| SEP | |
|---|---|
| Title | Combinatorial Design |
| Authors | Matthew Pocock, Jacob Beal, Nicholas Roehner ([email protected]) |
| Editor | Raik Gruenberg |
| Type | Data Model |
| SBOL Version | 2.2 |
| Status | Accepted |
| Created | 19-Aug-2016 |
| Last modified | 12-Sep-2017 |
| Issue | #21 |
We propose adding two new classes, CombinatorialDerivation and VariableComponent, to allow users to represent basic combinatorial designs in SBOL without having to enumerate every possible design variant. For example, a user may wish to encode a library of reporter gene variants that have different promoters and ribosome binding sites (RBS) without having to create a ComponentDefinition for every possible combination of a promoter, RBS, and coding sequence (CDS) in their library. A CombinatorialDerivation refers to a single template ComponentDefinition from which new ComponentDefinition objects can be derived. Each VariableComponent in a CombinatorialDerivation specifies one or more possible definitions for any new sub-Component object derived from a Component in the template ComponentDefinition.
We also propose adding http://sbols.org/v2#differentFrom to the list of recommended URIs for the restriction property of the SequenceConstraint class. This would enable users to specify combinatorial designs in which the choice of a definition for one Component during a derivation can preclude the choice of that definition for another Component during the same derivation.
This SEP was initiated in response to SBOL-Specification/#31. Currently, there is no way to specify the composition of a genetic library or another combinatorial design for common use cases in synthetic biology, such as tuning the performance of a genetic circuit or biosynthetic pathway through combinatorial DNA assembly and screening. While a user could derive multiple ComponentDefinition objects from an abstract ComponentDefinition that lacks a Sequence or a total ordering of its sub-Component objects via SequenceConstraint objects, they would still be unable to use SBOL to specify a finite set of alternative structures to choose from during such a derivation. This SEP is intended to enable users of SBOL to explicitly denote the structural choices to be made and the basic strategy to be used (enumerate vs. sample) during the derivation of a ComponentDefinition in accordance with a combinatorial design.
Here we define two new classes, CombinatorialDerivation and VariableComponent, and provide an update to Table 9 of the SBOL 2.1.0 specification, adding http://sbols.org/v2#differentFrom to the list of recommended URIs for the restriction property of the SequenceConstraint class.
The CombinatorialDerivation class can be used to specify a combinatorial design. ComponentDefinition objects that realize the design can be derived in accordance with the class properties template, variableComponents, and strategy (Figure 1).
Figure 1: Diagram of the CombinatorialDerivation class and its associated properties
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. Consequently, its components property SHOULD contain one or more Component objects that describe its substructure (referred to hereafter as template Component objects), and its sequenceConstraints property MAY also contain one or more SequenceConstraint objects that constrain this substructure.
When a ComponentDefinition is derived in accordance with a CombinatorialDerivation, the wasDerivedFrom property of the derived ComponentDefinition SHOULD refer to the CombinatorialDerivation. When multiple ComponentDefinition objects are derived in accordance with the same CombinatorialDerivation, they MAY be referred to by the members property of a Collection, in which case the wasDerivedFrom property of the Collection SHOULD also refer to this CombinatorialDerivation.
If the types property of the template ComponentDefinition contains one or more URIs, then the types property of the derived ComponentDefinition SHOULD also contain those URIs. The same holds true for the roles properties of these ComponentDefinition objects.
The variableComponents property is OPTIONAL and MAY contain a set of VariableComponent objects. These VariableComponent objects are expected to denote the choices available when deriving the substructure of a new ComponentDefinition in accordance with a CombinatorialDerivation. The variableComponents property MUST NOT contain two or more VariableComponent objects that refer to the same template Component via their variable properties.
If the variable property of one of these VariableComponent objects refers to a template Component, then the components property of the derived ComponentDefinition SHOULD contain as many Component objects derived from the template Component as specified by the operator property of the VariableComponent (see Section 2.2.5 and Table 2). In addition, the definition properties of these derived Component objects MUST refer to ComponentDefinition objects specified by the variants, variantCollections, or variantDerivations property of the VariableComponent (see Section 2.2.1).
If no variable property of one of these VariableComponent objects refers to a template Component, then the components property of the derived ComponentDefinition SHOULD contain exactly one Component with a wasDerivedFrom property that refers to the template Component. The definition property of this derived Component MUST refer to the ComponentDefinition referred to by the definition property of the template Component.
