[Bioperl-l] Re: No joins

[Jason Stajich]

b/c swiss prot and genbank have different formats.
Not sure how agave,bsml,game, represent them.

-jason

On Fri, 16 Aug 2002, Lincoln Stein wrote:

> Why not store them in an auxiliary text field, then, for round-tripping
> purposes?
>
> Lincoln
>
> On Friday 16 August 2002 11:14 am, Matthew Pocock wrote:
> > If you talk to the curation teams, either for EMBL or SWISSPROT, they
> > always say that fuzzies are purely for human consumption and come with a
> > public health warning stronger than that attached to any tobacco products.
> >
> > IMHO the only point in representing them in all their goarey detail is
> > that some people want to be able to round-trip fuzzies through our
> > object models, and the effort associated with producing an API that does
> > much more than this is not worth the hastle.
> >
> > Matthew
> >
> > Lincoln Stein wrote:
> > > Can someone point me to an example of an algorithm that makes use of
> > > fuzzies, either from the ASCII art representation or from ASN.1.  Or are
> > > the fuzzies intended only for human consumption?
> > >
> > > Lincoln
> > >
> > > On Thursday 15 August 2002 12:36 pm, Ewan Birney wrote:
> > >>Brian -
> > >>
> > >>
> > >>I would certainly agree with you that joins are bad, and in fact Bioperl
> > >>originally had a heirarchical feature only system and joins implicitly
> > >>went into these cases.
> > >>
> > >>
> > >>
> > >>However as more people used it being able to store and process 100% of
> > >>EMBL/GenBank became a priority, and we bolted on the location stuff -
> > >>location stuff was really driven in by the fuzzies (aaaah, the fuzzies)
> > >>which are distinctly hard to handle inside heirarichal features (what
> > >> does biojava do with the fuzzies?) but most fuzzies are also joins, (in
> > >> fact alot of joins have fuzzy ends) so... it became the defacto way to
> > >> handle joins.
> > >>
> > >>
> > >>Of course the frustrating thing is that noone *can* use the fuzzies but
> > >>the semantic interpretation of fuzzies is just... impossible to remain
> > >>cosnsistent across more than 2 records. Fuzzies are for human warm-fuzzy
> > >>feelings that the data format is representing everything they know and is
> > >>just a semantic mire for computers.
> > >>
> > >>
> > >>
> > >>I agree it gives us so much semantic rope to hang ourselves with it is
> > >>scary. But there is not an obvious ideal solution:
> > >>
> > >>   - somehow represent all things inside hierarchial features, including
> > >>the fuzzies (brain-ache)
> > >>
> > >>   - not handle 100% of Genbank (means a large number of uses cases fail)
> > >>
> > >>
> > >>
> > >>If there is something obvious I am missing here, shout, but this is
> > >>somewhere between rock-and-hard-place in my experience.
> > >>
> > >>
> > >>
> > >>Practical question - what does BioJava do with the Fuzzies?
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>-----------------------------------------------------------------
> > >>Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > >><birney@ebi.ac.uk>.
> > >>-----------------------------------------------------------------
> > >>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu