IRI:
http://sbols.org/v2
Current version:
1.0

Abstract

The OWL version of the SBOL data model

Table of Content

  1. Classes
  2. Object Properties
  3. Data Properties
  4. Named Individuals
  5. General Axioms
  6. Namespace Declarations

Classes

Accessc back to ToC or Class ToC

IRI: http://sbols.org/v2#Access

Not represented in SBOL directly. It is used in the OWL representation to enforce choosing an access type using one of its subclasses.

is equivalent to
private c or public c
has super-classes
SBOLVocabulary c
has sub-classes
private c, public c
is in range of
access op
is disjoint with
CombinatorialDerivationStrategy c, Direction c, Orientation c, Refinement c, Restriction c, RoleIntegration c, VariableOperator c

Attachmentc back to ToC or Class ToC

IRI: http://sbols.org/v2#Attachment

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.

has super-classes
TopLevel c
is in domain of
format op, hash dp, size dp
is disjoint with
Collection c, CombinatorialDerivation c, ComponentDefinition c, GenericTopLevel c, Implementation c, Model c, ModuleDefinition c, Sequence c

CDSc back to ToC or Class ToC

IRI: http://sbols.org/v2#CDS

CDS DNA component

is equivalent to
role op some s o:0000316 c
has super-classes
DNA c
is disjoint with
EngineeredGene c, Gene c, Operator c, Promoter c, RBS c, Terminator c

Collectionc back to ToC or Class ToC

IRI: http://sbols.org/v2#Collection

Groups together a set of TopLevel objects that have something in common.

has super-classes
TopLevel c
is in domain of
member op
is in range of
variantCollection op
is disjoint with
Attachment c, CombinatorialDerivation c, ComponentDefinition c, GenericTopLevel c, Implementation c, Model c, ModuleDefinition c, Sequence c

CombinatorialDerivationc back to ToC or Class ToC

IRI: http://sbols.org/v2#CombinatorialDerivation

The purpose of the CombinatorialDerivation class is to specify combinatorial genetic designs without having to specify every possible design variant. For example, a CombinatorialDerivation can be used to specify a library of reporter gene variants that include different promoters and RBSs without having to specify a ComponentDefinition for every possible combination of promoter, RBS, and CDS in the library. ComponentDefinition objects that realize a CombinatorialDerivation can be derived in accordance with the class properties template, variableComponents, and strategy.

has super-classes
TopLevel c
template op some ComponentDefinition c
is in domain of
strategy op, template op, variableComponent op
is in range of
variantDerivation op
is disjoint with
Attachment c, Collection c, ComponentDefinition c, GenericTopLevel c, Implementation c, Model c, ModuleDefinition c, Sequence c

CombinatorialDerivationStrategyc back to ToC or Class ToC

IRI: http://sbols.org/v2#CombinatorialDerivationStrategy

Specifies strategy types for combinatorial derivations.

is equivalent to
enumerate c or sample c
has super-classes
SBOLVocabulary c
has sub-classes
enumerate c, sample c
is in range of
strategy op
is disjoint with
Access c, Direction c, Orientation c, Refinement c, Restriction c, RoleIntegration c, VariableOperator c

Complexc back to ToC or Class ToC

IRI: http://sbols.org/v2#Complex

Complex component definition

is equivalent to
ComponentDefinition c and ( type op some complex c)
has super-classes
ComponentDefinition c
is disjoint with
DNA c, Protein c, RNA c, SmallMolecule c

Componentc back to ToC or Class ToC

IRI: http://sbols.org/v2#Component

The Component class is used to compose ComponentDefinition objects into a structural hierarchy. For example,the ComponentDefinition of a gene could contain four Component objects: a promoter, RBS, CDS, and terminator. In turn, the ComponentDefinition of the promoter Component could contain Component objects defined as various operator sites.

has super-classes
ComponentInstance c
is in domain of
isComponentOf op, isObjectOf op, isSubjectOf op, roleIntegration op
is in range of
component op, object op, subject op, variable op
is disjoint with
FunctionalComponent c

ComponentDefinitionc back to ToC or Class ToC

IRI: http://sbols.org/v2#ComponentDefinition

Can be used to represent biological design components such as DNA, RNA and small molecules.

is equivalent to
Complex c or DNA c or Protein c or RNA c or SmallMolecule c
has super-classes
TopLevel c
has sub-classes
Complex c, DNA c, Protein c, RNA c, SmallMolecule c
is in domain of
sequence op, sequenceAnnotation op, sequenceConstraint op
is in range of
isSequenceOf op, template op, variant op
is disjoint with
Attachment c, Collection c, CombinatorialDerivation c, GenericTopLevel c, Implementation c, Model c, ModuleDefinition c, Sequence c

ComponentInstancec back to ToC or Class ToC

IRI: http://sbols.org/v2#ComponentInstance

The ComponentInstance abstract class is inherited by SBOL classes that represent the usage or occurrence of a ComponentDefinition within a larger design (that is, another ComponentDefinition or ModuleDefinition).

is equivalent to
Component c or FunctionalComponent c
has super-classes
Identified c
access op some Access c
definition op some ComponentDefinition c
has sub-classes
Component c, FunctionalComponent c
is in domain of
access op
is in range of
local op, remote op

Cutc back to ToC or Class ToC

IRI: http://sbols.org/v2#Cut

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 that corresponds to the index of a character in the elements String of a Sequence.

has super-classes
Location c
is in domain of
at dp
is disjoint with
GenericLocation c, Range c

differentFromc back to ToC or Class ToC

IRI: http://sbols.org/v2#differentFrom

The definition property of the subject Component MUST NOT refer to the same ComponentDefinition as that of the object Component.

has super-classes
Restriction c
is disjoint with
oppositeOrientationAs c, precedes c, sameOrientationAs c

Directionc back to ToC or Class ToC

IRI: http://sbols.org/v2#Direction

Not represented in SBOL directly. It is used in the OWL representation to enforce choosing a direction type using one of its subclasses.

is equivalent to
in c or inout c or none c or out c
has super-classes
SBOLVocabulary c
has sub-classes
in c, inout c, none c, out c
is in range of
direction op
is disjoint with
Access c, CombinatorialDerivationStrategy c, Orientation c, Refinement c, Restriction c, RoleIntegration c, VariableOperator c

DNAc back to ToC or Class ToC

IRI: http://sbols.org/v2#DNA

DNA component definition

is equivalent to
ComponentDefinition c and ( type op some dna region c)
has super-classes
ComponentDefinition c
has sub-classes
CDS c, EngineeredGene c, Gene c, Operator c, Promoter c, RBS c, Terminator c
is disjoint with
Complex c, Protein c, RNA c, SmallMolecule c

