[obs] Joining DwC, OBOE, PO and PATO

[Hilmar Lapp]

Yeah, I agree, I've been thinking that before. Though aren't you  
referring here more to IAO than OBI?

	-hilmar

On Oct 27, 2010, at 4:25 PM, Chris Mungall wrote:

>
> It seems there is a large overlap between what OBOE is doing and  
> what OBI (the Ontology of Biomedical Investigations) is doing.  
> Although the domains have different focus (ecology vs experimental  
> biology and biomedicine) most examples will be analagous, just  
> switch apples for tissue samples. It might benefit to have some  
> cross-talk here.
>
> On Oct 27, 2010, at 1:11 PM, Shawn Bowers wrote:
>
>> Hi,
>>
>> Jumping in a bit late to the discussion ...
>>
>>> Although keeping all phenotype observations within the OBO model is
>>> attractive (i.e., not using OBOE after all).  If DwC were to  
>>> accept an
>>> Observation class, then this could be directly of a bfo:Entity  
>>> which was a
>>> bearer_of a Quality, making life much simpler.
>>
>> There is a fundamental difference between PATO (more generally EQ)  
>> and
>> OBOE when talking about properties of individuals. The focus of OBOE
>> is on defining measurements of individuals (e.g., "field
>> observations"). A measurement states that a particular entity (an
>> individual) had a specific value for a property within some context,
>> where the context could be a variety of spatial, temporal, or even
>> experimental settings. The measurement is not by definition essential
>> to the individual (e.g., the height of a tree varies over time, each
>> individual tree has a different height, etc.). PATO, from what I've
>> read, is not designed to express measurements and measurement  
>> context,
>> but instead is focused on describing the types of properties and  
>> their
>> associated values (e.g., spherical shape or green color). These could
>> be used within a measurement setting, or to classify entity types
>> (e.g., a curved wing is a wing that has a curved quality).
>>
>> A strength of OBOE is that we can describe the properties of
>> individuals that change over space/time/experiment/etc. This is also
>> true of other observation models (not just OBOE).
>>
>> In OBOE, going back to your original example, one way you could
>> specify the measurement of the individual using PATO terms might be
>> something like this:
>>
>> _:o2
>> a oboe:Observation ;
>> oboe:ofEntity [
>>   a po:PO_0009001 ;  # fruit entity
>>   ] ;
>> oboe:hasContext _:o1 ;
>> oboe:hasMeasurement [
>>   oboe:ofCharacteristic [
>>     a po:PATO_0000014 ; # color
>>     ] ;
>>   oboe:hasValue [
>>     a po:PATO_0000320 ; # green
>>     ] ;
>>   ] .
>>
>> _:o1
>> a oboe:Observation ;
>> oboe:ofEntity _:blank1 .  # an Occurrence
>>
>> Again, this does not say that the color of the individual is green.
>> Instead, it says someone observed within the occurrence that the
>> individual was green. And these are fundamentally different  
>> statements
>> ...
>>
>> Note above that I'm using Green as the value of the measurement,  
>> which
>> also implies the characteristic Color. However, one could imagine
>> wanting to attribute something more specific to the characteristic
>> than just color (at least for some qualities). This also becomes
>> important for numeric values (e.g., the Wavelength is 515nm).
>>
>> Shawn
>>
>> On Tue, Oct 26, 2010 at 9:29 PM, Cam Webb <cwebb at oeb.harvard.edu>  
>> wrote:
>>> Dear Chris,
>>>
>>>> You would be more interoperable with other OBO-compliant  
>>>> resources if you
>>>> model it this way, using the bfo bearer_of property to connect a  
>>>> fruit
>>>> individual with a color individual:
>>>>
>>>> [] a oboe:Observation ;
>>>>   oboe:ofEntity [
>>>>       a oboe:Entity ;
>>>>       a po:PO_0009001 ;
>>>>       bfo:bearer_of [
>>>>           a pato:PATO_0000320
>>>>       ] ;
>>>>   ] ;
>>>
>>> Thanks for this suggestion (although bearer_of doesn't seem to be  
>>> a term in
>>> bfo 1.1, but only in ro_proposed?).  A possible problem with this  
>>> solution
>>> may be that such an oboe:Observation has no oboe:Measurement  
>>> (though an
>>> oboe:Measurement is not specified in the oboe ontology as being  
>>> required for
>>> a oboe:Observation...).  Perhaps another solution is to simply  
>>> make the
>>> observed quality an instance of the PATO term:
>>>
>>> []   a oboe:Observation ;
>>>   oboe:ofEntity [
>>>       a oboe:Entity ;
>>>       a po:PO_0009001 ;
>>>       ] ;
>>>   oboe:hasMeasurement [
>>>       a pato:PATO_0000320 .  # <----------
>>>       ] .
>>>
>>> Although keeping all phenotype observations within the OBO model is
>>> attractive (i.e., not using OBOE after all).  If DwC were to  
>>> accept an
>>> Observation class, then this could be directly of a bfo:Entity  
>>> which was a
>>> bearer_of a Quality, making life much simpler.
>>>
>>> [] a dwcnew:Observation ;
>>>   dwcnew:ofEntity [
>>>       a po:PO_0009001 ;
>>>       bfo:bearer_of [
>>>           a pato:PATO_0000320
>>>           ] ;
>>>       ] .
>>>
>>>> I don't know much about the oboe ontology, an dhow these can  
>>>> interoperate
>>>> with OBO ontologies. Is oboe:Entity intended to be the maximally  
>>>> general
>>>> class? If so then it may be redundant to declare this individual  
>>>> as being
>>>> both type oboe:Entity and of type fruit (since presumably fruits  
>>>> are
>>>> entities).
>>>
>>> True, I was just adding it for extra information (for me).
>>>
>>> Thanks again,
>>>
>>> Cam
>>>
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>
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: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
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