[obs] Joining DwC, OBOE, PO and PATO

[Shawn Bowers]

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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