Effectorc back to ToC or Class ToC

IRI: http://sbols.org/v2#Effector

Effector small molecule

is equivalent to
role op some c h e b i:35224 c
has super-classes
SmallMolecule c

EngineeredGenec back to ToC or Class ToC

IRI: http://sbols.org/v2#EngineeredGene

EngineeredGene DNA component

is equivalent to
role op some s o:0000280 c
has super-classes
DNA c
is disjoint with
CDS c, Gene c, Operator c, Promoter c, RBS c, Terminator c

enumeratec back to ToC or Class ToC

IRI: http://sbols.org/v2#enumerate

A user SHOULD derive all possible ComponentDefinition objects specified by the CombinatorialDerivation.

has super-classes
CombinatorialDerivationStrategy c
has members
enumerate ni
is disjoint with
sample c
is also defined as
named individual

FunctionalComponentc back to ToC or Class ToC

IRI: http://sbols.org/v2#FunctionalComponent

A FunctionalComponent is an instance of a ComponentDefinition being used as part of a ModuleDefinition. The ModuleDefinition describes how the that describes how the FunctionalComponent interacts with others and summarizes their aggregate function

has super-classes
ComponentInstance c
direction op some Direction c
is in domain of
direction op
is in range of
functionalComponent op, participant op
is disjoint with
Component c

Genec back to ToC or Class ToC

IRI: http://sbols.org/v2#Gene

Gene DNA component

is equivalent to
role op some s o:0000704 c
has super-classes
DNA c
is disjoint with
CDS c, EngineeredGene c, Operator c, Promoter c, RBS c, Terminator c

GenericLocationc back to ToC or Class ToC

IRI: http://sbols.org/v2#GenericLocation

While the Range and Cut classes are best suited to specifying regions on Sequence objects with IUPAC encodings, the GenericLocation class is included as a starting point for specifying regions on Sequence objects with different encoding properties and potentially nonlinear structure. This class can also be used to set the orientation of a SequenceAnnotation and any associated Component when their parent ComponentDefinition is a partial design that lacks a Sequence.

has super-classes
Location c
is disjoint with
Cut c, Range c

GenericTopLevelc back to ToC or Class ToC

IRI: http://sbols.org/v2#GenericTopLevel

The GenericTopLevel class is used to represent top-level entities whose purpose is to contain a set of annotations that are independent of any other class of SBOL object.

has super-classes
TopLevel c
is disjoint with
Attachment c, Collection c, CombinatorialDerivation c, ComponentDefinition c, Implementation c, Model c, ModuleDefinition c, Sequence c

Identifiedc back to ToC or Class ToC

IRI: http://sbols.org/v2#Identified

Represents SBOL objects that can be identified uniquely using URIs.

has sub-classes
ComponentInstance c, Interaction c, Location c, MapsTo c, Module c, Participation c, SequenceAnnotation c, SequenceConstraint c, TopLevel c, VariableComponent c
is in domain of
displayId dp, persistentIdentity op, version dp

Implementationc back to ToC or Class ToC

IRI: http://sbols.org/v2#Implementation

An Implementation represents an instance of a synthetic biological construct, and describes the build phase of a design-built-test-learn workflow. Importantly, an Implementation can be associated with a laboratory sample that was already built, or that is to be built in the future. An Implementation can also represent virtual and simulated instances. An Implementation may be linked back to its original design (either a ModuleDefinition or ComponentDefinition) using the wasDerivedFroms property inherited from the Identified superclass. An Implementation may also link to a ModuleDefinition or ComponentDefinition that specifies its realized structure and/or function.

has super-classes
TopLevel c
is in domain of
built op
is disjoint with
Attachment c, Collection c, CombinatorialDerivation c, ComponentDefinition c, GenericTopLevel c, Model c, ModuleDefinition c, Sequence c

inc back to ToC or Class ToC

IRI: http://sbols.org/v2#in

Indicates that the FunctionalComponent is an input.

has super-classes
Direction c
has members
in ni
is disjoint with
inout c, none c, out c
is also defined as
named individual

inlinec back to ToC or Class ToC

IRI: http://sbols.org/v2#inline

The region specified by this Location is on the elements of a Sequence.

has super-classes
Orientation c
has members
inline ni
is disjoint with
reverseComplement c
is also defined as
named individual

inoutc back to ToC or Class ToC

IRI: http://sbols.org/v2#inout

Indicates that the FunctionalComponent is both an input and output.

has super-classes
Direction c
has members
inout ni
is disjoint with
in c, none c, out c
is also defined as
named individual

Interactionc back to ToC or Class ToC

IRI: http://sbols.org/v2#Interaction

Provides more detailed description of how the FunctionalComponent objects of a ModuleDefinition are intended to work together.

has super-classes
Identified c
is in domain of
participation op
is in range of
interaction op

Locationc back to ToC or Class ToC

IRI: http://sbols.org/v2#Location

Extended by the Range, Cut, and GenericLocation classes.

is equivalent to
Cut c or GenericLocation c or Range c
has super-classes
Identified c
has sub-classes
Cut c, GenericLocation c, Range c
is in domain of
orientation op
is in range of
location op

MapsToc back to ToC or Class ToC

IRI: http://sbols.org/v2#MapsTo

When ComponentDefinition and ModuleDefinition objects are composed into structural and functional hierarchies using ComponentInstance and Module objects, it is often the case that some ComponentInstance objects are intended to represent the same entity in the overall design. The purpose of the MapsTo class is to make these identity relationships clear and explicit. For example, consider a ModuleDefinition for a genetic inverter that includes a FunctionalComponent for an abstract repressor protein. When this ModuleDefinition is instantiated within a “higher level” ModuleDefinition that includes a FunctionalComponent for a LacI protein, the MapsTo object can be used to indicate that the repressor protein in the first ModuleDefinition is LacI in the context of the composite design.

has super-classes
Identified c
local op some ComponentInstance c
refinement op some Refinement c
remote op some ComponentInstance c
remote op only access op some public c
is in domain of
local op, refinement op, remote op
is in range of
mapsTo op

mergec back to ToC or Class ToC

IRI: http://sbols.org/v2#merge

In the context of the ComponentDefinition or ModuleDefinition that contains the owner of the MapsTo, all references to the local ComponentInstance or the remote ComponentInstance MUST dereference to both objects.