Finally, all of these derived Component objects MUST follow the restriction properties of any SequenceConstraint objects that refer to their corresponding template Component objects.
The strategy property is OPTIONAL and has a data type of URI. Table 1 provides a list of REQUIRED strategy URIs. If the strategy property is not empty, then it MUST contain a URI from Table 1. This property recommends how many ComponentDefinition objects a user SHOULD derive from the template ComponentDefinition.
Table 1: REQUIRED URIs for the strategy property
| Strategy URI | Description |
|---|---|
| http://sbols.org/v2#enumerate | A user SHOULD derive all possible ComponentDefinition objects specified by the Component objects contained by the template ComponentDefinition and the VariableComponent objects contained by the CombinatorialDerivation. |
| http://sbols.org/v2#sample | A user SHOULD derive a subset of all possible ComponentDefinition objects specified by the Component objects contained by the template ComponentDefinition and the VariableComponent objects contained by the CombinatorialDerivation. The manner in which this subset is chosen is for the user to decide. |
The VariableComponent class can be used to specify a choice of ComponentDefinition objects for any new Component derived from a template Component in the template ComponentDefinition. This specification is made using the class properties variable, variants, variantCollections, and variantDerivations (Figure 2). While the variants, variantCollections, and variantDerivations properties are OPTIONAL, at least one of them MUST NOT be empty.
Figure 2: Diagram of the VariableComponent class and its associated properties
The variable property is REQUIRED and MUST contain a URI that refers to a template Component in the template ComponentDefinition. If the wasDerivedFrom property of a Component refers to this template Component, then the definition property of the derived Component MUST refer to either (1) a ComponentDefinition referred to by the variants property of the VariableComponent, (2) a ComponentDefinition from a Collection referred to by the variantCollections property of the VariableComponent, or (3) a ComponentDefinition derived from a CombinatorialDerivation referred to by the variantDerivations property of the VariableComponent.
If the roles property of the template Component contains one or more URIs, then the roles property of the derived Component SHOULD also contain those URIs.
The variants property is OPTIONAL and MAY contain zero or more URIs that each refer to a ComponentDefinition. The variants property MUST NOT contain duplicate URIs. This property specifies individual ComponentDefinition objects to serve as options when deriving a new Component from the template Component.
The variantCollections property is OPTIONAL and MAY contain zero or more URIs that each refer to a Collection. The variantCollections property MUST NOT contain duplicate URIs. The members property of each Collection referred to in this way MUST NOT be empty, MUST refer only to ComponentDefinition objects, and MUST NOT contain duplicate URIs. 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.
The variantDerivations property is OPTIONAL and MAY contain zero or more URIs that each refer to a CombinatorialDerivation. The variantDerivations property MUST NOT contain duplicate URIs. 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. The variantDerivations property of a VariableComponent MUST NOT refer to the CombinatorialDerivation that contains this VariableComponent. Furthermore, VariableComponent objects MUST NOT form a cyclical chain of references via their variantDerivations properties and the ComponentDerivation objects that contain them. For example, consider the VariableComponent objects A and B and the ComponentDerivation objects X and Y. The reference chain X contains A, A has variant derivation Y, Y contains B, and B has variant derivation X is cyclical.
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. The URI value of this property MUST come from the REQUIRED operator URIs provided in Table 2.
Table 2: REQUIRED URIs for the operator property
| Operator URI | Description |
|---|---|
| http://sbols.org/v2#zeroOrOne | No more than one Component in the derived ComponentDefinition SHOULD have a wasDerivedFrom property that refers to the template Component. |
| http://sbols.org/v2#one | Exactly one Component in the derived ComponentDefinition SHOULD have a wasDerivedFrom property that refers to the template Component. |
| http://sbols.org/v2#zeroOrMore | Any number of Component objects in the derived ComponentDefinition MAY have wasDerivedFrom properties that refer to the template Component. |
| http://sbols.org/v2#oneOrMore | At least one Component in the derived ComponentDefinition SHOULD have a wasDerivedFrom property that refers to the template Component. |
In addition to the two new classes outlined above, we propose adding a new URI to the list of RECOMMENDED URIs for the restriction property of the SequenceConstraint class (Table 3). Previously, the SequenceConstraint class could be used to assert restrictions on the relative, sequence-based positions of a pair of Component objects, the subject and the object. This new URI raises the possibility of using the SequenceConstraint class to assert pairwise restrictions on Component identity and structure.
