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SEP 038 -- Merging ComponentDefinition and ModuleDefinition through Inheritance Pattern

SEP 038
Title Merging ComponentDefinition and ModuleDefinition through Inheritance Pattern
Authors Bryan Bartley (bartleyba@sbolstandard.org)
Editor
Type Data Model
SBOL Version 2.4/3.0
Replaces
Status Draft
Created 28-August-2019
Last modified

Abstract

This proposal will make ModuleDefinition a subclass of ComponentDefinition, effectively merging ModuleDefinition into ComponentDefinition. This change is intended for the 3.0 milestone, but if necessary there is a migration path though 2.4

Motivation

The goal here is in keeping with the spirit of SEP035, and all of the following (quoted from that SEP) still applies:

...the boundary between structural and functional composition is often unclear, and can cause miscategorizations that are problematic to correct. For example, we are using ModuleDefinition to represent mixtures (e.g., growth media) while ComponentDefinition is used to represent covalently bonded structures (e.g., DNA, pure chemicals).

In short, there doesn't seem to be any value to separating structure and function, so we are going to let one object contain both types of information.

Another important point that distinguishes the approach advocated in this SEP compared with SEP035 is that it help harmonize the SBOL data model with SBOL visual, so that the semantics map better from one standard to another. This is demonstrated in the provided Example below. Unlike SEP035, which eliminates ModuleDefinitions altogether, this proposal allows us to retain a ModuleDefinition class, while correcting some of its problems. In SBOL Visual, a module is represented by a box, often with dashed lines, that groups subcomponents into an abstraction hierarchy. This SEP provides a simplified and unambiguous specification that will help automated visualization tools to interpret SBOL data and render a diagram with the appropriate visual semantics.

A natural language description of the conceptualization offered by this proposal is as follows:

A module is a component of a system that has a specified functional interaction with other components through an interface of inputs and outputs.

This conceptualization is quite easy to understand, consistent with an engineer's understanding of the concept of modularity, and easy to explain to new users, reviewers, and the synthetic biology community.

Specification

Merging ComponentDefinition and ModuleDefinition through Inheritance Pattern

Figure 1: Diagram of ModuleDefinition class as subclass of ComponentDefinition

Adjustments to Component

  • The definition property of Component can now reference either a ComponentDefinition or ModuleDefinition, thus integrating the previously separate structural and functional hierarchies into a single hierarchy.
  • The direction field is moved from FunctionalComponent to Component

Adjustments to FunctionalComponent

  • FunctionalComponent is deprecated

Adjustments to ModuleDefinition

  • ModuleDefinition is subclassed from ComponentDefinition
  • The modules property is deprecated. The components property is used instead for hierarchical composition.
  • The functionalComponents property is deprecated.
  • The types property remains an optional field, unlike the superclass, ComponentDefinition

Adjustments to Participation

For Participation objects, the participant property is generalized to allow ComponentInstance objects, not just FunctionalComponent.

Additional validation rules to add are:

  • During the 2.4 transition stage to full deprecation, there may be 2.3 ModuleDefinitions using the old modules hierarchy that coexist with 2.4 ModuleDefinitions using the new components hierarchy. There we may need validation rules to enforce consistency between these two options. One possibility is to allow a ModuleDefinition to use one or the other hierarchy, but not both simultaneously.
  • Like SEP035, a weak REQUIRED condition for ModuleDefinition: there must only be a sequence or sequenceAnnotaiton if all components can be linearized onto a single sequence.

Backwards Compatibility

Backwards compatibility can be temporarily maintained by retaining all of ModuleDefinitions current properties, while going ahead and implementing the inheritance relationship with ComponentDefinition.

In SBOL 3, FunctionalComponent, and Module will all be deleted, which will obviously not be backward compatible, while ModuleDefinition will be retained. Once Modules and FunctionalComponents are fully deprecated, there is still a straightforward conversion from 2.4 to 3.0 ModuleDefinition.

Discussion

A concern raised is that this change may require type casting triple stores. If necessary, we will demonstrate how easy it is to implement this change using pySBOL and validate it on existing SynBioHub instances.

Competing SEPs

This proposal is in the same spirit as SEP035, though the approach to implementation is different. It accomplishes much of the same as SEP035, because it adds Interactions and Models to ComponentDefinition, thus integrating the structural and functional hierarchies.

Example

Following is an SBOL visual representation of a module with DNA, RNA, and protein subcomponents. Example serialization based on the SEP038 specification also follows. Note how the semantics of the data model now align nicely with the diagram. (Of particular importance to how the ModuleDefinition is now integrated with the ComponentDefinition hierarchy by using the component property). Finally is the pySBOL code that was used to generate the example serialization.