has super-classes
Refinement c
has members
merge ni
is disjoint with
useLocal c, useRemote c, verifyIdentical c
is also defined as
named individual

mergeRolesc back to ToC or Class ToC

IRI: http://sbols.org/v2#mergeRoles

Indicates to use the union of the two sets: both the set of zero or more roles given for this Component as well as the set of zero or more roles given for the included subComponentDefinition.

has super-classes
RoleIntegration c
is disjoint with
overrideRoles c

Modelc back to ToC or Class ToC

IRI: http://sbols.org/v2#Model

Serves as a placeholder for an external computational model and provide additional meta-data to enable better reasoning about the contents of this model.

has super-classes
TopLevel c
is in domain of
framework op, language op
is in range of
model op
is disjoint with
Attachment c, Collection c, CombinatorialDerivation c, ComponentDefinition c, GenericTopLevel c, Implementation c, ModuleDefinition c, Sequence c

Modulec back to ToC or Class ToC

IRI: http://sbols.org/v2#Module

Represents the usage or occurrence of a ModuleDefinition within a larger design.

has super-classes
Identified c
definition op some ModuleDefinition c
is in range of
module op

ModuleDefinitionc back to ToC or Class ToC

IRI: http://sbols.org/v2#ModuleDefinition

Represents a grouping of structural and functional entities in a biological design.

has super-classes
TopLevel c
is in domain of
functionalComponent op, interaction op, model op, module op
is disjoint with
Attachment c, Collection c, CombinatorialDerivation c, ComponentDefinition c, GenericTopLevel c, Implementation c, Model c, Sequence c

mRNAc back to ToC or Class ToC

IRI: http://sbols.org/v2#mRNA

mRNA RNA component

is equivalent to
role op some s o:0000234 c
has super-classes
RNA c

NASequencec back to ToC or Class ToC

IRI: http://sbols.org/v2#NASequence

Nucleic acid sequence

has super-classes
Sequence c
encoding op some naseq.html c
isSequenceOf op only DNA c or RNA c
is disjoint with
ProteinSequence c, SMILES c

nonec back to ToC or Class ToC

IRI: http://sbols.org/v2#none

Indicates that the FunctionalComponent is neither an input or output.

has super-classes
Direction c
has members
none ni
is disjoint with
in c, inout c, out c
is also defined as
named individual

onec back to ToC or Class ToC

IRI: http://sbols.org/v2#one

Exactly one Component in the derived ComponentDefinition SHOULD have a wasDerivedFroms property that refers to the template Component.

has super-classes
VariableOperator c
has members
one ni
is disjoint with
oneOrMore c, zeroOrMore c, zeroOrOne c
is also defined as
named individual

oneOrMorec back to ToC or Class ToC

IRI: http://sbols.org/v2#oneOrMore

At least one Component in the derived ComponentDefinition SHOULD have a wasDerivedFroms property that refers to the template Component.

has super-classes
VariableOperator c
has members
oneOrMore ni
is disjoint with
one c, zeroOrMore c, zeroOrOne c
is also defined as
named individual

Operatorc back to ToC or Class ToC

IRI: http://sbols.org/v2#Operator

Operator DNA component

is equivalent to
role op some s o:0000057 c
has super-classes
DNA c
is disjoint with
CDS c, EngineeredGene c, Gene c, Promoter c, RBS c, Terminator c

oppositeOrientationAsc back to ToC or Class ToC

IRI: http://sbols.org/v2#oppositeOrientationAs

The subject and object Component objects MUST have opposite orientations. If each one is associated with a SequenceAnnotation, then the orientation URIs of the Location objects of one SequenceAnnotation MUST NOT be among those of the other SequenceAnnotation.

has super-classes
Restriction c
is disjoint with
differentFrom c, precedes c, sameOrientationAs c

Orientationc back to ToC or Class ToC

IRI: http://sbols.org/v2#Orientation

Provides values for the orientation of a Sequence entity.

is equivalent to
inline c or reverseComplement c
has super-classes
SBOLVocabulary c
has sub-classes
inline c, reverseComplement c
is in range of
orientation op
is disjoint with
Access c, CombinatorialDerivationStrategy c, Direction c, Refinement c, Restriction c, RoleIntegration c, VariableOperator c

outc back to ToC or Class ToC

IRI: http://sbols.org/v2#out

Indicates that the FunctionalComponent is an output.

has super-classes
Direction c
has members
out ni
is disjoint with
in c, inout c, none c
is also defined as
named individual

overrideRolesc back to ToC or Class ToC

IRI: http://sbols.org/v2#overrideRoles

Indicates that in the context of a Component, ignore any roles given for the included subComponentDefinition. Instead use only the set of zero or more roles given for this Component.

has super-classes
RoleIntegration c
is disjoint with
mergeRoles c

Participationc back to ToC or Class ToC

IRI: http://sbols.org/v2#Participation

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

has super-classes
Identified c
participant op some FunctionalComponent c
is in domain of
participant op
is in range of
participation op

precedesc back to ToC or Class ToC

IRI: http://sbols.org/v2#precedes

The position of the subject Component MUST precede that of the object Component. If each one is associated with a SequenceAnnotation, then the SequenceAnnotation associated with the subject Component MUST specify a region that starts before the region specified by the SequenceAnnotation associated with the object Component.

has super-classes
Restriction c
is disjoint with
differentFrom c, oppositeOrientationAs c, sameOrientationAs c

privatec back to ToC or Class ToC

IRI: http://sbols.org/v2#private

Indicates that a ComponentInstance MUST NOT be referred to by remote MapsTo objects.

has super-classes
Access c
has members
private ni
is disjoint with
public c
is also defined as
named individual

Promoterc back to ToC or Class ToC

IRI: http://sbols.org/v2#Promoter

Promoter DNA component

is equivalent to
role op some s o:0000167 c
has super-classes
DNA c
is disjoint with
CDS c, EngineeredGene c, Gene c, Operator c, RBS c, Terminator c

Proteinc back to ToC or Class ToC

IRI: http://sbols.org/v2#Protein

Protein component definition

is equivalent to
ComponentDefinition c and ( type op some protein c)
has super-classes
ComponentDefinition c
is disjoint with
Complex c, DNA c, RNA c, SmallMolecule c

ProteinSequencec back to ToC or Class ToC

IRI: http://sbols.org/v2#ProteinSequence

Protein sequence

has super-classes
Sequence c
encoding op some http://www.chem.qmul.ac.uk/iupac/AminoAcid/ c
isSequenceOf op only Protein c
is disjoint with
NASequence c, SMILES c

publicc back to ToC or Class ToC

IRI: http://sbols.org/v2#public

Indicates that a ComponentInstance MAY be referred to by remote MapsTo objects.

