Provides a controlled vocabulary for describing restrictions between pairs of Feature objects, including identity, topology, sequence order, and orientation relationships.
The Collection class is a class that groups together a set of TopLevel objects that have something in common.
The purpose of the CombinatorialDerivation class is to specify combinatorial biological designs without having to specify every possible design variant.
Controlled vocabulary for the strategies that can be used to derive new Components from a template Component.
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.
The ComponentReference class is a subclass of Feature that can be used to reference Features within SubComponents.
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.
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.
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).
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.
Represents a control interaction, with the type of SBO:control, that involves at least one modifier participation and at least one modified participation.
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.)
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.
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.
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 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 -.
Represents a degradation interaction, with the type of SBO:degradation, that involves at least one reactant participation.
Represents an effector simple chemical component, with the role of CHEBI:effector.
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.
Represents an engineered region DNA component, with the role of SO:engineered_region.
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 Experiment class is to aggregate ExperimentalData objects for subsequent analysis, usually in accordance with an experimental design.
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.
The ExternallyDefined class has been introduced so that external definitions in databases like ChEBI or UniProt can be referenced.
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.
Represents a functional entity component, with the type of SBO:functional_entity.
Represents a gene DNA component, with the role of SO:gene.
Represents a generic DNA component, with the role of SO:sequence_feature.
The GenericTopLevel class is a way to create a placeholder for a top-level entity that is not defined in the SBOL data model.
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.
All SBOL-defined classes are directly or indirectly derived from the Identified abstract class.
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.
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.
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.
Represents a participation of a feature that is inhibited in an interaction, with the role of SBO:inhibited.
Represents an inhibition interaction, with the type of SBO:inhibition, that involves at least one inhibitor participation and at least one inhibited participation.
Represents a participation of a feature that inhibits an interaction, with the role of SBO:inhibitor.
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).
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.
The Interface class is a way of explicitly specifying the interface of a Component.
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.
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.
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.
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.
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.
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.
Represents a participation of a feature that is modified in an interaction, with the role of SBO:modified.
Represents a participation of a feature that is a modifier in an interaction, with the role of SBO:modifier.
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.
Represents a non-covalent complex Component, with the type SBO:non-covalent complex.
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.
Represents an operator DNA component, with the role of SO:operator.
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.
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.
Each Participation represents how a particular Feature behaves in its parent Interaction.
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.
Represents a participation of a feature that is a product in an interaction, with the role of SBO:product.
Represents a promoter DNA component, with the role of SO:promoter.
Represents a participation of a feature that is a promoter in an interaction, with the role of SBO:promoter.
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.
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.
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 -.
Represents a ribosome binding site DNA component, with the role of SO:RBS.
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.
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.
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 -.
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.
Represents a participation of a feature that is a reactant in an interaction, with the role of SBO:reactant.
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.
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.
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.
A wrapper class to enable the use of OM BinaryPrefixes in SBOL. This class allows adding custom SBOL relationships.
A wrapper class to enable the use of OM CompoundUnits in SBOL. This class allows adding custom SBOL relationships.
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.
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.
A wrapper class to enable the use of OM Prefixes in SBOL. This class allows adding custom SBOL relationships.
A wrapper class to enable the use of OM PrefixedUnits in SBOL. This class allows adding custom SBOL relationships.
A wrapper class to enable the use of OM SIPrefixes in SBOL. This class allows adding custom SBOL relationships.
A wrapper class to enable the use of OM SingularUnits in SBOL. This class allows adding custom SBOL relationships.
The SBOLTerm class is a way to create a placeholder for a term in an SBOL-controlled vocabulary.
A wrapper class to enable the use of OM Units in SBOL. This class allows adding custom SBOL relationships.
A wrapper class to enable the use of OM UnitDivisions in SBOL. This class allows adding custom SBOL relationships.
A wrapper class to enable the use of OM UnitExponentiations in SBOL. This class allows adding custom SBOL relationships.
A wrapper class to enable the use of OM UnitMultiplications in SBOL. This class allows adding custom SBOL relationships.
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.
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.
The purpose of the Sequence class is to represent the primary structure of a Component object and the manner in which it is encoded.
The SequenceFeature class describes one or more regions of interest on the Sequence objects referred to by its parent Component.
A SequenceWithElements is a Sequence that contains elements and an encoding.
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.
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.
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.
Represents a participation of a feature that is stimulated in an interaction, with the role of SBO:stimulated.
Represents a stimulation interaction, with the type of SBO:stimulation, that involves at least one stimulator participation and at least one stimulated participation.
Represents a participation of a feature that stimulates an interaction, with the role of SBO:stimulator.
The SubComponent class is a subclass of the Feature class that can be used to specify structural hierarchy.
Represents a participation of a feature that is a template in an interaction, with the role of SBO:template.
Represents a terminator DNA component, with the role of SO:terminator.
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.
Topology restrictions are a subset of the ConstraintRestriction class that are used to express topological relationships between pairs of Features within a template Component. The value of a TopologyRestriction must be one of the following: contains, strictlyContains, equals, covers, overlaps, meets, or isDisjointFrom.