Table 3: RECOMMENDED URIs for the restriction property
| Restriction URI | Description |
|---|---|
| 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. In addition, if the sequence properties of these ComponentDefinition objects are both not empty, then they MUST have different elements properties. |
Here we will specify the combinatorial design for a library of GFP reporters and enumerate all possible ComponentDefinition objects in accordance with it.
Given an abstract template ComponentDefinition that contains four sub-Component objects and three SequenceConstraint objects to fix their ordering,
gfp_reporter_template : ComponentDefinition
description = "An abstract GFP reporter"
component : Component
identity = p1_template
definition = abstract_glucose-sensitive_promoter
component : Component
identity = r1_template
definition = elowitz_rbs
component : Component
identity = c1_template
definition = abstract_gfp
component : Component
identity = t1_template
definition = double_terminator
sequenceConstraint = p1_template precedes r1_template
sequenceConstraint = r1_template precedes c1_template
sequenceConstraint = c1_template precedes t1_template
a Collection of GFP CDS ComponentDefinition variants,
gfp_library : Collection
description = "A library of various GFP CDSes"
member = gfp1
member = gfp2
member = gfp3
two glucose-sensitive promoter ComponentDefinition variants,
glucose-sensitive_promoter1 : ComponentDefinition
description = "Glucose-sensitive promoter"
type = DNA
role = Promoter
glucose-sensitive_promoter2 : ComponentDefinition
description = "Glucose-sensitive promoter"
type = DNA
role = Promoter
a ribosome binding site, and a terminator,
elowitz_rbs : ComponentDefinition
description = "Elowitz RBS"
type = DNA
role = Ribosome Entry Site
double_terminator: ComponentDefinition
description = "Double terminator"
type = DNA
role = Terminator
we can define a CombinatorialDerivation that specifies a full enumeration using the GFP reporter as its template and the glucose-sensitive promoter and GFP library as its variableComponents.
gfp_reporter_derivation1 : CombinatorialDerivation
description = "Derive various concrete designs from an abstract GFP reporter template by choosing replacements for the promoter and CDS."
template = gfp_reporter_template
strategy = enumerate
variableComponent : VariableComponent
operator = one
variable = p1_template
variant = glucose-sensitive_promoter1
variant = glucose-sensitive_promoter2
variableComponent : VariableComponent
operator = one
variable = c1_template
variantCollection = gfp_library
This CombinatorialDerivation can then serve as the basis for deriving a Collection of all six possible GFP reporter variants:
expanderbot2000 : prov:Agent
name = "Expanderbot 2000"
version = "0.1.3"
gfp_reporter_expansion1 : Collection
description = "Expansions of GFP reporter derivation"
wasDerivedFrom = gfp_reporter_derivation1
prov:wasGeneratedBy : prov:Activity
identity = gfp_reporter_expansion1_activity
prov:qualifiedUsage : prov:Usage
hadRole = source
entity = gfp_reporter_derivation1
prov:qualifiedAssociation : prov:Association
hadRole = enumerator
prov:agent = expanderbot2000
member : ComponentDefinition
wasDerivedFrom = gfp_reporter_derivation1
prov:wasGeneratedBy : prov:Activity
prov:wasInformedBy = gfp_reporter_expansion1_activity
type = DNA
role = Gene
component : Component
identity = p1
definition = glucose-sensitive_promoter1
wasDerivedFrom = p1_template
component : Component
identity = r1
definition = elowitz_rbs
wasDerivedFrom = r1_template
component : Component
identity = c1
definition = gfp1
wasDerivedFrom = c1_template
component : Component
identity = t1
definition = double_terminator
wasDerivedFrom = t1_template
sequenceConstraint = p1 precedes r1
sequenceConstraint = r1 precedes c1
sequenceConstraint = c1 precedes t1
member : ComponentDefinition
wasDerivedFrom = gfp_reporter_derivation1
prov:wasGeneratedBy : prov:Activity
prov:wasInformedBy = gfp_reporter_expansion1_activity
type = DNA
role = Gene
component : Component
identity = p1
definition = glucose-sensitive_promoter2
wasDerivedFrom = p1_template
component : Component
identity = r1
definition = elowitz_rbs
wasDerivedFrom = r1_template
component : Component
identity = c1
definition = gfp1
wasDerivedFrom = c1_template
component : Component
identity = t1
definition = double_terminator
wasDerivedFrom = t1_template
sequenceConstraint = p1 precedes r1
sequenceConstraint = r1 precedes c1
sequenceConstraint = c1 precedes t1
member : ComponentDefinition
wasDerivedFrom = gfp_reporter_derivation1
prov:wasGeneratedBy : prov:Activity
prov:wasInformedBy = gfp_reporter_expansion1_activity
type = DNA
role = Gene
component : Component
identity = p1
definition = sensitive_promoter1
wasDerivedFrom = p1_emplate
component : Component
identity = r1
definition = elowitz_rbs
wasDerivedFrom = r1_template
component : Component
identity = c1
definition = gfp2
wasDerivedFrom = c1_template
component : Component
identity = t1
definition = double_terminator
wasDerivedFrom = t1_template
sequenceConstraint = p1 precedes r1
sequenceConstraint = r1 precedes c1
sequenceConstraint = c1 precedes t1
...