has super-classes
Access c
has members
public ni
is disjoint with
private c
is also defined as
named individual

Rangec back to ToC or Class ToC

IRI: http://sbols.org/v2#Range

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.

has super-classes
Location c
is in domain of
end dp, start dp
is disjoint with
Cut c, GenericLocation c

RBSc back to ToC or Class ToC

IRI: http://sbols.org/v2#RBS

RBS DNA component

is equivalent to
role op some s o:0000139 c
has super-classes
DNA c
is disjoint with
CDS c, EngineeredGene c, Gene c, Operator c, Promoter c, Terminator c

Refinementc back to ToC or Class ToC

IRI: http://sbols.org/v2#Refinement

Not represented in SBOL directly. It is used in the OWL representation to enforce choosing a refinement using one of its subclasses.

is equivalent to
merge c or useLocal c or useRemote c or verifyIdentical c
has super-classes
SBOLVocabulary c
has sub-classes
merge c, useLocal c, useRemote c, verifyIdentical c
is in range of
refinement op
is disjoint with
Access c, CombinatorialDerivationStrategy c, Direction c, Orientation c, Restriction c, RoleIntegration c, VariableOperator c

Restrictionc back to ToC or Class ToC

IRI: http://sbols.org/v2#Restriction

Specifies relative positions of sub components in a design.

is equivalent to
differentFrom c or oppositeOrientationAs c or precedes c or sameOrientationAs c
has super-classes
SBOLVocabulary c
has sub-classes
differentFrom c, oppositeOrientationAs c, precedes c, sameOrientationAs c
is in range of
restriction op
is disjoint with
Access c, CombinatorialDerivationStrategy c, Direction c, Orientation c, Refinement c, RoleIntegration c, VariableOperator c

reverseComplementc back to ToC or Class ToC

IRI: http://sbols.org/v2#reverseComplement

The region specified by this Location is on the reverse-complement translation of the elements of a Sequence. The exact nature of this translation depends on the encoding of the Sequence

has super-classes
Orientation c
has members
reverseComplement ni
is disjoint with
inline c
is also defined as
named individual

RNAc back to ToC or Class ToC

IRI: http://sbols.org/v2#RNA

RNA component definition

is equivalent to
ComponentDefinition c and ( type op some rna region c)
has super-classes
ComponentDefinition c
has sub-classes
mRNA c
is disjoint with
Complex c, DNA c, Protein c, SmallMolecule c

RoleIntegrationc back to ToC or Class ToC

IRI: http://sbols.org/v2#RoleIntegration

Not represented in SBOL directly. It is used in the OWL representation to enforce choosing a role integration using one of its subclasses.

is equivalent to
mergeRoles c or overrideRoles c
has super-classes
SBOLVocabulary c
has sub-classes
mergeRoles c, overrideRoles c
is in range of
roleIntegration op
is disjoint with
Access c, CombinatorialDerivationStrategy c, Direction c, Orientation c, Refinement c, Restriction c, VariableOperator c

sameOrientationAsc back to ToC or Class ToC

IRI: http://sbols.org/v2#sameOrientationAs

The subject and object Component objects MUST have the same orientation. If each one is associated with a SequenceAnnotation, then the orientation URIs of the Location objects of the first SequenceAnnotation MUST be among those of the second SequenceAnnotation, and vice versa.

has super-classes
Restriction c
is disjoint with
differentFrom c, oppositeOrientationAs c, precedes c

samplec back to ToC or Class ToC

IRI: http://sbols.org/v2#sample

A user SHOULD derive a subset of all possible ComponentDefinition objects specified by CombinatorialDerivation. The manner in which this subset is chosen is for the user to decide.

has super-classes
CombinatorialDerivationStrategy c
has members
sample ni
is disjoint with
enumerate c
is also defined as
named individual

SBOLVocabularyc back to ToC or Class ToC

IRI: http://sbols.org/v2#SBOLVocabulary

Not represented in SBOL directly. It is used to group SBOL specific terms.

is equivalent to
Access c or CombinatorialDerivationStrategy c or Direction c or Orientation c or Refinement c or Restriction c or RoleIntegration c or VariableOperator c
has sub-classes
Access c, CombinatorialDerivationStrategy c, Direction c, Orientation c, Refinement c, Restriction c, RoleIntegration c, VariableOperator c

Sequencec back to ToC or Class ToC

IRI: http://sbols.org/v2#Sequence

The purpose of the Sequence class is to represent the primary structure of a ComponentDefinition object and the manner in which it is encoded. This representation is accomplished by means of the elements property and encoding property.

has super-classes
TopLevel c
elements dp some string
has sub-classes
NASequence c, ProteinSequence c, SMILES c
is in domain of
elements dp, encoding op, isSequenceOf op
is in range of
sequence op
is disjoint with
Attachment c, Collection c, CombinatorialDerivation c, ComponentDefinition c, GenericTopLevel c, Implementation c, Model c, ModuleDefinition c

SequenceAnnotationc back to ToC or Class ToC

IRI: http://sbols.org/v2#SequenceAnnotation

The SequenceAnnotation class describes one or more regions of interest on the Sequence objects referred to by its parent ComponentDefinition. In addition, SequenceAnnotation objects can describe the substructure of their parent ComponentDefinition through association with the Component objects contained by this ComponentDefinition.

has super-classes
Identified c
location op some Location c
is in domain of
location op
is in range of
sequenceAnnotation op

SequenceConstraintc back to ToC or Class ToC

IRI: http://sbols.org/v2#SequenceConstraint

The SequenceConstraint class can be used to assert restrictions on the relative, sequence-based positions of pairs of Component objects contained by the same parent ComponentDefinition. The primary purpose of this class is to enable the specification of partially designed ComponentDefinition objects, for which the precise positions or orientations of their contained Component objects are not yet fully determined. Each SequenceConstraint includes the restriction, subject, and object properties.

has super-classes
Identified c
object op some Component c
restriction op some Restriction c
subject op some Component c
is in domain of
object op, restriction op, subject op
is in range of
isObjectOf op, isSubjectOf op, sequenceConstraint op

SmallMoleculec back to ToC or Class ToC

IRI: http://sbols.org/v2#SmallMolecule

SmallMolecule component definition

is equivalent to
ComponentDefinition c and ( type op some small molecule c)
has super-classes
ComponentDefinition c
has sub-classes
Effector c
is disjoint with
Complex c, DNA c, Protein c, RNA c

