[obs] Joining DwC, OBOE, PO and PATO

[Chris Mungall]

Best starting point:

http://purl.obolibrary.org/obo/OBI

There's a paper in the works I believe. But the best way to understand  
some of the equivalent issues that have come up re: measurements and  
PATO is to trawl through some fairly dense email threads, I'm afraid -  
unless Alan has better suggestions

On Oct 27, 2010, at 1:32 PM, Shawn Bowers wrote:

> 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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>>
>>