The provenance objects are OPTIONAL, but ensure that there is a full history of how these entities were derived.
The operon ComponentDefinition has SequenceConstraint objects to position two CDSes between a promoter and terminator, but does not constrain the relative ordering of the CDSes themselves. For simplicity, the complete sub-Component objects and OPTIONAL provenance objects are omitted from this example.
operon_template : ComponentDefinition
type = DNA
role = Operon
sequenceConstraint = p1_template precedes c1_template
sequenceConstraint = p1_template precedes c2_template
sequenceConstraint = c1_template precedes t1_template
sequenceConstraint = c2_template precedes t1_template
This time we will specify a CombinatorialDerivation that does not contain VariableComponent objects since we only want to enumerate all possible orderings of these non-abstract Component objects.
operon_order_derivation : CombinatorialDerivation
description = "Derive the various unambiguous orderings"
template = operon_template
strategy = enumerate
This CombinatorialDerivation will give us a Collection of two ComponentDefinition objects:
operon_order_expansion : Collection
wasDerivedFrom = operon_order_derivation
member : ComponentDefinition
wasDerivedFrom = operon_order_derivation
type = DNA
role = Operon
sequenceConstraint = p1 precedes c1
sequenceConstraint = c1 precedes c2
sequenceConstraint = c2 precedes t1
member : ComponentDefinition
wasDerivedFrom = operon_order_derivation
type = DNA
role = Operon
sequenceConstraint = p1 precedes c2
sequenceConstraint = c2 precedes c1
sequenceConstraint = c1 precedes t1
The ordering of sub-Component objects within each newly derived ComponentDefinition is fixed with a new set of SequenceConstraint objects. Note that, instead of using SequenceConstraint objects to indicate sub-Component ordering in a derived ComponentDefinition, a user can associate the latter with a Sequence and a set of SequenceAnnotation objects that designate the Location of each sub-Component.
We can have more than one derivation from the same template ComponentDefinition. Given the previous ComponentDefinition for a GFP reporter, we can specify two different derivations, one that varies the promoter sub-Component, and one that varies the CDS sub-Component.
