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

Hilmar Lapp hlapp at gmx.net
Tue Jun 27 10:27:55 EDT 2006

I would have suggested initiating a quantitation type ontology, not  
one individual per module.

An ontology would capture all your semantic information (min/max or  
range, higher or lower is better, what is a reasonable default [not  
sure there would be one], etc) and you would have a hierarchical  

You type a score by associating it with an ontology term:

	BLAST_e-value is-a expectation_value
	expectation_value has-min-value 0
	expectation_value has-max-value positive_infinity
	BLAST_p-value is-a probability_value
	probability_value has-min-value 0
	probability_value has-max-value 1
etc and then something being an expectation_value for instance would  
imply several attributes laid down in the ontology (probably through  
has-a statements).

It seems to me that essentially what you are trying to do is  
capturing knowledge for particular types of scores, which you would  
then use in more general purpose programs to sort from more to less  
significant, and possibly filter? If so, then hard-coding this into  
objects (all over the place or in a single place) is typically not  
the best practice; rather, the usual best-practice approach is using  
(and if necessary, constructing) an ontology. This is also the most  
re-usable approach.


On Jun 27, 2006, at 8:52 AM, Sendu Bala wrote:

> 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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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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