Re: [Obi-plan-branch] protocol parameters

[Alan R. <ala...@gm...>]

I'll give it a first pass, though it may not be completely baked.

On Jun 13, 2008, at 1:08 PM, Fostel, Jennifer (NIH/NIEHS) [C] wrote:
> Hello, all!
>
> we have several very similar protocols which differ at the  
> parameter specification.  we were thinking of these as the "same"  
> protocol with different parameters.
>
One can see the conflict even in your phrasing. Are they very  
similar? or the same? I think we should reserve "the same" to mean  
the same, and instead consider this a standard situation of having a  
class and subclasses. (assuming protocol is a class, but that's a  
separate discussion).

So:
> for example, dosing-a-rat protocols within a study would be  
> identical except for the dose level
> can we use OBI to annotate this?
>
For the sake of discussion, suppose that the drug is aspirin measured  
by mass, and let's not get into the question of whether we know the  
mass exactly or just have a measurement of it. I'll write "mass of n  
grams" as the name of a mass quality for this purpose. It probably  
means the instance of mass quality that was measured to be n grams.

I'm writing this at the class level, since I'm assuming that that's  
what you requested, though it may be appropriate to consider this at  
the instance level.

portion_of_aspirin: acetylsalicylic acid and has_role some drug_role

Dosing-a-rat-with-aspirin: material transformation and has_input some  
rat and has_input some portion_of_aspirin and has_output some (rat  
and has_role treated_role) and (exactly 1 has_input (has_role some  
drug_role))

Dosing-a-rat at 10mg:  Dosing-a-rat and has_input some (aspirin and  
(has_quality some (mass of  10mg)))
Dosing-a-rat at 20mg:  Dosing-a-rat and has_input some (aspirin and  
(has_quality some (mass of  20mg)))
...

This doesn't preclude the description of a larger protocol with  
multiple dosings.

-Alan



>
> (the protocol actually has about a dozen parameters, but to make it  
> straightforward i list only one)
>
> thanks!
>
> ...jennifer
>
>
> Jennifer Fostel, Ph.D.
> CEBS Scientific Administrator
> SRA International
>
> Laboratory of Respiratory Biology
> NIEHS, NIH
> PO Box 12233 Mail Drop F1-05
> 111 Alexander Drive
> Research Triangle Park NC 27709-2233
>
> phone 919 541 5055
> fax 919 541 1460
>
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