SMILESc back to ToC or Class ToC

IRI: http://sbols.org/v2#SMILES

SMILES sequence

has super-classes
Sequence c
encoding op some opensmiles.html c
isSequenceOf op only SmallMolecule c
is disjoint with
NASequence c, ProteinSequence c

Terminatorc back to ToC or Class ToC

IRI: http://sbols.org/v2#Terminator

Terminator DNA component

is equivalent to
role op some s o:0000141 c
has super-classes
DNA c
is disjoint with
CDS c, EngineeredGene c, Gene c, Operator c, Promoter c, RBS c

TopLevelc back to ToC or Class ToC

IRI: http://sbols.org/v2#TopLevel

Can be used to represent biological design components such as DNA, RNA and small molecules.

has super-classes
Identified c
has sub-classes
Attachment c, Collection c, CombinatorialDerivation c, ComponentDefinition c, GenericTopLevel c, Implementation c, Model c, ModuleDefinition c, Sequence c
is in range of
member op

useLocalc back to ToC or Class ToC

IRI: http://sbols.org/v2#useLocal

In the context of the ComponentDefinition or ModuleDefinition that contains the owner of the MapsTo, all references to the remote ComponentInstance MUST dereference to the local ComponentInstance instead.

has super-classes
Refinement c
has members
useLocal ni
is disjoint with
merge c, useRemote c, verifyIdentical c
is also defined as
named individual

useRemotec back to ToC or Class ToC

IRI: http://sbols.org/v2#useRemote

Indicates that all references to the local ComponentInstance MUST dereference to the remote ComponentInstance instead.

has super-classes
Refinement c
has members
useRemote ni
is disjoint with
merge c, useLocal c, verifyIdentical c
is also defined as
named individual

VariableComponentc back to ToC or Class ToC

IRI: http://sbols.org/v2#VariableComponent

The VariableComponent class can be used to specify a choice of ComponentDefinition objects for any new 35 Component derived from a template Component in the template ComponentDefinition.

has super-classes
Identified c
operator op some VariableOperator c
variable op some Component c
is in domain of
operator op, variable op, variant op, variantCollection op, variantDerivation op
is in range of
variableComponent op

VariableOperatorc back to ToC or Class ToC

IRI: http://sbols.org/v2#VariableOperator

Specifies the operator types for combinatorial derivations.

is equivalent to
one c or oneOrMore c or zeroOrMore c or zeroOrOne c
has super-classes
SBOLVocabulary c
has sub-classes
one c, oneOrMore c, zeroOrMore c, zeroOrOne c
is in range of
operator op
is disjoint with
Access c, CombinatorialDerivationStrategy c, Direction c, Orientation c, Refinement c, Restriction c, RoleIntegration c

verifyIdenticalc back to ToC or Class ToC

IRI: http://sbols.org/v2#verifyIdentical

Indicates that the definition properties of the local and remote ComponentInstance objects MUST refer to the same ComponentDefinition.

has super-classes
Refinement c
has members
verifyIdentical ni
is disjoint with
merge c, useLocal c, useRemote c
is also defined as
named individual

zeroOrMorec back to ToC or Class ToC

IRI: http://sbols.org/v2#zeroOrMore

Any number of Component objects in the derived ComponentDefinition MAY have wasDerivedFroms properties that refer to the template Component.

has super-classes
VariableOperator c
is disjoint with
one c, oneOrMore c, zeroOrOne c
is also defined as
named individual

zeroOrOnec back to ToC or Class ToC

IRI: http://sbols.org/v2#zeroOrOne

No more than one Component in the derived ComponentDefinition SHOULD have a wasDerivedFroms property that refers to the template Component.

has super-classes
VariableOperator c
has members
zeroOrMore ni, zeroOrOne ni
is disjoint with
one c, oneOrMore c, zeroOrMore c
is also defined as
named individual

Object Properties

accessop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#access

The access property is a REQUIRED URI that indicates whether the ComponentInstance can be referred to remotely by a MapsTo on another ComponentInstance or Module contained by a different parent ComponentDefinition or ModuleDefinition (one that does not contain this ComponentInstance)

has characteristics: functional

has domain
ComponentInstance c
has range
Access c

builtop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#built

The built property is OPTIONAL and MAY contain a URI that MUST refer to a TopLevel object that is either a ComponentDefinition or ModuleDefinition. This ComponentDefinition or ModuleDefinition is intended to describe the actual physical structure and/or functional behavior of the Implementation.

has characteristics: functional

has domain
Implementation c
has range
ComponentDefinition c or ModuleDefinition c

componentop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#component

The components property is OPTIONAL and MAY specify a set of Component objects that are contained by the ComponentDefinition. The set of relations between Component and ComponentDefinition objects is strictly acyclic.

has domain
ComponentDefinition c or SequenceAnnotation c
has range
Component c
is inverse of
isComponentOf op

definitionop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#definition

The definition property is a REQUIRED URI that refers to the ComponentDefinition of the ComponentInstance. As described in the previous section, this ComponentDefinition effectively provides information about the types and roles of the ComponentInstance.

has characteristics: functional

has domain
ComponentInstance c or Module c
has range
ComponentDefinition c or ModuleDefinition c
is inverse of
isDefinitionOf op

directionop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#direction

Each FunctionalComponent MUST specify via the direction property whether it serves as an input, output, both, or neither for its parent ModuleDefinition object.

has characteristics: functional

has domain
FunctionalComponent c
has range
Direction c

encodingop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#encoding

The encoding property is REQUIRED and has a data type of URI. This property MUST indicate how the elements property of a Sequence MUST be formed and interpreted.

has characteristics: functional

has domain
Sequence c

formatop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#format

The format property is OPTIONAL and MAY contain a URI that specifies the format of the attached file. It is RECOMMENDED that this URI refer to a term from the EMBRACE Data and Methods (EDAM) ontology

has characteristics: functional

has domain
Attachment c

frameworkop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#framework

The framework property is REQUIRED and MUST contain a URI that specifies the framework in which the model is implemented. It is RECOMMENDED this URI refer to a term from the modeling framework branch of the SBO when possible.

has characteristics: functional

has domain
Model c

functionalComponentop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#functionalComponent

The property is OPTIONAL and MAY be used specify a set of FunctionalComponent objects contained by the ModuleDefinition.

has domain
ModuleDefinition c
has range
FunctionalComponent c

interactionop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#interaction

The interaction property is OPTIONAL and MAY be used specify a set of Interaction objects within the ModuleDefinition.

has domain
ModuleDefinition c
has range
Interaction c
is inverse of
isInteractionOf op

isComponentOfop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#isComponentOf

