[Bioperl-l] Bio::Score of interest?

Sendu Bala bix at sendu.me.uk
Tue Jun 27 08:52:05 EDT 2006

Hilmar Lapp wrote:
> So you basically want to attach semantic information to a number, and 
> type the number thereby?

Basically, I want to be able to stick a bunch of (different kinds of) 
numbers into an object, and later get the 'best' one out (of a 
particular kind), or sort multiple of those objects.

> If so, an ontology would be the more natural choice (and in the end more 
> flexible one) for expressing this kind of information.

I'm not really sure I understand 'and type the number', or what (useful) 
flexibility doing it with an ontology would provide.

> Have you looked at the concept of 'quantitation types', e.g. in MAGE 
> (the XML [MGAE-ML] or the object model [MAGE-OM])?

I had a quick look, but not really sure what you intended to suggest here.

> There is no quantitation type ontology at a repository I know of. I have 
> used my own ones in the past and they have been pretty useful.

Can you provide a brief example of what you mean?

If it would be appropriate to implement a Bio::Score with an ontology 
that's fine. Would we want a Bio::Score implemented though? Or are you 
suggesting each module make it's own quantitation type ontology when it 
wants to deal with numerous scores?

I like the idea of a Bio::Score because then you can compare complex 
scores from multiple different unrelated modules.

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