[Open-bio-l] Re: [Bioperl-l] seq namespace method

[Steve Chervitz]

Glad we're all thinking alike here. However, why not use containment instead of
inheritance, to allow a Bio::IdentifiableI to contain one or more
Bio::Identifiers? 

If an IdentifiableI also has a preferred identifier slot, then it could have
methods such as namespace(), id(), version() that would delegate to their
preferred identifier. This would allow us to maintain the current interface yet
still be I3C-compliant.

For those that don't know about it, the I3C thingy that Ewan mentions is called
the LSID (Life Science Identifier), a draft specification of which can be found
at http://www.i3c.org/workgroups/technical_architecture/index.html. It's
generated a bunch of interesting discussion.

The LSID concept is still evolving, but current thinking is to have at least
these fields: authority, namespace, id. A version field will probably be added
and security info may be dropped.

Steve

--- Lincoln Stein <lstein@cshl.org> wrote:
> Yes.
> 
> Lincoln
> 
> On Monday 15 July 2002 04:48 am, Ewan Birney wrote:
> > I would claim the right pattern here is to have
> >
> >
> >   Bio::IdentifiableI
> >
> > which Bio::PrimarySeqI inheriets from and Bio::PrimarySeq implements.
> >
> >
> >   Bio::IdentifiableI would have slots for namespace, version, id (NB
> > **no** type) and would be compatiable with the 13C naming convention
> > thingy to produce I3C style names (so it might also have "authority" as a
> > slot).
> >
> >
> >
> >
> >
> >
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>.
> > -----------------------------------------------------------------
> >
> >
> > _______________________________________________
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> 
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein@cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
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=====
Steve Chervitz
sac@bioperl.org

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