Inverse of the component property.

has domain
Component c
has range
ComponentDefinition c or SequenceAnnotation c
is inverse of
component op

isDefinitionOfop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#isDefinitionOf

Inverse of the definition property.

is inverse of
definition op

isInteractionOfop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#isInteractionOf

Inverse of the interaction property.

is inverse of
interaction op

isMemberOfop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#isMemberOf

Inverse of the member property.

is inverse of
member op

isModuleOfop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#isModuleOf

Inverse of the module property.

is inverse of
module op

isObjectOfop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#isObjectOf

Inverse of the object property

has domain
Component c
has range
SequenceConstraint c
is inverse of
object op

isSequenceOfop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#isSequenceOf

Inverse of the sequence property.

has characteristics: functional

has domain
Sequence c
has range
ComponentDefinition c
is inverse of
sequence op

isSubjectOfop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#isSubjectOf

Inverse of the subject property.

has domain
Component c
has range
SequenceConstraint c
is inverse of
subject op

languageop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#language

The language property is REQUIRED and MUST contain a URI that specifies the language in which the model is implemented. It is RECOMMENDED that this URI refer to a term from the EMBRACE Data and Methods (EDAM) ontology.

has characteristics: functional

has domain
Model c

localop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#local

This REQUIRED property has a data type of URI and is used to refer to the ComponentInstance contained by the “higher level” ComponentDefinition or ModuleDefinition. This local ComponentInstance MUST be contained by the ComponentDefinition or ModuleDefinition that contains the ComponentInstance or Module that owns the MapsTo.

has characteristics: functional

has domain
MapsTo c
has range
ComponentInstance c

locationop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#location

The location property is REQUIRED to specify one or more Location objects that indicate which elements of a Sequence are described by the SequenceAnnotation.

has domain
SequenceAnnotation c
has range
Location c

mapsToop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#mapsTo

The mapsTo property is OPTIONAL and MAY contain a MapsTo object that refers to and links together a ComponentInstance object (both Component objects and FunctionalComponent objects) within a larger design.

has domain
ComponentInstance c or Module c
has range
MapsTo c

memberop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#member

Contains a reference to a top level entity.

has domain
Collection c
has range
TopLevel c
is inverse of
isMemberOf op

modelop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#model

The model property is OPTIONAL and MAY be used to specify a set of URI references to Model objects.

has domain
ModuleDefinition c
has range
Model c

moduleop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#module

The property is OPTIONAL and MAY be used specify a set of Module objects contained by the ModuleDefinition. Note that the set of relations between Module and ModuleDefinition objects is strictly acyclic.

has domain
ModuleDefinition c
has range
Module c
is inverse of
isModuleOf op

objectop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#object

The object property is REQUIRED and MUST contain a URI that refers to a Component contained by the same parent ComponentDefinition that contains the SequenceConstraint. This Component MUST NOT be the same Component that the SequenceConstraint refers to via its subject property.

has characteristics: functional

has domain
SequenceConstraint c
has range
Component c
is inverse of
isObjectOf op

operatorop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#operator

The operator property is REQUIRED and has a data type of URI. This property specifies how many Component objects SHOULD be derived from the template Component during the derivation of a new ComponentDefinition.

has characteristics: functional

has domain
VariableComponent c
has range
VariableOperator c

orientationop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#orientation

Indicates the type of a component's orientation. All subclasses of Location share this property, which can be used to indicate how the region specified by the SequenceAnnotation and any associated double-stranded Component is oriented on the elements of a Sequence from their parent ComponentDefinition

has characteristics: functional

has domain
Location c
has range
Orientation c

participantop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#participant

The participant property MUST specify precisely one FunctionalComponent object that plays the designated role in its parent Interaction object.

has characteristics: functional

has domain
Participation c
has range
FunctionalComponent c

participationop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#participation

The participation property is an OPTIONAL and MAY contain a Participation object, which identifies the roles that its referenced FunctionalComponent plays in the Interaction.

has domain
Interaction c
has range
Participation c

persistentIdentityop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#persistentIdentity

It is used to refer to a set of SBOL objects that are different versions of each other.

has characteristics: functional

has domain
Identified c

refinementop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#refinement

The refinement property is REQUIRED and has a data type of URI. Each MapsTo object MUST specify the rela- 27 tionship between its local and remote ComponentInstance objects.

has characteristics: functional

has domain
MapsTo c
has range
Refinement c

remoteop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#remote

This REQUIRED property has a data type of URI and is used to refer to the ComponentInstance contained by the “lower level” ComponentDefinition or ModuleDefinition. This remote ComponentInstance MUST be contained by the ComponentDefinition or ModuleDefinition that is the definition of the ComponentInstance or Module that owns the MapsTo. Lastly, the access property of the remote ComponentInstance MUST be set to “public.

has characteristics: functional

has domain
MapsTo c
has range
ComponentInstance c

restrictionop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#restriction

The restriction property is REQUIRED and has a data type of URI. This property MUST indicate the type of structural restriction on the positions, orientations, or structural identities of the subject and object Component objects in relation to each other.

has characteristics: functional

has domain
SequenceConstraint c
has range
Restriction c

roleop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#role

Clarifies the potential function of an entity in a biochemical or physical context. When it is used for ComponentDefinitions, it MUST identify terms from ontologies that are consistent with the types property of the ComponentDefinition. For example, the roles property of a DNA or RNA ComponentDefinition could contain URIs identifying terms from the Sequence Ontology (SO).

has domain
Component c or ComponentDefinition c or ModuleDefinition c or Participation c or SequenceAnnotation c

roleIntegrationop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#roleIntegration

A roleIntegration specifies the relationship between a Component instance’s own set of roles and the set of roles on the included sub-ComponentDefinition.

has characteristics: functional

has domain
Component c
has range
RoleIntegration c

sequenceop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#sequence

The sequences property is OPTIONAL and MAY include a set of URIs that refer to Sequence objects. These objects define the primary structure of the ComponentDefinition.

has domain
ComponentDefinition c
has range
Sequence c
is inverse of
isSequenceOf op

sequenceAnnotationop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#sequenceAnnotation

The sequenceAnnotations property is OPTIONAL and MAY contain a set of SequenceAnnotation objects. Each SequenceAnnotation specifies and describes a potentially discontiguous region on the Sequence objects referred to by the ComponentDefinition.

has domain
ComponentDefinition c
has range
SequenceAnnotation c

sequenceConstraintop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#sequenceConstraint

