[Bioperl-l] Re: No joins

[Matthew Pocock]

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



__________________________________________________
Do You Yahoo!?
Everything you'll ever need on one web page
from News and Sport to Email and Music Charts
http://uk.my.yahoo.com