[Biocorba-l] Re: [Biojava-l] Re: CORBADEV: LSR news - new RFP about biomolecular entities

[Dickson, Mike]

In the current LSR model facts on a sequence are described as SeqAnnotations
and they have positional info, a label and an Any which represents the data
association with that position.  I think Philip is suggesting that a
standard type be defined for floating point info and as he says the obvious
answer is to use a native IDL type (like float or double) for this.  A
typedef, if there is an obvious name for the concept might also be nice.

The alignment approach you suggest could also be made to work but it doesn't
map nicely onto the current sequence model.  There's no concept of a symbol
being anything other than a string character.   I actually like the biojava
model quite a bit.  BTW, I also understand that there has been some
discussion regarding wether the next RFP should allow changes to the current
BSA model.  I won't attempt to summarize the discussion at the meeting since
I didn't attend (Scott perhaps you could?).  My personal opinion is that
some modifications are probably necessary.

BTW, since I'm giving opinions :) I do have one other.  I believe the next
RFP should focus on submissions that submit models (using UML and the UML
Corba profile) as opposed to directly requiring IDL.  Doing so would support
a normative mapping to IDL but also allow use of the model in other contexts
(i.e. anything that supports mapping UML to an implementation language).

Mike

> -----Original Message-----
> From: Matthew Pocock [mailto:mrp@sanger.ac.uk]
> Sent: Tuesday, September 19, 2000 9:03 AM
> To: lijnzaad@ebi.ac.uk
> Cc: senger@ebi.ac.uk; konnerth@incyte.com; corbadev@ebi.ac.uk;
> biocorba-l@biocorba.org; biojava-l@biojava.org; bioxml-dev@bioxml.org
> Subject: [Biocorba-l] Re: [Biojava-l] Re: CORBADEV: LSR news - new RFP
> about biomolecular entities
> 
> 
> Afternoon.
> 
> > I have just two suggestions for addition:
> >
> > - a type for representing floating point information on 
> sequence positions,
> >   such as hydrophobicity plots. I am not going to insist on 
> this, because the
> >   (nearly) obvious solution is to just use a IDL::float. Or 
> was that double ...
> >
> 
> This can be cleanly represented as an alignment containing a 
> sequence (protein) and
> hydrophobicity (floats). This would require either a special 
> type within alignments
> that has numbers, or a re-working of how sequences are 
> represented so that an
> individual symbol could be a float (the neater solution). 
> This may be covered by the
> BioSequence alphabet extensions. I don't know how the 
> alignment object works in BSA
> so I may be way of mark.
> 
> Matthew
> 
> _______________________________________________
> Biocorba-l mailing list
> Biocorba-l@biocorba.org
> http://biocorba.org/mailman/listinfo/biocorba-l
>