Represents a transcription factor protein component, with the role of GO:DNA-binding transcription factor activity.
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.
The subject contains the object and they might or might not share a boundary.
The subject contains the object but also shares a boundary.
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.
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.
The subject and object occupy the same location in space.
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.
Inline is an attribute of the feature, where the feature is in the 5' to 3' direction.
The subject and object do not overlap in space.
The subject and object are connected at a shared boundary.
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.
Exactly one Feature in the derived Component SHOULD have a prov:wasDerivedFrom property that refers to the template Feature.
At least one Feature in the derived Component SHOULD have a prov:wasDerivedFrom property that refers to the template Feature.
The subject and object Component objects MUST have opposite orientations.
The subject and object overlap in space, but portions of each are outside of the other.
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 less than the start of the location for object.
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.
Reverse complement is an attribute of the feature, where the feature is in the 3' to 5' direction.
The subject and object Component objects MUST have the same orientation.
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 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.
The subject entirely contains the object: they do not share a boundary.
The end of the location for subject is less than the start of the location for object.
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.
Any number of Feature objects in the derived Component MAY have prov:wasDerivedFrom properties that refer to the template Feature.
No more than one Feature in the derived Component SHOULD have a prov:wasDerivedFrom property that refers to the template Feature.
The purpose of the om:BinaryPrefix class is to describe standard binary prefixes such as "kibi", "mebi", "gibi", etc.
om:CompoundUnit is an abstract class that is extended by other classes to describe units of measure that can be represented as combinations of multiple other units of measure.
The purpose of the om:Measure class is to link a numerical value to a om:Unit.
om:Prefix is an abstract class that is extended by other classes to describe factors that are commonly represented by standard unit prefixes.
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.
The purpose of the om:SIPrefix class is to describe standard SI prefixes such as "milli", "centi", "kilo", etc.
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.
om:Unit is an abstract class that is extended by other classes to describe units of measure using a shared set of properties.
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.
The purpose of the om:UnitExponentiation class is to describe a unit of measure that is raised to an integer power.
The purpose of the om:UnitMultiplication class is to describe a unit of measure that is the multiplication of two other units of measure.
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).
A role is particular behaviour which a material entity may exhibit.
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.
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.
DNA-binding transcription factor activity
Representation of an entity used in a systems biology knowledge reconstruction, such as a model, pathway, network.
The function of a physical or conceptual entity, that is its role, in the execution of an event or process.
Set of assumptions that underlay a mathematical description.
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.
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.
Substance that changes the velocity of a process without itself being consumed or transformed by the reaction.
Substance that decreases the probability of a chemical reaction without itself being consumed or transformed by the reaction.
Modelling approach where the quantities of participants are considered continuous, and represented by real values. The associated simulation methods make use of differential equations.
Modelling approach where the quantities of participants are considered discrete, and represented by integer values. The associated simulation methods can be deterministic or stochastic.
An event involving physical entities that results in modification of structure, location, or free energy.
Negative modulation of the execution of a process.
Positive modulation of the execution of a process.
An event involving one or more chemical entities that modifies the electrochemical structure of at least one of the participants.
Complete disappearance of a physical entity.
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.
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.
A real thing, defined by its properties or the actions it performs, rather than it physico-chemical structure.
Naturally occurring macromolecule formed by the repetition of amino-acid residues linked by peptidic bonds. A polypeptide chain is synthesized by the ribosome.
Entity composed of several independant components that are not linked by covalent bonds.
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.
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 region of DNA to which various transcription factors and RNA polymerase must bind in order to initiate transcription for a gene.
Conceptual or material entity that is the object of an inhibition process, and is acted upon by an inhibitor.
Conceptual or material entity that is the object of a stimulation process, and is acted upon by a stimulator.
Conceptual or material entity that is the object of a modification process, and is acted upon by a modifier.
An entity that acts as the starting material for genetic production (http://identifiers.org/biomodels.sbo/SBO:0000589).
Modeling approach which combines multiple canonical modeling frameworks. For example, a hybrid model could consider both continuous (represented by real values) and discrete (represented by integers) participants. Hybrid models are executed with hybrid simulation algorithms. For example, a hybrid continuous-discrete model may be simulation using a combination of stochastic simulation and ordinary differential equations.
Modelling approach which captures bounds on the possible behavior of a system, which may be further reduced using an objective function.
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.
Any extent of continuous biological sequence.
Region in mRNA where ribosome assembles.
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.
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.
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.
A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
An attribute describes a quality of sequence.
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.
Attributes added to describe the different kinds of replicon. SO workshop, September 2006. When a nucleotide polymer has only one strand.
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.
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.
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.
Forward is an attribute of the feature, where the feature is in the 5' to 3' direction.
Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer.
Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation.
Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation.
Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters.
Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters.
A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.
Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation.
BioPAX is an exchange format for pathway data, with its data model defined in OWL.
CellML, the format for mathematical models of biological and other networks.
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.
An Agent is something that bears some form of responsibility for an Activity taking place, such as a person, organization, or software agent.
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.
A Plan is used to describe a set of actions or steps intended to achieve a specific goal or outcome.
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.