[Bioperl-l] Re: No joins

[Lincoln Stein]

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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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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