gfp_reporter_derivation2 : CombinatorialDerivation
template = gfp_reporter_template
strategy = enumerate
variableComponent : VariableComponent
operator = one
variable = p1_template
variant = glucose-sensitive_promoter1
variant = glucose-sensitive_promoter2
gfp_reporter_derivation3 : CombinatorialDerivation
template = gfp_reporter_template
strategy = enumerate
variableComponent : VariableComponent
operator = one
variable = c1_template
variantCollection = gfp_library
These derivations give rise to two independent families of enumerations from the same template design (again omitting OPTIONAL provenance objects):
gfp_reporter_expansion2 : Collection
wasDerivedFrom = gfp_reporter_derivation2
member : ComponentDefinition
wasDerivedFrom = gfp_reporter_derivation2
component : Component
identity = p1
definition = glucose-sensitive_promoter1
wasDerivedFrom = p1_template
component : Component
identity = r1
definition = elowitz_rbs
wasDerivedFrom = r1_template
component : Component
identity = c1
definition = abstract_gfp
wasDerivedFrom = c1_template
component : Component
identity = t1
definition = double_terminator
wasDerivedFrom = t1_template
sequenceConstraint = p1 precedes r1
sequenceConstraint = r1 precedes c1
sequenceConstraint = c1 precedes t1
member : ComponentDefinition
wasDerivedFrom = gfp_reporter_derivation2
component : Component
identity = p1
definition = glucose-sensitive_promoter2
wasDerivedFrom = p1_template
component : Component
identity = r1
definition = elowitz_rbs
wasDerivedFrom = r1_template
component : Component
identity = c1
definition = abstract_gfp
wasDerivedFrom = c1_template
component : Component
identity = t1
definition = double_terminator
wasDerivedFrom = t1_template
sequenceConstraint = p1 precedes r1
sequenceConstraint = r1 precedes c1
sequenceConstraint = c1 precedes t1
gfp_reporter_expansion3 : Collection
wasDerivedFrom = gfp_reporter_derivation3
member : ComponentDefinition
wasDerivedFrom = gfp_reporter_derivation3
component : Component
identity = p1
definition = abstract_glucose-sensitive_promoter
wasDerivedFrom = p1_template
component : Component
identity = r1
definition = elowitz_rbs
wasDerivedFrom = r1_template
component : Component
identity = c1
definition = gfp1
wasDerivedFrom = c1_template
component : Component
identity = t1
definition = double_terminator
wasDerivedFrom = t1_template
sequenceConstraint = p1 precedes r1
sequenceConstraint = r1 precedes c1
sequenceConstraint = c1 precedes t1
member : ComponentDefinition
wasDerivedFrom = gfp_reporter_derivation3
component : Component
identity = p1
definition = abstract_glucose-sensitive_promoter
wasDerivedFrom = p1_template
component : Component
identity = r1
definition = elowitz_rbs
wasDerivedFrom = r1_template
component : Component
identity = c1
definition = gfp2
wasDerivedFrom = c1_template
component : Component
identity = t1
definition = double_terminator
wasDerivedFrom = t1_template
sequenceConstraint = p1 precedes r1
sequenceConstraint = r1 precedes c1
sequenceConstraint = c1 precedes t1
member : ComponentDefinition
wasDerivedFrom = gfp_reporter_derivation3
component : Component
identity = p1
definition = abstract_glucose-sensitive_promoter
wasDerivedFrom = p1_template
component : Component
identity = r1
definition = elowitz_rbs
wasDerivedFrom = r1_template
component : Component
identity = c1
definition = gfp3
wasDerivedFrom = c1_template
component : Component
identity = t1
definition = double_terminator
wasDerivedFrom = t1_template
sequenceConstraint = p1 precedes r1
sequenceConstraint = r1 precedes c1
sequenceConstraint = c1 precedes t1
Since each CombinatorialDerivation is external to its template ComponentDefinition, we could use this template as the target of another CombinatorialDerivation to further expand it out.
Starting again with the GFP reporter template ComponentDefinition, we can specify a CombinatorialDerivation that uses the sample strategy rather than the enumerate strategy that we have used so far.
gfp_reporter_derivation4 : CombinatorialDerivation
template = gfp_reporter_template
strategy = sample
variableComponent : VariableComponent
operator = one
variable = p1_template
variant = glucose-sensitive_promoter1
variant = glucose-sensitive_promoter2
variableComponent : VariableComponent
operator = one
variable = c1_template
variantCollection = gfpLibrary
We can sample once to derive the following ComponentDefinition:
samplebot3000 : prov:Agent
name = "samplebot3000"
version = "9.1"
randomSeed = "9837453"^^xs:long
sampled_gfp_reporter1 : ComponentDefinition
wasDerivedFrom = gfp_reporter_derivation4
prov:wasGeneratedBy : prov:Activity
prov:qualifiedUsage : prov:Usage
hadRole = source
entity = gfp_reporter_derivation4
prov:qualifiedAssociation : prov:Association
hadRole = sampler
prov:agent = samplebot3000
component : Component
identity = p1
definition = glucose-sensitive_promoter1
wasDerivedFrom = p1_template
component : Component
identity = r1
definition = elowitz_rbs
wasDerivedFrom = r1_template
component : Component
identity = c1
definition = gfp2
wasDerivedFrom = c1_template
component : Component
identity = t1
definition = double_terminator
wasDerivedFrom = t1_template
sequenceConstraint = p1 precedes r1
sequenceConstraint = r1 precedes c1
sequenceConstraint = c1 precedes t1
Once again, the provenance objects are OPTIONAL, but ensure that there is a full history of how these entities were derived.
