[obs] Joining DwC, OBOE, PO and PATO

[Hilmar Lapp]

Hi Cam,

thanks for writing this up and posting here! I think it's a perfectly  
valid place to discuss your questions, or more generally how to use  
possibly applicable emerging standards for expressing observation data  
in an interoperable way with machine-interpretable semantics.

Aside from Chris' response just a few comments below.

On Oct 26, 2010, at 5:31 AM, Cam Webb wrote:

> 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.

> 2. *part_of* If we want to record an observation of part of an  
> organism, we could use the ro:part_of property to link the  
> Observation of that part to the Individual which has that part.  Two  
> issues here, i) is it meristically valid to say that the Occurrence  
> (the space-time instance of the continuant Individual) can have a  
> part?

If you treat the occurrence of an individual as the same as the  
individual itself then yes. But they are not the same, are they? An  
individual can occur at a certain place at a certain time, but the  
occurrence isn't the individual, right?

> 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.

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.

> 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.

> Matt Jones mentioned that there was an effort underway by  
> participants of SONet, DataONE, and the Data Conservancy, and  
> possibly the Plant Trait observations ontology group to ``try to  
> harmonize many of the existing observations models, including OBOE, O 
> +M, and EQ, as well as more traditional models like Darwin Core.''  
> I'm wondering if there are any documents available describing this  
> ontology interoperability development process?

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.

>
> 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?

> The options for someone in my position are to design a model that  
> represents the data as I see it, coining various new terms where  
> needed, or to find/wait for a semantic template, with standardized  
> terms, and fit my 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.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================