[obs] Joining DwC, OBOE, PO and PATO

[Cam Webb]

Dear Hilmar,

>> There is an active discussion on the tdwg-content mailing list right now 
>> about using Darwin Core in a semantic web context
>
> My own view on this is that this is problematic - DwC is a common vocabulary, 
> with rather weakly defined semantics, and certainly not in a computable form 
> (i.e., there are usage guidelines, but very little you can reason over). For 
> a LOD view that may still be enough, though. But I wouldn't try too hard to 
> nail down the formal semantics of DwC terms - there really aren't any.

Looking at that tdwg-content conversation I think you are right, but this 
calls for the need for a more semantically formal set of DwC terms, a fork 
to create a `Darwin SW' to stand alongside Darwin Core.  The LSID-voc 
ontology at http://rs.tdwg.org/ontology/voc/ is a start I guess.  The 
formal acceptance of such a new standard would take a long time.  What do 
you suggest doing in the meantime?

>> I think a fruit_txyz0 is indeed part of plant_txyz0
>
> An instance of the Fruit is ro:part_of some instance of Plant, yes, unless it 
> has fallen down, or is being eaten by an animal (does PO assert that Fruit 
> ro:part_of Plant?). But the instance of the fruit isn't ro:part_of the 
> occurrence of the instance of the plant.

Hmm [scratches head], I guess so...  Then how about this for a more 
satisfying (but slightly more complex) way to do this (dropping the 
prefixes):

@prefix : <#> .
:Indiv123 a :Individual ;
     :hasOccurrence [
     a :SpaceTimeDefinedOccurrence ;
     :hasToken [
         a :Observation ;
         :ofEntity [
             :part_of :Indiv123 ;
             a :Fruit ;
             :bearer_of [
                 a :GreenColor
                 ] ;
             ] ;
         ] ;
      ] .

(Figure at: http://phylodiversity.net/cwebb/img/obs-eg2.jpg )

> You said earlier in the discussion on tdwg-content, if I paraphrase 
> correctly (and correct me if I'm wrong) that the occurrence is the 
> intersection between the individual, space, and time. I would argue that 
> it's not: there is no non-empty intersection set between the set of all 
> living (or formerly living) individuals, the set of all points in space, 
> and the set of all time points. Rather, an instance of an occurrence has 
> properties, namely the individual, the point (or region) in space, and 
> the point in time.

Sorry - sloppy use of `intersection' by me I guess.  I see the occurrence 
as the Individual frozed in a particular space and time.  So I agree that 
an instance of an occurrence has properties, namely the individual, the 
point (or region) in space, and the point in time, and is not the same as 
the Individual.

>> I.e. is it fair to assert that a pato:Quality is a oboe;Measurement?
>
> Would you say that pato:shape is_a oboe:Measurement (which would follow from 
> the above)? I think not; I would think that a oboe:Measurement would be for a 
> pato:shape.

I would say that pato:RoundShaped is_a oboe:Measurement (consisting of 
oboe:Characteristic "Shape" and oboe:Value "Round") but not that 
pato:Shape (the parent quality of pato:RoundShaped) is_a oboe:Measurement. 
But I accept that this may be tricky semantically; I don't see how to 
demarcate the level of hierarchy in PATO where a pato:Quality shifts from 
just a oboe:Characteristic to a combination of oboe:Characteristic and 
oboe:Value. Chris, any insight here, if you have time?

> We are working on making this all available via the collaborative site 
> of SONet (http://sonet.ecoinformatics.org/). The site is being 
> transitioned as we speak to become as open as this list. We will also be 
> posting the meeting report from the TDWG workshop there once it is 
> written (see 
> http://sonet.ecoinformatics.org/workshops/tdwg-2010-meeting). Anyone who 
> would like an account on the site right away should let Mark Schildhauer 
> or Matt Jones know, or hang on a little more for all content having been 
> made open.

Standing by.  Thanks.

>> An alternative to using the OBOE ontology at all is to use a 
>> phenotype-focussed ontology (i.e., an OBO one emerging from the phenoscape 
>> group), where a pato:quality ro:inheres_in a po:Fruit.  However, I'm not 
>> sure there are terms yet published that can be used in RDF.  Any updates on 
>> this would be vaulable.
>
> Why can the PATO terms not be used in RDF?

Sorry, I meant that the phenoscape terms (e.g. hasPhenotype) are not 
available yet in RDF, AFAIK.  This is not a problem if a new vocabulary is 
coined, with Observation terms, either `Darwin SW,' or something else.

>> data into it.  For data re-use (especially LOD applications) the latter is 
>> preferable, but I don't think we are at the stage yet of having an agreed 
>> upon template.
>
> I agree on both accounts.

Hoping we can push forward as fast as possible to such a template.

Best,

Cam