[obs] proportional phenotypes

[Hilmar Lapp]

I thought this would be an interesting question for the Observations  
list as well, and am hence forwarding it.

How would "petiole 5x longer than wide" best be represented in an OBOE  
model?

Jim -

your revised suggestion below is exactly along my reaction to your  
original question. Often questions such as yours are framed as "what  
is the correct way to represent this using model Y". Many data models  
have indeed only one or very few correct way of representing some  
data, but I think this is much less true for the EQ model. Obviously  
something that is syntactically wrong or logically inconsistent in OWL  
would have to be considered "incorrect".

The rationale I was trying to follow in thinking how best to represent  
this wasn't so much about what is the "correct" way, but rather what  
inferences do you want to support with it. Is it important to the  
ability to reason over the semantics that it is a proportionality that  
inheres in the petiole, or that it is a length, and the length in this  
case just happens to be stated relative to some other length, but that  
doesn't change that what is of interest here semantically is that it  
is a length characteristic that is being observed.

Even so, that doesn't mean that in other cases it would really be the  
proportionality that's important.

	-hilmar

On Feb 17, 2011, at 2:36 PM, Jim Balhoff wrote:

> I've been thinking a little more about this and wonder about  
> modeling proportions in a way that is more in line with how we are  
> modeling relative phenotypes and phenotypes with absolute values. At  
> a PATO/Phenoscape/HAO workshop in September, we decided on modeling  
> relative phenotypes something like this:
>
> length that inheres_in some petiole and  
> increased_in_magnitude_relative_to some (length that inheres_in some  
> head)
>
> where the petiole is described as longer than the head.
>
> An absolute value for the length would be like this:
>
> length that inheres_in some petiole and has_value some  
> (has_magnitude value 5 and has_unit value cm)
>
> By the way I'm not sure what the standard properties are to be used  
> to relate the magnitude, unit, etc.
>
> So if we want to explicitly describe the length of one part as  
> proportional to some other part, perhaps we could use the comparison  
> quality as a unit:
>
> length that inheres_in some petiole and has_value some  
> (has_magnitude value 5 and has_unit some (length that inheres_in  
> some head))
>
> Any opinions?
>
> Thanks,
> Jim
>
> On Feb 16, 2011, at 4:00 PM, Jim Balhoff wrote:
>
>> Hi,
>>
>> Is there an accepted model for representing a proportional  
>> phenotype in OWL? I've taken a look at the properties in PATO such  
>> as has_dividend_quality and has_divisor_quality, but I'm not sure  
>> how to put it all together. Here is the phenotype description:
>>
>> character: petiole length
>> state: petiole 5x longer than wide
>>
>> This is what I came up with:
>>
>> has_part some (petiole and bearer_of some ('proportionality to' and  
>> (has_dividend_quality some width) and (has_divisor_quality some  
>> length)))
>>
>> Firstly I'm not sure if I've constructed that correctly. Also, what  
>> data property can I use to connect 'proportionality to' with the  
>> value 5?
>>
>> Thanks,
>> Jim
>>
>
> ____________________________________________
> James P. Balhoff, Ph.D.
> National Evolutionary Synthesis Center
> 2024 West Main St., Suite A200
> Durham, NC 27705
> USA
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: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
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