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

[Lincoln Stein]

I think it's important to separate the notion of an identifier from the notion 
of a collection of identifiers assigned to an object.

Lincoln

On Monday 15 July 2002 04:08 pm, Ewan Birney wrote:
> On Mon, 15 Jul 2002, Steve Chervitz wrote:
> > 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?
>
> Hmmm. Doable.
>
> Is this ideal - this is saying that one object is usually represented by a
> "cloud" of identifiers?
>
>
> I would claim that the opposite pattern is more true - on object usually
> has one "main" identifier and then points to a cloud of related
> identifers, the DBxREFs
>
> Certainly merging the idea of DBxREFs - or DBLinks in Bioperl which should
> also be Identifiable would be a good idea.
>
>
> I can see your arguement, but I would marginally favour the strict
> one-object-one-identifier and not factor out the identifier objects as a
> separate thing - claiming that in those cases most people want an
> Identifiable object that is an AnnotationCollectionI and has a cloud of
> Identifiable DBxREFs
>
>
> But... not a clear cut decision. Any other views
>
>
> (PS - I liked Lincoln's simple "yes")
>
> > 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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> > >
> > > --
> > > =======================================================================
> > >= Lincoln D. Stein                           Cold Spring Harbor
> > > Laboratory lstein@cshl.org			                  Cold Spring Harbor, NY
> > > =======================================================================
> > >= _______________________________________________
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> > > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> > =====
> > Steve Chervitz
> > sac@bioperl.org
> >
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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