[Bioperl-l] How is is_circular recorded in BioSQL (by BioPerl)?

[Peter Cock]

Hi all,

I'm trying to check how (currently) BioSQL should be used to record
if a sequence is circular or linear. I know this property is exposed in
BioPerl as the boolean is_circular() method from Bio::PrimarySeq,
and based on this old thread the value gets stored in BioSQL as a
sequence level annotation:

http://www.bioperl.org/pipermail/biosql-l/2005-June/000843.html
http://www.bioperl.org/pipermail/biosql-l/2005-June/000846.html
http://www.bioperl.org/pipermail/biosql-l/2005-June/000849.html
http://www.bioperl.org/pipermail/biosql-l/2005-June/000859.html

The term is_circular also matches nicely with GFF3, other than a
possible difference in capitalisation:

"Is_circular A flag to indicate whether a feature is circular."

and:

"For a circular genome, the landmark feature should include
Is_circular=true in column 9."

http://www.sequenceontology.org/gff3.shtml.

Can anyone confirm how exactly the is_circular (or Is_circular?)
annotation is used in BioSQL by BioPerl? I am guessing that
it is in the standard bioentry_qualifier_value table, with the
term_id referencing "is_circular" (check case), rank 0, and
value of "true" or "false" (check case).

I want to make Biopython's BioSQL usage consistent, see:
https://redmine.open-bio.org/issues/2578

Thanks,

Peter