[Bioperl-l] Bio::Ontology overhaul

[Hilmar Lapp]

First off, I'm not in particular favor of creating two interface name 
monsters that nobody else is used to from anywhere else. My viewpoint 
is that you can solve the problem by having different methods 
reflecting identifiers which are valid locally and those which are also 
valid globally. We had a discussion about that 5 minutes before we left 
off in Singapore. Lincoln's proposal hasn't been discussed on the list 
yet, so it may or may not finally happen.

Second, we made a decision a while ago to separate interfaces from one 
another wherever sensibly possible. In this case, OntologyI will not 
inherit off of <whichever>IdentifiableI, but an implementation may do 
so, and can then provide the alias if appropriate. (Similarly, SeqI 
doesn't inherit from IdentifiableI, but Seq does implement both.)

So, bottom line, if an ontology wants to be <whichever>IdentifiableI, 
my take is it will inherit from that interface and appropriately alias.

As for the TermI interface, it doesn't inherit from IdentifiableI 
either, but in fact I forgot to mention that I changed the 
Bio::Ontology::Term implementation to implement both Bio::IdentifiableI 
and Bio::DescribableI. TermI::identifier() is not meant to be an 
arbitrary identifier (as opposed to OntologyI::identifier); it will 
usually be assigned by the authority of the ontology.

	-hilmar

On Wednesday, February 26, 2003, at 05:16  PM, Paul Edlefsen wrote:

> My immediate concern is compatability with Lincoln's proposed 
> LocallyIdentifiableI and GloballyIdentifiableI interfaces (already 
> checked in on the freaky dev branch).  If there is going to be a 
> unique identifier it should, for compatability with 
> LocallyIdentifiableI, be called (or aliased) 'unique_id'.  You are 
> proposing that, in TermI, 'name' be unique and 'identifier' be 
> arbitrary.  Even if you were to add 'unique_id' as an alias to 'name', 
> the homonymity of 'identifier' and 'unique_id' would be confusing.
>
> :Paul
>
>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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