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SEP 045 -- Expand set of SequenceConstraint relations

SEP
Title Expand set of SequenceConstraint relations
Authors Jacob Beal (jakebeal@ieee.org)
Editor
Type Data Model
SBOL Version 3.0 or 3.1
Replaces
Status Accepted
Created 24-Jan-2020
Last modified 6-Feb-2020
Issue #93

Abstract

The precedes relationship covers only one of the seven basic relationships of standard interval algebra. This SEP proposes to add the other six (along with some key unions) and to clarify the definition of precedes.

1. Rationale

The precedes relationship is valuable for ordering items in a sequence, but there are other relationships that we may wish to express as well, such as one sequence being contained within another (e.g., an intron in an RNA transcript) or one sequence overlapping with another (e.g., oligos in an assembly plan).

The standard reference for such relations is Allen's interval algebra [1]. Although designed for reasoning about time, it is applicable to any asymmetric linear sequence, including nucleic acid and amino acid sequences.

Allen's interval algebra provides 7 basic relationships, of which precedes is one. These can also be joined together in unions to specify a number of additional possibilities, some of which are more likely than others to be relevant restrictions for describing biological designs.

Finally, the current definition of precedes is ambiguous, not defining whether the ordering relates to the beginnings or ends of intervals, and so this needs to be cleaned up as well.

[1] Allen, James F. (26 November 1983). "Maintaining knowledge about temporal intervals" (PDF). Communications of the ACM. 26 (11): 832–843.

2. Specification

In the table of recommended restrictions for SequenceConstraint, the entry for http://sbols.org/v2#precedes will be replaced by the following:

Restriction URI Description
http://sbols.org/v2#precedes The start of the location for subject is less than the start of the location for object (i.e., union of strictlyPrecedes, meets, and overlaps). Example: a promoter precedes a ribosome entry site, but the exact boundary between the two will be determined by sequence optimization and assembly planning.
http://sbols.org/v2#strictlyPrecedes The end of the location for subject is less than the start of the location for object. Example: a promoter strictly precedes a terminator (with a CDS between them).
http://sbols.org/v2#meets The end of the location for subject is equal to the start of the location for object. Example: the 3' region adjacent to a blunt restriction site meets the 5' region adjacent to the site.
http://sbols.org/v2#overlaps The start of the location for subject is before the start of the location for object and the end of the location for subject is before the end of the location for object. Example: two oligos in a Gibson assembly plan
http://sbols.org/v2#contains The start of the location for subject is less than or equal to the start of the location for object and the end of the location for subject is greater than or equal to the end of the location for object (i.e., union of strictlyContains, equals, finishes, and starts). Example: a composite part contains a promoter
http://sbols.org/v2#strictlyContains The start of the location for subject is before the start of the location for object and the end of the location for subject is after the end of the location for object. Example: an RNA transcript strictly contains an intron.
http://sbols.org/v2#equals The start and end of the location for subject are equal to the start and end of the location for object. Example: the transcribed region of a CDS part equals the entire part.
http://sbols.org/v2#finishes The start of the location for subject is after the start of the location for object and the end of the location for subject is equal to the end of the location for object. Example: a terminator finishes an expression cassette.
http://sbols.org/v2#starts The start of the location for subject is equal to the start of the location for object and the end of the location for subject is before the end of the location for object. Example: a promoter starts an expression cassette.

Note that here we name the Allen relations precedes as strictlyPrecedes and contains as strictlyContains, leaving the more intuitive names for the unions.

3. Examples

See examples embedded in table.

4. Backwards Compatibility

No conversion is needed, as the SBOL 2 relations are still valid in SBOL 3 and the additional relations are allowed in SBOL 2.

Note, however, that some algorithms designed for SBOL 2 may have been using precedes incorrectly, and this may cause bugs of that type to come to light.

5. Discussion

A number of relation names are shared between this SEP and the topological restrictions in SEP 044. This need not be problematic, but if it is judged to be so, one or the other can have a prefix added to differentiate them.

6. Relation to Other SEPs

If SEP 037 passes, SequenceConstraint will be renamede to Constraint.

As noted above, some of the relation names in this SEP are identical to relation names in SEP 044. If both SEP 044 and SEP 037 pass, the descriptions of the shared terms will be merged with an explanation of how they apply to ordered vs. unordered elements.

Copyright

CC0
To the extent possible under law, SBOL developers has waived all copyright and related or neighboring rights to SEP 045. This work is published from: United States.