Clarification on comments re NucleicAcidSequenceFeature.orientation

Return to BRIDG

Need clarification on comments re NucleicAcidSequenceFeature.orientation (rows 35)

Current Definition

DEFINITION: The orientation of the feature relative to the sequence upon which it is annotated.

EXAMPLE(S): "forward", "for", "F", "+", "reverse", "rev", "R", "-"

OTHER NAME(S):

NOTE(S): Features that are annotated on the same strand as the underlying sequence are usually indicated by "forward", "for", "F", or "+". Features that are on the opposite strand (the reverse-complement of the underlying sequence) are usually indicated by "reverse", "rev", "R", or "-".

Ballot Comment

This is confusing. Can it be constrained to orientation relative to the genomic context?

Current Disposition

Pending Input From Submitter

Proposed Disposition Comment

Need confirmation from LSDAM SMEs that this proposed change is OK with their use case. Does the note in the attribute description help clarify?

• 'NOTE(S): Features that are annotated on the same strand as the underlying sequence are usually indicated by "forward", "for", "F", or "+". Features that are on the opposite strand (the reverse-complement of the underlying sequence) are usually indicated by "reverse", "rev", "R", or "-".'

Outstanding Questions

• Is this comment actually proposing a change in definition to the following?
  • DEFINITION: The orientation of the feature relative to the genomic context.
• Life Science SMEs: Is such a change consistent with the original LSDAM concept?

Responses

DISCUSSION 20160225: This may be in the CG message, in fact probably is, but is a very specific concept that we should probably model by reference. Deferred until an approach can be established.

Return to BRIDG