[obs] Species occurrences in OBOE

[Shawn Bowers]

Hilmar --

I'll let Matt comment further. But indeed we discussed most of your
points below when creating this representation. We modeled it this way
since this seemed closest to what was being represented in DwC.

As for this statement:

> Also, if OBOE is indeed confined to direct observational measurements (as
> Shawn recently suggested), then  those properties and assignment should be
> represented differently indeed, shouldn't they?

I don't know what you mean here by "direct observational
measurements". So, I don't think I suggested this :-)

Shawn


On Wed, Dec 15, 2010 at 9:10 AM, Hilmar Lapp <hlapp at nescent.org> wrote:
> Hi Matt,
> thanks for this, very useful, and I wish I had had time to look more closely
> at this earlier. Some comments, specifically about the example for the bird
> observation:
> 1 - It seems weird to have to represent every property of a particular
> (individual in OWL) as a measurement, even if for many of those we know that
> nobody measured them, and even if someone did that there aren't alternative
> outcomes possible. Is this a modeling pattern for OBOE?
> To they seem like an artifact of the entirely flat and redundant structure
> of DwC, and I'm not sure it'd be good practice to keep those artifacts in a
> more expressive (and semantically better defined) representation such as
> OBOE.
> For example, the countryCode of Argentina is a property of the particular
> Argentina, and it is set. Also, that the province Neuquén is located within
> Argentina can perhaps be an observation one can make, but that knowledge
> should be encoded in a Gazetteer (and it is indeed [1]), or if that's not
> available, shouldn't there be a direct assertion between the two?  Other
> examples include: geodeticDatum (a property of the lat/long measurement),
> URI IDs for spatialLocation and samplingEvent and occurrenceID (are
> assignments, not measurements), institutionCode and collectionCode (also
> assignments, not measurements), basisOfRecord (standard or protocol, not
> measurement).
> 2 - Measurements resulting in multiple values become multiple measurements
> (presumably as a result of hasValue being a functional property?). Example:
> lat/long - this is probably from a single GPS reading, not two.
> 3 - Similar to the above, genus, class and specific epithet are not
> independent "measurements" from scientificName. One determines the other.
> 4 - Where can I find oboe-rel definitions? oboe-rel:within seems to be used
> with very heterogenous semantics (geographically located in, at the time of,
> result of).
> Also, if OBOE is indeed confined to direct observational measurements (as
> Shawn recently suggested), then  those properties and assignment should be
> represented differently indeed, shouldn't they?
> -hilmar
> [1]
> http://bioportal.bioontology.org/visualize/40651/?conceptid=GAZ%3A00004077
>
> On Nov 24, 2010, at 6:27 PM, Matt Jones wrote:
>
> Hi Hilmar,
> I spent a bit of time with Shawn and Ben working up two Darwin Core examples
> in OBOE.  One example is a Darwin Core record of a specimen record, and the
> other is a Darwin Core record of a bird observation where they counted birds
> in a survey. They both should clarify how OBOE makes relationships clear
> and, in particular, makes the contextual relationships among different
> observations explicit (that were otherwise implicit in the Darwin Core
> record).
> The examples show how OBOE can flexibly incorporate terms from other
> ontologies that represent, for example, Entities and Characteristics.  Note
> that I needed ontology classes in several areas, so I was lazy and just used
> a hypothetical 'foobar' ontology namespace for classes I needed.  But the
> idea is that any proper OWL ontology that has the right mappings to OBOEs
> classes can be used.
> https://sonet.ecoinformatics.org/observational-data-use-cases/oboe-representation-examples
> This approach would be relevant to use case 1 on kelp/nitrogen and on use
> case DC2 on mammal observations.
> Matt
>
> On Mon, Nov 22, 2010 at 5:25 PM, Matt Jones <jones at nceas.ucsb.edu> wrote:
>>
>> Hi Hilmar,
>> Its definitely possible to represent a DarwinCore (DwC) record or set of
>> records using OBOE.  The model is general enough to accomodate these types
>> of scientific observations, including specimen occurrence records, which are
>> really just a specialized form of population survey in which the specimens
>> are at times preserved.  The crux, of course, is having an appropriate OBOE
>> extension ontology that captures the essence of Darwin Core's model in OWL.
>>  We have not worked on that, and given the discussion of DwC concepts that
>> has been occurring on tdwg-content over the last few weeks about the meaning
>> of DwC terms, that might be a challenge.
>> Nevertheless, I'll try to work up a DwC record represented in OBOE as a
>> point for discussion, and I'll send it here. And I'll probably add it to the
>> use case pages on the SONet site somehow.
>> Matt
>>
>> On Sat, Nov 20, 2010 at 2:04 PM, Hilmar Lapp <hlapp at nescent.org> wrote:
>>>
>>> Specimen records and species occurrence records are probably most
>>> typically transported in Darwin Core (DwC). Bob Morris and I are wondering
>>> whether anyone has thought yet about wrapping such a DwC record in an OBOE
>>> document.
>>>
>>> The OBOE paper doesn't provide a treatment of this, and my recollection
>>> from the TDWG Task Group meeting is that it hasn't been thought through yet.
>>> Also, looking at OBOE, DwC terms might be used to describe the Entity, but a
>>> direct wrapping does not seem obvious if not impossible. That's not to say
>>> that a DwC occurrence (an observation) couldn't be mapped to an equivalent
>>> OBOE document, but in my recollection such a mapping has not been defined
>>> yet.
>>>
>>> Can those who are more familiar with OBOE confirm this or provide
>>> pointers to where this question is being dealt with?
>>>
>>>        -hilmar
>>> --
>>> ===========================================================
>>> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
>>> ===========================================================
>>>
>>>
>>>
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>>
>
>
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
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