The sequenceConstraints property is OPTIONAL and MAY contain a set of SequenceConstraint objects. These objects describe any restrictions on the relative, sequence-based positions and/or orientations of the Component objects contained by the ComponentDefinition. For example, the ComponentDefinition of a gene might specify that the position of its promoter Component precedes that of its CDS Component. This is particularly useful when a ComponentDefinition lacks a Sequence and therefore cannot specify the precise, sequence-based positions of its Component objects using SequenceAnnotation objects.

has domain
ComponentDefinition c
has range
SequenceConstraint c

sourceop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#source

The source property is REQUIRED and MUST contain a URI reference to the source file for a model.

has characteristics: functional

has domain
Attachment c or Model c

strategyop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#strategy

Indicates combinatorial derivation strategy.

has characteristics: functional

has domain
CombinatorialDerivation c
has range
CombinatorialDerivationStrategy c

subjectop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#subject

The subject property is REQUIRED and MUST contain a URI that refers to a Component contained by the same parent ComponentDefinition that contains the SequenceConstraint.

has characteristics: functional

has domain
SequenceConstraint c
has range
Component c
is inverse of
isSubjectOf op

templateop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#template

The template property is REQUIRED and MUST contain a URI that refers to a ComponentDefinition. This ComponentDefinition is expected to serve as a template for the derivation of new ComponentDefinition objects.

has characteristics: functional

has domain
CombinatorialDerivation c
has range
ComponentDefinition c

typeop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#type

Specifies the category of biochemical or physical entity. For example DNA, protein, or small molecule that a ComponentDefinition object abstracts for the purpose of engineering design. For DNA or RNA entities, additional types fields are used to describe nucleic acid topology (circular / linear) and strandedness (double- or single-stranded).

has domain
ComponentDefinition c or Interaction c

variableop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#variable

The variable property is REQUIRED and MUST contain a URI that refers to a template Component in the template ComponentDefinition.

has characteristics: functional

has domain
VariableComponent c
has range
Component c

variableComponentop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#variableComponent

The variableComponent property is OPTIONAL and MAY contain a set of VariableComponent objects.

has domain
CombinatorialDerivation c
has range
VariableComponent c

variantop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#variant

The variants property is OPTIONAL and MAY contain zero or more URIs that each refer to a ComponentDefinition. This property specifies individual ComponentDefinition objects to serve as options when deriving a new Component from the template Component.

has domain
VariableComponent c
has range
ComponentDefinition c

variantCollectionop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#variantCollection

This property is OPTIONAL and MAY contain zero or more URIs that each refer to a Collection. The members property of each Collection referred to in this way MUST NOT be empty. This property enables the convenient specification of existing groups of ComponentDefinition objects to serve as options when deriving a new Component from the template Component.

has domain
VariableComponent c
has range
Collection c

variantDerivationop back to ToC or Object Property ToC

IRI: http://sbols.org/v2#variantDerivation

The variantDerivations property is OPTIONAL and MAY contain zero or more URIs that each refer to a CombinatorialDerivation. This property enables the convenient specification of ComponentDefinition objects derived in accordance with another CombinatorialDerivation to serve as options when deriving a new Component from the template Component.

has domain
VariableComponent c
has range
CombinatorialDerivation c

Data Properties

atdp back to ToC or Data Property ToC

IRI: http://sbols.org/v2#at

specifies a discrete position that that corresponds to the index of a character in the elements String of a Sequence.

has characteristics: functional

has domain
Cut c

displayIddp back to ToC or Data Property ToC

IRI: http://sbols.org/v2#displayId

The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity.

has characteristics: functional

has domain
Identified c
has range
string

elementsdp back to ToC or Data Property ToC

IRI: http://sbols.org/v2#elements

The elements property is a REQUIRED String of characters that represents the constituents of a biological or chemical molecule. For example, these characters could represent the nucleotide bases of a molecule of DNA, the amino acid residues of a protein, or the atoms and chemical bonds of a small molecule.

has characteristics: functional

has domain
Sequence c
has range
string

enddp back to ToC or Data Property ToC

IRI: http://sbols.org/v2#end

Specifies the inclusive ending position of the Range.

has characteristics: functional

has domain
Range c

hashdp back to ToC or Data Property ToC

IRI: http://sbols.org/v2#hash

The hash property is OPTIONAL and MAY contain a SHA-1 hash of the file contents represented as a hexadecimal digest.

has characteristics: functional

has domain
Attachment c
has range
string

sizedp back to ToC or Data Property ToC

IRI: http://sbols.org/v2#size

The size property is OPTIONAL and MAY contain a long indicating the file size in bytes.

has characteristics: functional

has domain
Attachment c

startdp back to ToC or Data Property ToC

IRI: http://sbols.org/v2#start

Specifies the inclusive starting position of the Range.

has characteristics: functional

has domain
Range c

versiondp back to ToC or Data Property ToC

IRI: http://sbols.org/v2#version

The version property is OPTIONAL and has a data type of String. This property can be used to compare two SBOL objects with the same persistentIdentity.

has characteristics: functional

has domain
Identified c
has range
string

Named Individuals

complexni back to ToC or Named Individual ToC

IRI: http://www.biopax.org/release/biopax-level3.owl#Complex

belongs to
complex c
is also defined as
class

dna regionni back to ToC or Named Individual ToC

IRI: http://www.biopax.org/release/biopax-level3.owl#DnaRegion

belongs to
dna region c
is also defined as
class

enumerateni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#enumerate

A user SHOULD derive all possible ComponentDefinition objects specified by the CombinatorialDerivation.

belongs to
enumerate c
is disjoint with
sample
is also defined as
class

inni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#in

Indicates that the FunctionalComponent is an input.

belongs to
in c
is disjoint with
inout, none, out
is also defined as
class

inlineni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#inline

The region specified by this Location is on the elements of a Sequence.

belongs to
inline c
is disjoint with
reverseComplement
is also defined as
class

inoutni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#inout

Indicates that the FunctionalComponent is both an input and output.

belongs to
inout c
is disjoint with
in, none, out
is also defined as
class

mergeni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#merge

In the context of the ComponentDefinition or ModuleDefinition that contains the owner of the MapsTo, all references to the local ComponentInstance or the remote ComponentInstance MUST dereference to both objects.

belongs to
merge c
is disjoint with
useLocal, useRemote, verifyIdentical
is also defined as
class

noneni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#none

Indicates that the FunctionalComponent is neither an input or output.

belongs to
none c
is disjoint with
in, inout, out
is also defined as
class

oneni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#one

Exactly one Component in the derived ComponentDefinition SHOULD have a wasDerivedFroms property that refers to the template Component.

