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SEP 036 -- Externally grounded components

SEP 036
Title Externally grounded components
Authors Jacob Beal (jakebeal@ieee.org)
Editor Zach Palchick
Type Data Model
SBOL Version 3.0
Replaces
Status Accepted
Issue #81
Created 14-July-2019
Last modified 26-Jan-2020

Abstract

This proposal adds an option for a ComponentInstance to use reference external definitions in databases like CHEBI or UniProt.

Motivation

When designs include small molecules, proteins, and reagents, right now they often cause a proliferation of "empty" ComponentDefinition objects that essentially only serve to be a link to an external definition in a database like CHEBI and UniProt.

Doing this tends to obfuscate the sharing of reagents, by causing there to be many copies of the same reagent in different namespaces (or even the same namespace, due to accidental duplications).

Instead, we propose to provide an option for a ComponentInstance sibling class to SubComponent that goes directly to a non-SBOL grounding term rather than having to go through an "empty" ComponentDefinition.

Specification

In harmony with SEP 015, the new ExternalReference class is taken to be a sibling class of SubComponent, below the new unifying ComponentInstance class.

examples

Note that this class diagram assumes SBOL 3 implementation of SEP 025, SEP 015, and SEP 010.

The ExternalReference class has the following three fields:

  • The definition field is a link to a canonical definition external to SBOL.
  • The types field is identical to its use in ComponentDefinition

The roles and direction fields are shared, and thus placed on ComponentInstance.

The access field is also dropped as generally unused and redundant with direction.

We may also add a weak validation rule that definition SHOULD refer to a non-SBOL canonical definition using an identifiers.org URI.

Backwards Compatibility

This is an SBOL 3 change because it depends on changes being made in the SubComponent and related class hierarchy.

An ExternalReference can be down-converted to SBOL 2 by creating an "empty" ComponentDefinition and linking it with an appropriate type of SBOL 2 Component.

Upconversion of SBOL 2 is a "nice to have", since an "empty" ComponentDefinition is still valid under this proposal, just no longer necessary. Implementing upconversion may be complicated, as one has to detect "empty" ComponentDefinition objects and figure out what convention was being used for linking to the external reference. This has typically been either a wasDerivedFrom link or a non-standard type, but may not be entirely automatable.

Discussion

The original proposal was to just modify SubComponent by allowing an optional type and making definition optional. Since SEP 037 is creating a "pointer" class sibling to ComponentInstance, however, it seems sensible to do the same rather than unnecessarily complicating SubComponent, since there is no benefit here to accessing additional fields like sourceLocations and roleIntegration.

The names of SubComponent and ComponentInstance have been swapped.

Competing SEPs

No SEPs are directly competing.

This SEP assumes adoption of SEP 010, SEP 015, and SEP 025.

This SEP is compatible with SEP 037 and SEP 043

References

Copyright

CC0
To the extent possible under law, SBOL developers has waived all copyright and related or neighboring rights to SEP 036. This work is published from: United States.