[Bioperl-l] seq namespace method

[Steve Chervitz]

The namespace concept is useful, only I think that the correct place for it is
at the level of the identifier, not the sequence object, because a namespace
applies to a name, not a sequence. 

Bioperl doesn't encapsulate sequence identifiers with objects, but doing so
would help manage the sequence-identifier relationship and also make it easier
to work with identifiers in general.

A Bio::Identifier object could have slots for: namespace, type, version, id,
and  perhaps, is_unique. It could have a method to stringify itself with a
specified delimiter and with or without namespace/version/type info.

Identifiable objects such as sequences could have methods that returned
Bio::Identifiers such as: all_identifiers(), preferred_identifier(). Perhaps
there could be a Bio::IdentifiableI interface for this. 

Identifiable object would not have to store Bio::Identifiers internally. They
could construct them on the fly (perhaps via an associated Bio::Factory::
object).

This would model the object-to-identifier relationship more generally than we
do  now. For example, PrimarySeqs can have display_id, primary_id, and
accession_number, which I always find a bit confusing/limiting.

I know this is more of a substantial undertaking than just adding a namespace()
method to PrimarySeqI, but could be worth the effort. What do you think?

Steve

--- Hilmar Lapp <hlapp@gnf.org> wrote:
> According to BioSQL, sequences (bioentries) live in a namespace, e.g., the
> name of the databank that maintains and/or serves them.
> 
> None of the Bio:: seq objects/interfaces have a method for that.
> 
> I propose to add one, specifically to the lowest level Bio::PrimarySeqI
> (bioentries are pretty general, and a namespace is needed for /any and all/
> bioentries). To me, the namespace doesn't have to do much with whether this
> seq is going to be stored in BioSQL or not. A sequence with an accession
> number has (implicitly or explicitly) a namespace in which this accession
> number is valid. PrimarySeqI has an accession.
> 
> Anyone has other suggestions, objections?
> 
> 	-hilmar
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
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=====
Steve Chervitz
sac@bioperl.org

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