[obs] Joining DwC, OBOE, PO and PATO

[Chris Mungall]

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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