[Bioperl-l] Question - Primary_id

[Ewan Birney]

On Mon, 23 Dec 2002, Hilmar Lapp wrote:

>
> On Monday, December 23, 2002, at 05:29  AM, Ewan Birney wrote:
>
> > Out of these three, both display_id and accession_number have pretty
> > consistent semantics and usage, whereas primary_id frankly should
> > probably
> > be junked - it is too complex an idea to be enforced, and by
> > definition is
> > implementation specific.
>
> My $.02 are that it's the definition that should be junked, not the
> method itself. I think there should be a place to store a
> datastore-specific ID which may be different from an accession number.
> GenBank's GI number is a perfect example (and the genbank parser
> presently uses primary_id to store the GI number).

Well, should we call it:

  "implementation_specific_id" or something


BTW - if genbank parser uses it for GI number, i am tempted to put some
super smarts into a method called gi_number on richseq which will issue a
warning if it didn't come from genbank or something like that. Hmmmm....






>
> The semantics I'm using it with for bioperl-db, for example, is that it
> is an alternate key by itself, which is helpful as opposed to the
> accession/version/namespace triple you'd have to use otherwise. That
> might not hold though ...
>
> 	-hilmar
>
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>