NOR device

Figure 2: SBOL Visual depiction of a CRISPRi NOR logic device, from Communication Structure and Function in Synthetic Biology Diagrams

Example Serialization

<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/"
   xmlns:prov="http://www.w3.org/ns/prov#"
   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
   xmlns:sbol="http://sbols.org/v2#"
   xmlns:sys-bio="http://sys-bio.org#">
  <sbol:ModuleDefinition rdf:about="http://examples.org/ModuleDefinition/nor_gate/1">
    <sbol:component>
      <sbol:Component rdf:about="http://examples.org/ModuleDefinition/nor_gate/dcas9_mix1_0/1">
        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
        <sbol:definition rdf:resource="http://examples.org/ComponentDefinition/dcas9_mix1/1"/>
        <sbol:displayId>dcas9_mix1_0</sbol:displayId>
        <sbol:persistentIdentity rdf:resource="http://examples.org/ModuleDefinition/nor_gate/dcas9_mix1_0"/>
        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
        <sbol:version>1</sbol:version>
      </sbol:Component>
    </sbol:component>
    <sbol:component>
      <sbol:Component rdf:about="http://examples.org/ModuleDefinition/nor_gate/dcas9_mix1_grna_x_0/1">
        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
        <sbol:definition rdf:resource="http://examples.org/ComponentDefinition/dcas9_mix1_grna_x/1"/>
        <sbol:displayId>dcas9_mix1_grna_x_0</sbol:displayId>
        <sbol:persistentIdentity rdf:resource="http://examples.org/ModuleDefinition/nor_gate/dcas9_mix1_grna_x_0"/>
        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
        <sbol:version>1</sbol:version>
      </sbol:Component>
    </sbol:component>
    <sbol:component>
      <sbol:Component rdf:about="http://examples.org/ModuleDefinition/nor_gate/dcas9_mix1_grna_y_0/1">
        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
        <sbol:definition rdf:resource="http://examples.org/ComponentDefinition/dcas9_mix1_grna_y/1"/>
        <sbol:displayId>dcas9_mix1_grna_y_0</sbol:displayId>
        <sbol:persistentIdentity rdf:resource="http://examples.org/ModuleDefinition/nor_gate/dcas9_mix1_grna_y_0"/>
        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
        <sbol:version>1</sbol:version>
      </sbol:Component>
    </sbol:component>
    <sbol:component>
      <sbol:Component rdf:about="http://examples.org/ModuleDefinition/nor_gate/dcas9_mix1_grna_z_0/1">
        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
        <sbol:definition rdf:resource="http://examples.org/ComponentDefinition/dcas9_mix1_grna_z/1"/>
        <sbol:displayId>dcas9_mix1_grna_z_0</sbol:displayId>
        <sbol:persistentIdentity rdf:resource="http://examples.org/ModuleDefinition/nor_gate/dcas9_mix1_grna_z_0"/>
        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
        <sbol:version>1</sbol:version>
      </sbol:Component>
    </sbol:component>
    <sbol:component>
      <sbol:Component rdf:about="http://examples.org/ModuleDefinition/nor_gate/grna_z_0/1">
        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
        <sbol:definition rdf:resource="http://examples.org/ComponentDefinition/grna_z/1"/>
        <sbol:displayId>grna_z_0</sbol:displayId>
        <sbol:persistentIdentity rdf:resource="http://examples.org/ModuleDefinition/nor_gate/grna_z_0"/>
        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
        <sbol:version>1</sbol:version>
      </sbol:Component>
    </sbol:component>
    <sbol:component>
      <sbol:Component rdf:about="http://examples.org/ModuleDefinition/nor_gate/z_expression_cassette_0/1">
        <sbol:access rdf:resource="http://sbols.org/v2#public"/>
        <sbol:definition rdf:resource="http://examples.org/ComponentDefinition/z_expression_cassette/1"/>
        <sbol:displayId>z_expression_cassette_0</sbol:displayId>
        <sbol:persistentIdentity rdf:resource="http://examples.org/ModuleDefinition/nor_gate/z_expression_cassette_0"/>
        <sbol:roleIntegration rdf:resource="http://sbols.org/v2#mergeRoles"/>
        <sbol:version>1</sbol:version>
      </sbol:Component>
    </sbol:component>
    <sbol:displayId>nor_gate</sbol:displayId>
    <sbol:interaction>
      <sbol:Interaction rdf:about="http://examples.org/Interaction/dcas9_mix1_grna_z_formation/1">
        <sbol:displayId>dcas9_mix1_grna_z_formation</sbol:displayId>
        <sbol:persistentIdentity rdf:resource="http://examples.org/dcas9_mix1_grna_z_formation"/>
        <sbol:type rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000343"/>
        <sbol:version>1</sbol:version>
      </sbol:Interaction>
    </sbol:interaction>
    <sbol:interaction>
      <sbol:Interaction rdf:about="http://examples.org/Interaction/x_repression/1">
        <sbol:displayId>x_repression</sbol:displayId>
        <sbol:persistentIdentity rdf:resource="http://examples.org/x_repression"/>
        <sbol:type rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000343"/>
        <sbol:version>1</sbol:version>
      </sbol:Interaction>
    </sbol:interaction>
    <sbol:interaction>
      <sbol:Interaction rdf:about="http://examples.org/Interaction/y_repression/1">
        <sbol:displayId>y_repression</sbol:displayId>
        <sbol:persistentIdentity rdf:resource="http://examples.org/y_repression"/>
        <sbol:type rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000343"/>
        <sbol:version>1</sbol:version>
      </sbol:Interaction>
    </sbol:interaction>
    <sbol:interaction>
      <sbol:Interaction rdf:about="http://examples.org/Interaction/z_production/1">
        <sbol:displayId>z_production</sbol:displayId>
        <sbol:persistentIdentity rdf:resource="http://examples.org/z_production"/>
        <sbol:type rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000343"/>
        <sbol:version>1</sbol:version>
      </sbol:Interaction>
    </sbol:interaction>
    <sbol:persistentIdentity rdf:resource="http://examples.org/ModuleDefinition/nor_gate"/>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:version>1</sbol:version>
  </sbol:ModuleDefinition>
  <sbol:ComponentDefinition rdf:about="http://examples.org/ComponentDefinition/dcas9_mix1/1">
    <sbol:displayId>dcas9_mix1</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://examples.org/ComponentDefinition/dcas9_mix1"/>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:version>1</sbol:version>
  </sbol:ComponentDefinition>
  <sbol:ComponentDefinition rdf:about="http://examples.org/ComponentDefinition/dcas9_mix1_grna_x/1">
    <sbol:displayId>dcas9_mix1_grna_x</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://examples.org/ComponentDefinition/dcas9_mix1_grna_x"/>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:version>1</sbol:version>
  </sbol:ComponentDefinition>
  <sbol:ComponentDefinition rdf:about="http://examples.org/ComponentDefinition/dcas9_mix1_grna_y/1">
    <sbol:displayId>dcas9_mix1_grna_y</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://examples.org/ComponentDefinition/dcas9_mix1_grna_y"/>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:version>1</sbol:version>
  </sbol:ComponentDefinition>
  <sbol:ComponentDefinition rdf:about="http://examples.org/ComponentDefinition/dcas9_mix1_grna_z/1">
    <sbol:displayId>dcas9_mix1_grna_z</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://examples.org/ComponentDefinition/dcas9_mix1_grna_z"/>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:version>1</sbol:version>
  </sbol:ComponentDefinition>
  <sbol:ComponentDefinition rdf:about="http://examples.org/ComponentDefinition/grna_z/1">
    <sbol:displayId>grna_z</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://examples.org/ComponentDefinition/grna_z"/>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:version>1</sbol:version>
  </sbol:ComponentDefinition>
  <sbol:ComponentDefinition rdf:about="http://examples.org/ComponentDefinition/z_expression_cassette/1">
    <sbol:displayId>z_expression_cassette</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="http://examples.org/ComponentDefinition/z_expression_cassette"/>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:version>1</sbol:version>
  </sbol:ComponentDefinition>
</rdf:RDF>

Code

from sbol import *

# Redefine ModuleDefinition as a subclass of ComponentDefinition
class ModuleDefinition(ComponentDefinition):

    def __init__(self, displayId):
        ComponentDefinition.__init__(self, SBOL_MODULE_DEFINITION, displayId, BIOPAX_DNA, '1')
        self.interactions = OwnedPythonObject(self, SBOL_INTERACTIONS, Interaction, '0', '*')
        self.models = OwnedPythonObject(self, SBOL_MODELS, SBOL_MODEL, '0', '*')



doc = Document()

# Define the module (dotted line in figure)
nor_gate = ModuleDefinition('nor_gate')

# Define subcomponents of the module (corresponding to glyphs in the figure)
z_expression_cassette = ComponentDefinition('z_expression_cassette')
dcas9_mix1_grna_x = ComponentDefinition('dcas9_mix1_grna_x')
dcas9_mix1_grna_y = ComponentDefinition('dcas9_mix1_grna_y')
dcas9_mix1 = ComponentDefinition('dcas9_mix1')
grna_z = ComponentDefinition('grna_z')
dcas9_mix1_grna_z = ComponentDefinition('dcas9_mix1_grna_z') 

# Add the subcomponents to the nor gate module
nor_gate.assemble([z_expression_cassette, dcas9_mix1_grna_x, dcas9_mix1_grna_y, dcas9_mix1, grna_z, dcas9_mix1_grna_z], doc)

# Define interactions corresponding to arcs in the figure
x_repression = Interaction('x_repression')
y_repression = Interaction('y_repression')
z_production = Interaction('z_production')
dcas9_mix1_grna_z_formation = Interaction('dcas9_mix1_grna_z_formation')

# Add the interactions to the module
nor_gate.interactions.add(x_repression)
nor_gate.interactions.add(y_repression)
nor_gate.interactions.add(z_production)
nor_gate.interactions.add(dcas9_mix1_grna_z_formation)

doc.write('sep_038.xml')

References

Copyright

CC0
To the extent possible under law, SBOL developers has waived all copyright and related or neighboring rights to SEP 038. This work is published from: United States.