Here we will specify the combinatorial design for a synthetic eukaryotic promoter that contains a variable number of upstream operator sites1.
Given an abstract template ComponentDefinition that contains two sub-Component objects and one SequenceConstraint object to fix their ordering,
synthetic_cmv_template : ComponentDefinition
description = "Template for a synthetic eukaryotic promoter (CMV)"
component : Component
identity = o1_template
definition = abstract_operator
component : Component
identity = p1_template
definition = cmv
sequenceConstraint = o1_template precedes p1_template
a Collection of operator site ComponentDefinition variants,
operator_library : Collection
description = "A library of operator site variants"
member = operator1
member = operator2
member = operator3
member = operator4
and a CMV promoter ComponentDefinition,
cmv : ComponentDefinition
description = "CMV promoter"
type = DNA
role = Promoter
we can define a CombinatorialDerivation that specifies a sampling using the synthetic CMV promoter ComponentDefinition as its template and the operator library as the variantCollection of a VariableComponent from which to derive one or more sub-Component objects.
synthetic_cmv_derivation1 : CombinatorialDerivation
description = "Derive various concrete designs for the synthetic CMV promoter by choosing one or more upstream operator sites."
template = synthetic_cmv_template
strategy = sample
variableComponent : VariableComponent
operator = oneOrMore
variable = o1_template
variantCollection = operator_library
This CombinatorialDerivation can then serve as the basis for deriving a Collection of synthetic CMV promoters with different numbers of upstream operator sites.
samplebot300 : prov:Agent
name = "samplebot3000"
version = "9.1"
randomSeed = "9837453"^^xs:long
synthetic_cmv_expansion1 : Collection
description = "Expansions of the synthetic CMV promoter"
wasDerivedFrom = synthetic_cmv_derivation1
prov:wasGeneratedBy : prov:Activity
identity = synthetic_cmv_expansion1_activity
prov:qualifiedUsage : prov:Usage
hadRole = source
entity = synthetic_cmv_derivation1
prov:qualifiedAssociation : prov:Association
hadRole = sampler
prov:agent = samplebot3000
member : ComponentDefinition
identity = cmv1
wasDerivedFrom = synthetic_cmv_derivation1
prov:wasGeneratedBy : prov:Activity
prov:wasInformedBy = synthetic_cmv_expansion1_activity
type = DNA
role = Promoter
component : Component
identity = o1
definition = operator2
wasDerivedFrom = o1_template
component : Component
identity = o2
definition = operator3
wasDerivedFrom = o1_template
component : Component
identity = o3
definition = operator2
wasDerivedFrom = o1_template
component : Component
identity = p1
definition = cmv
wasDerivedFrom = p1_template
sequenceConstraint = o1 precedes o2
sequenceConstraint = o2 precedes o3
sequenceConstraint = o3 precedes p1
member : ComponentDefinition
identity = cmv2
wasDerivedFrom = synthetic_cmv_derivation1
prov:wasGeneratedBy : prov:Activity
prov:wasInformedBy = synthetic_cmv_expansion1_activity
type = DNA
role = Promoter
component : Component
identity = o1
definition = operator1
wasDerivedFrom = o1_template
component : Component
identity = o2
definition = operator4
wasDerivedFrom = o1_template
component : Component
identity = o3
definition = operator2
wasDerivedFrom = o1_template
component : Component
identity = o4
definition = operator3
wasDerivedFrom = o1_template
component : Component
identity = o5
definition = operator3
wasDerivedFrom = o1_template
component : Component
identity = p1
definition = cmv
wasDerivedFrom = p1_template
sequenceConstraint = o1 precedes o2
sequenceConstraint = o2 precedes o3
sequenceConstraint = o3 precedes o4
sequenceConstraint = o4 precedes o5
sequenceConstraint = o5 precedes p1
...
Here we will specify the combinatorial design for a eukaryotic transcriptional unit (TU) by using our previous combinatorial design for a synthetic eukaryotic promoter.