belongs to
one c
is disjoint with
oneOrMore, zeroOrMore, zeroOrOne
is also defined as
class

oneOrMoreni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#oneOrMore

At least one Component in the derived ComponentDefinition SHOULD have a wasDerivedFroms property that refers to the template Component.

belongs to
oneOrMore c
is disjoint with
one, zeroOrMore, zeroOrOne
is also defined as
class

outni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#out

Indicates that the FunctionalComponent is an output.

belongs to
out c
is disjoint with
in, inout, none
is also defined as
class

privateni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#private

Indicates that a ComponentInstance MUST NOT be referred to by remote MapsTo objects.

belongs to
private c
is disjoint with
public
is also defined as
class

proteinni back to ToC or Named Individual ToC

IRI: http://www.biopax.org/release/biopax-level3.owl#Protein

belongs to
protein c
is also defined as
class

publicni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#public

Indicates that a ComponentInstance MAY be referred to by remote MapsTo objects.

belongs to
public c
is disjoint with
private
is also defined as
class

reverseComplementni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#reverseComplement

The region specified by this Location is on the reverse-complement translation of the elements of a Sequence. The exact nature of this translation depends on the encoding of the Sequence

belongs to
reverseComplement c
is disjoint with
inline
is also defined as
class

rna regionni back to ToC or Named Individual ToC

IRI: http://www.biopax.org/release/biopax-level3.owl#RnaRegion

belongs to
rna region c
is also defined as
class

s o:0000057ni back to ToC or Named Individual ToC

IRI: http://identifiers.org/so/SO:0000057

belongs to
s o:0000057 c
is also defined as
class

s o:0000139ni back to ToC or Named Individual ToC

IRI: http://identifiers.org/so/SO:0000139

belongs to
s o:0000139 c
is also defined as
class

s o:0000141ni back to ToC or Named Individual ToC

IRI: http://identifiers.org/so/SO:0000141

belongs to
s o:0000141 c
is also defined as
class

s o:0000167ni back to ToC or Named Individual ToC

IRI: http://identifiers.org/so/SO:0000167

belongs to
s o:0000167 c
is also defined as
class

s o:0000234ni back to ToC or Named Individual ToC

IRI: http://identifiers.org/so/SO:0000234

belongs to
s o:0000234 c
is also defined as
class

s o:0000280ni back to ToC or Named Individual ToC

IRI: http://identifiers.org/so/SO:0000280

belongs to
s o:0000280 c
is also defined as
class

s o:0000316ni back to ToC or Named Individual ToC

IRI: http://identifiers.org/so/SO:0000316

belongs to
s o:0000316 c
is also defined as
class

s o:0000704ni back to ToC or Named Individual ToC

IRI: http://identifiers.org/so/SO:0000704

belongs to
s o:0000704 c
is also defined as
class

sampleni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#sample

A user SHOULD derive a subset of all possible ComponentDefinition objects specified by CombinatorialDerivation. The manner in which this subset is chosen is for the user to decide.

belongs to
sample c
is disjoint with
enumerate
is also defined as
class

small moleculeni back to ToC or Named Individual ToC

IRI: http://www.biopax.org/release/biopax-level3.owl#SmallMolecule

belongs to
small molecule c
is also defined as
class

useLocalni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#useLocal

In the context of the ComponentDefinition or ModuleDefinition that contains the owner of the MapsTo, all references to the remote ComponentInstance MUST dereference to the local ComponentInstance instead.

belongs to
useLocal c
is disjoint with
merge, useRemote, verifyIdentical
is also defined as
class

useRemoteni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#useRemote

Indicates that all references to the local ComponentInstance MUST dereference to the remote ComponentInstance instead.

belongs to
useRemote c
is disjoint with
merge, useLocal, verifyIdentical
is also defined as
class

verifyIdenticalni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#verifyIdentical

Indicates that the definition properties of the local and remote ComponentInstance objects MUST refer to the same ComponentDefinition.

belongs to
verifyIdentical c
is disjoint with
merge, useLocal, useRemote
is also defined as
class

zeroOrMoreni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#zeroOrMore

Any number of Component objects in the derived ComponentDefinition MAY have wasDerivedFroms properties that refer to the template Component.

belongs to
zeroOrOne c
is disjoint with
one, oneOrMore, zeroOrOne
is also defined as
class

zeroOrOneni back to ToC or Named Individual ToC

IRI: http://sbols.org/v2#zeroOrOne

No more than one Component in the derived ComponentDefinition SHOULD have a wasDerivedFroms property that refers to the template Component.

belongs to
zeroOrOne c
is disjoint with
one, oneOrMore, zeroOrMore
is also defined as
class

General Axioms

All Disjoint Classes back to ToC

Accessc, CombinatorialDerivationStrategyc, Directionc, Orientationc, Refinementc, Restrictionc, RoleIntegrationc, VariableOperatorc

All Disjoint Classes back to ToC

Attachmentc, Collectionc, CombinatorialDerivationc, ComponentDefinitionc, GenericTopLevelc, Implementationc, Modelc, ModuleDefinitionc, Sequencec

All Disjoint Classes back to ToC

CDSc, EngineeredGenec, Genec, Operatorc, Promoterc, RBSc, Terminatorc

All Disjoint Classes back to ToC

Complexc, DNAc, Proteinc, RNAc, SmallMoleculec

All Disjoint Classes back to ToC

Cutc, GenericLocationc, Rangec

All Disjoint Classes back to ToC

NASequencec, ProteinSequencec, SMILESc

All Disjoint Classes back to ToC

differentFromc, oppositeOrientationAsc, precedesc, sameOrientationAsc

All Disjoint Classes back to ToC

inc, inoutc, nonec, outc

All Disjoint Classes back to ToC

mergec, useLocalc, useRemotec, verifyIdenticalc

All Disjoint Classes back to ToC

onec, oneOrMorec, zeroOrMorec, zeroOrOnec

Namespace Declarations back to ToC

default namespace
http://sbols.org/v2#
biopax-level3-owl
http://www.biopax.org/release/biopax-level3.owl#
chebi
http://identifiers.org/chebi/
misc
http://www.chem.qmul.ac.uk/iubmb/misc/
ontolink
http://www.purl.org/ontolink/
owl
http://www.w3.org/2002/07/owl#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
sbol
http://sbols.org/v2#
sbols-org
http://sbols.org/
so
http://identifiers.org/so/
tawny
http://www.purl.org/ontolink/tawny#
www-opensmiles-org
http://www.opensmiles.org/
xsd
http://www.w3.org/2001/XMLSchema#

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni.