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SEP 046 -- Changes in the new SBOL 3.0 specification

SEP
Title Changes in the new SBOL 3.0 specification
Authors Chris Myers (myers@ece.utah.edu), Jake Beal (jakebeal@gmail.com), James McLaughlin (james@mclgh.net), Bryan Bartley (bartleyba@sbolstandard.org), James Scott-Brown (james@jamesscottbrown.com), Pedro Fontanarrosa (pfontanarrosa@gmail.com), Prashant Vaidyanathan (t-prva@microsoft.com), Neil Wipat (neilwipat@gmail.com), Matthew Crowther (m.crowther1@ncl.ac.uk), Goksel Misirli (g.misirli@keele.ac.uk)
Editor Prashant Vaidyanathan (t-prva@microsoft.com), Pedro Fontanarrosa (pfontanarrosa@gmail.com), James McLaughlin (james@mclgh.net)
Type New Specification
SBOL Version SBOL 3.0
Replaces SBOL 2.x
Status Accepted
Created 12-March-2020
Last modified
Issue #98

Abstract

In this document, a brief and high level overview of the changes in the new SBOL 3 specification document is explained.

Table of Contents

1. Rationale

Sufficient SEPs accumulated proposing major data model changes that merited a change in the specification from version 2.x to 3.0. This SEP summarizes the changes that have been implemented from various SEPs that have been accepted by the community along with changes that have been proposed after discussion at HARMONY 2020.

2. Specification

2.1 List of SEPs implemented:

2.2 Summary of the changes to the specification

  • definition renamed as instanceOf
  • dcterms:title renamed as sbol:name
  • dcterms:description renamed as sbol:description
  • persistentIdentity removed from Identified
  • version removed from Identified
  • Interface has been introduced as a sub-class of Identified
  • NameSpace has been introduced as a sub-class of Collection
  • Added a new Abstract class Feature
    • Add role field to Feature
    • Add direction field to Feature
    • Add orientation field to Feature
  • SBOL 2.x Component renamed as SubComponent
    • Add location field to SubComponent
    • Remove access field from SubComponent
    • Remove direction field from SubComponent. This is now inherited from the parent class Feature
  • SubComponent is now a sub-class of Feature
  • SBOL 2.x SequenceAnnotation renamed as SequenceFeature
    • Remove component field from SequenceFeature
    • Remove roleIntegration field from SequenceFeature
  • SequenceFeature is now a sub-class of Feature
  • ComponentReference introduced as a sub-class of Feature
  • LocalSubComponent introduced as a sub-class of Feature
  • ExternallyDefined introduced as a sub-class of Feature
  • SBOL 2.x SequenceConstraint has been renamed as Constraint
    • Constraint.object and Constraint.subject now point to Feature
    • The table of recommended restrictions for Constraint has been updated.
  • The sequence property of Location is now required.
    • As a consequence, Sequence now has elements and encoding as optional rather than required.
  • Add order field to Location
  • SBOL 2.x GenericLocation has been removed
  • EntireSequence has been introduced as a sub-class of Location
  • SBOL 2.x ComponentDefinition renamed as Component
    • Add interface field to Component
  • SBOL 2.x ModuleDefinition properties moved to Component
    • SBO's FunctionalEntity term has been introduced as type for Component
    • SBOL 2.x ModuleDefinition has been removed
    • SBOL 2.x Module has been removed
  • SBOL 2.x FunctionalComponent has been removed and any references to it have been changed to references to SubComponent
  • SBOL 2.x MapTos has been removed.
  • BioPAX type values have been changed to their SBO equivalents.
  • SBOL has been made more Semantic Web friendly. This includes:
    • Differentiating SBOL entities (concepts) and properties. A few examples include:
      • The feature field of Component which points to a Feature object, has now been renamed as hasFeature
      • The variableComponent field of CombinatorialDerivation which points to a VariableComponent object, has now been renamed as hasVariableComponent
    • Consistent labelling of SBOL entities
      • For instance, Access values will be capitalised. E.g. 'public' has been changed to 'Public', 'private' has been changed to 'Private', etc.
    • rdf:type is now recommender over sbol:type to specify the type of an SBOL entity.
    • Enabling graph-based serialization of SBOL documents.
  • Properties/fields that were in plural form are now specified in singular form

2.3 Summary of the changes not included in previous SEPs

The following changes were proposed during HARMONY 2020 and have not been covered by any previous SEPs:

  • The operator field of VariableComponent has been changed to cardinality
  • order field has been added to Location
  • ComponentInstance class has been renamed as Feature
    • The ComponentInstance class was introduced as an abstract class in SEP 36, SEP 37, and SEP 43. This ComponentInstance class has now been renamed as Feature.
  • SequenceFeature class is now a sub-class of Feature
  • The hasSubComponent and hasFeature fields of the Component class have been merged as a single field: hasFeature which points to a Feature object
    • This was a consequence of making SequenceFeature and SubComponent sub-classes of Feature.
  • hasSequence field has been added back to Component
    • SEP 41 removed hasSequence from Component, however hasSequence has been added back to Component.
  • orientation field has been added to Feature
  • Experiment is now a sub-class of Collection
  • NameSpace is now a sub-class of Collection
  • Sequence now has elements and encoding as optional rather than required.
  • GenericLocation has been removed.
  • Location's EntireLocation sub-class has been renamed as EntireSequence
    • SEP 41 introduced EntireLocation. This new class has been renamed EntireSequence.
  • SequenceConstraint has been renamed as Constraint
  • ExternalReference has been renamed as ExternallyDefined
    • SEP 36 introduced ExternalReference as a subclass of Feature. This new class has been renamed as ExternallyDefined.
  • The VariableComponent class has 3 optional properties. There is a validation rule that states that at least one of them must not be empty. This validation rule has been deleted.
  • Added the hashAlgorithm property to the Attachment class. The hash property is OPTIONAL and MAY contain the name of the hash algorithm used to generate the value of the hash property. The value of this property SHOULD be a hash name string from the IANA Named Information Hash Algorithm Registry, of which sha3-256 is currently recommended. If the hash property is set, then hashAlgorithm MUST be set as well.

3. Example or Use Case

In this section, we show the UML diagrams of the classes that have undergone changes that were not part of any previous SEPs.

  • Collection UML

Collection UML

  • Component UML

Component UML

  • Feature UML

Feature UML

  • Location UML

Location UML

  • VariableComponent UML

VariableComponent UML

4. Backwards Compatibility

5. Discussion

6. Competing SEPs

None.

References

None.

Copyright

CC0
To the extent possible under law, SBOL developers has waived all copyright and related or neighboring rights to SEP 002. This work is published from: United States.