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SEP 015 -- Simplification of SBOL class names

SEP 015
Title Simplification of SBOL class names
Authors James Alastair McLaughlin ([email protected]); Raik Grünberg ([email protected])
Editor
Type Data Model
SBOL Version 3.0
Replaces
Status Draft
Created 28-Jun-2017
Last modified 28-Jul-2019
Issue #32

Abstract

The number of classes in the SBOL data model grew sharply with the introduction of SBOL 2.0. Prior to generalizations such as turning DnaComponent into ComponentDefinition, many discussions took place about the nomenclature, and eventually a quorum was reached and the class names were accepted.

SBOL2 has been released for some time now, and the community is now familiar with using the data model in practice. This SEP suggests that, given our experience actually using SBOL2, we reconsider the nomenclature once more for SBOL3.0. The intention would be to simplify names and to convey meaning more effectively.

  1. Motivation

SBOL2 can be very confusing to newcomers, and the verbosity of its class names doesn't help. The most common class in SBOL is likely ComponentDefinition, which is a verbose name usually abbreviated to "CD" or simply "component". Confusingly though, SBOL 2.x also defines a class Component which, however, actually describes a subcomponent. Similar issues exist with ModuleDefinition and Module.

The rationale for this SEP, using Component as an example, are that:

  • In SBOL2, Component must be contained by a ComponentDefinition and is therefore always a subcomponent. Changing the name to SubComponent is more expressive.

  • This change leaves the name Component free for ComponentDefinition to be renamed to. Removing "Definition" makes the name less verbose and less confusing. The simplified name Component matches what programmers currently use in colloqial conversations about SBOL.

  • In programming languages, classes are definitions implicitly and do not need to be explicitly named as such. For example, the File class in Java is called File, not FileDefinition, even before an instance of it has been created. Bringing SBOL in line with this makes SBOL more intuitive.

The FunctionalComponent class, though also confusingly named, will remain as-is for the purposes of this SEP.

  1. Specification

The following classes will be renamed:

  • ComponentDefinition to Component
  • Component to SubComponent
  • ModuleDefinition to Module
  • Module to SubModule
  • definition to instanceOf
  1. Backwards Compatibility

This is a major change, but only to the names of classes. (Note: a separate SEP will deal with removing FunctionalComponent). Consequently, updating the libraries should be straightforward. It is important to defer this change to SBOL 3.0 so that the namespace is different (otherwise, it would be ambiguous whether a Component was an SBOL 2.0 Component instance or a SBOL 3.0 Component).

More generally, tools solely programmed for SBOL 2.x will, in any case, run into trouble when opening an SBOL 3.0 document. SBOL2 documents use the URI prefix http://sbols.org/v2# for terms. Presumably, SBOL3 will use the http://sbols.org/v3# prefix, which will prevent SBOL2 and SBOL3 from clashing.

  1. Discussion

5.1 Related SEPs

The following SEPs make complementary suggestions for further simplification of the SBOL data model:

  • SEP 10 (Issue) -- a proposal to separate sequence feature annotations from sub-component (part) compositions

  • SEP 25 (Issue) -- merge Module(Definition) with Component(Definition) and remove FunctionalComponent

5.2 Implementation cost

Library developers may be concerned at the time cost of implementing such a significant change. However, as the proposed change is only to the nomenclature and not the semantics, it should generally be no less complicated than a find/replace operation.

5.2 Distinction between SBOL 2.x and 3.x documents

SBOL2 documents use the URI prefix http://sbols.org/v2# for terms. Presumably, SBOL3 will use the http://sbols.org/v3# prefix, which will prevent SBOL2 and SBOL3 from clashing. This has yet to be discussed.

  1. Competing SEPs

None.

References

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 Kingdom.