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SEP 026 -- Add a link from Location to Sequence

SEP 027
Title Add a link from Location to Sequence
Authors James Alastair McLaughlin (j.a.mclaughlin@ncl.ac.uk); Chris Myers (myers@ece.utah.edu)
Editor Zach Palchick
Type Data Model
SBOL Version 2.3
Replaces
Status Draft
Created 21-Jun-2018
Last modified 03-Sep-2018

Abstract

In SBOL2, ComponentDefinitions can have multiple Sequences, and ComponentDefinitions can also have SequenceAnnotations. Currently, it is ambiguous which Sequence the SequenceAnnotation(s) refer to. Adding an optional link from Location to the Sequence it is annotating would solve this.

Motivation

As abstract

Specification

Add an optional sequence property to Location that links to a Sequence.

Example or Use Case

The below listed use cases are examples where there could be multiple Sequences associated with a ComponentDefinition, but it is not clear which Sequence a SequenceAnnotation would refer to.

  • Different encodings of the same thing (e.g. smiles and inchi)
  • DNA sequence + methylation patterns

Backwards Compatibility

When loading older SBOL:

  • If there is exactly one sequence in a ComponentDefinition, make locations in the SequenceAnnotations of that ComponentDefinition point to that sequence
  • If more than one sequence, warn that the annotations are ambiguous

Backporting to older SBOL:

  • If exactly one sequence in a ComponentDefinition, remove the sequence property of locations in the SequenceAnnotations of that ComponentDefinition
  • If more than one sequence, cannot be represented in older SBOL, throw an error.

Discussion

Competing SEPs

SEP 23 which advocates associating at most one Sequence with a ComponentDefinition. It has since been revoked.

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.