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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 2.4
Replaces
Status Draft
Created 14-July-2019
Last modified

Abstract

This proposal adds an option for a ComponentInstance to use 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 to directly to a non-SBOL grounding term rather than having to go through an "empty" ComponentDefinition.

Specification

The ComponentInstance class is changed in the following ways:

  • A new externalDefinition field is added with cardinality [0..1] and type URI.
  • The definition cardinality changes from [1] to [0..1].
  • A new validation rule is added that says precisely one of externalDefinition and definition must be defined.

It is necessary to split the two fields because there is no way to tell from the URI alone whether one is referring to an SBOL object or a non-SBOL database entry.

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

Backwards Compatibility

The same pattern of component definitions being used to import reagents or other items can still be used, so there is no issue with backward compatibility.

For SBOL 3, we might rename definition to sbolDefinition for clarity and symmetry.

Discussion

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 036. This work is published from: United States.