[obs] Joining DwC, OBOE, PO and PATO

[Shawn Bowers]

Hi Chris,

Are there some specific papers / webpages that I could read to get an
understanding of OBI?  Any pointers would be great.

Thanks,
Shawn

On Wed, Oct 27, 2010 at 1:25 PM, Chris Mungall <CJMungall at lbl.gov> 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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>
>