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

[Matthew Pocock]

Hi.

My vote would be on containment/agregation. This is nearly always the 
answer over inheritance. Perhaps Bio::IdentifiableI provides an 
identifier method that returns a Bio::IdentifierI. Bio::SeqI implements 
Bio::IdentifiableI. Bio::IdentifierI stores all of the info necisary for 
regenerating the resource (in this case a sequence) and can exist 
potentialy (or even preferably) without a reference to the object it 
identifies. A Bio::Resolver class is used as the factory or hub for 
returning objects for identifiers.

XRefs are a different use case of identifiers, and may be better moddled 
by sticking Bio::Identifier objects in some well-known annotation 
bundle, totaly disjoint from any Bio::IdentifiableI API.

For cases where an identifiable object has a primary and several 
secondary identifiers, why not have the Bio::IdentifiableI::identifier 
method take an optional argument (something like "ACC" or "SID" or 
whatever). No argument returns the default identifier. An argument 
returns a list (possibly empty) of all identifiers of that type.

Sequences have identifiers, they are not themselves identifiers.

Matthew

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
>>>========================================================================
>>>_______________________________________________
>>>Bioperl-l mailing list
>>>Bioperl-l@bioperl.org
>>>http://bioperl.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>=====
>>Steve Chervitz
>>sac@bioperl.org
>>
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> 
> 
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