Given a template ComponentDefinition that contains three sub-Component objects and two SequenceConstraint objects to fix their ordering,
synthetic_eukaryotic_tu : ComponentDefinition
description = "A synthetic eukaryotic transcriptional unit"
component : Component
identity = p1_template
definition = abstract_promoter
component : Component
identity = c1_template
definition = abstract_cds
component : Component
identity = t1_template
definition = polyA
sequenceConstraint = p1_template precedes c1_template
sequenceConstraint = c1_template precedes t1_template
a Collection of enzyme CDS ComponentDefinition variants,
enzyme_cds_library : Collection
description = "A library of enzyme CDS variants"
member = enzyme1
member = enzyme2
member = enzyme3
member = enzyme4
and a eukaryotic terminator ComponentDefinition,
polyA : ComponentDefinition
description = "A poly-A sequence acting as a terminator signal"
type = DNA
role = Terminator
we can define a CombinatorialDerivation that specifies a sampling using the ComponentDefinition of a synthetic enzyme TU as its template, the enzyme CDS library as a variantCollection from which to choose one CDS, and the CombinatorialDerivation for the eukaryotic promoter as a variantDerivation from which to choose one promoter.
synthetic_eukaryotic_tu_derivation1 : CombinatorialDerivation
description = "Derive various concrete designs for a synthetic eukaryotic TU by choosing one enzyme CDS and one promoter with a variable number of operator sites."
template = synthetic_eukaryotic_tu
strategy = sample
variableComponent : VariableComponent
operator = one
variable = p1_template
variantDerivation = synthetic_cmv_derivation1
variableComponent : VariableComponent
operator = one
variable = c1_template
variantCollection = enzyme_cds_library
This CombinatorialDerivation can then serve as the basis for deriving a Collection of synthetic eukaryotic TUs with different promoters and enzyme CDSes.
samplebot300 : prov:Agent
name = "samplebot3000"
version = "9.1"
randomSeed = "9837453"^^xs:long
synthetic_eukaryotic_tu_expansion1 : Collection
description = "Expansions of a synthetic eukaryotic TU"
wasDerivedFrom = synthetic_eukaryotic_tu_derivation1
prov:wasGeneratedBy : prov:Activity
identity = synthetic_eukaryotic_tu_expansion1_activity
prov:qualifiedUsage : prov:Usage
hadRole = source
entity = synthetic_eukaryotic_tu_derivation1
prov:qualifiedAssociation : prov:Association
hadRole = sampler
prov:agent = samplebot3000
member : ComponentDefinition
wasDerivedFrom = synthetic_eukaryotic_tu_derivation1
prov:wasGeneratedBy : prov:Activity
prov:wasInformedBy = synthetic_eukaryotic_tu_expansion1_activity
type = DNA
role = Gene
component : Component
identity = p1
definition = cmv1
wasDerivedFrom = p1_template
component : Component
identity = c1
definition = enzyme2
wasDerivedFrom = c1_template
component : Component
identity = t1
definition = polyA
wasDerivedFrom = t1_template
sequenceConstraint = p1 precedes c1
sequenceConstraint = c1 precedes t1
member : ComponentDefinition
wasDerivedFrom = synthetic_eukaryotic_tu_derivation1
prov:wasGeneratedBy : prov:Activity
prov:wasInformedBy = synthetic_eukaryotic_tu_expansion1_activity
type = DNA
role = Gene
component : Component
identity = p1
definition = cmv2
wasDerivedFrom = p1_template
component : Component
identity = c1
definition = enzyme4
wasDerivedFrom = c1_template
component : Component
identity = t1
definition = polyA
wasDerivedFrom = t1_template
sequenceConstraint = p1 precedes c1
sequenceConstraint = c1 precedes t1
...
New classes and RECOMMENDED property value, no issues anticipated.
Advantages:
We have a complete log of the combinatorial expansion options and the individual expansions. We can also use provenance objects to document that a CombinatorialDerivation was executed using a specific software tool. The proposed extension also gives us a separation between an abstract design and the strategy used to refine it into a concrete design. We can take the same template and expand it in accordance with several CombinatorialDerivation objects that present different sets of VariableComponent objects.
Currently none.
- Brown et al., Synthetic promoters for CHO cell engineering, Biotechnol. and Bioeng., vol. 111, pp. 1638-1647, 2014.
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