[tdwg-content] Can all DwC be Simple DwC?

[joel sachs]

Hi Matt -

Thanks for the invitation - I've joined the list. One of the posts that 
caught my attention during October's tdwg-content avalanche was Cam Webb's 
discussion of some of the differences in the various approaches (OBOE, EQ, 
SDD, etc.) to representing character data [1].  Cam used the following 
example to show how observation ontologies could be worked into occurrence 
records:

----
@prefix oboe: <http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#> .
@prefix dwc: <http://rs.tdwg.org/dwc/terms/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix sernec: <http://bioimages.vanderbilt.edu/rdf/terms#> .
@prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
@prefix : <#> .

<http://phylodiversity.net/xmalesia/indiv/9>
      a sernec:Individual ;
      sernec:derivativeOccurrence _:blank1 .

_:blank1
      # The Occurrence of the Individual...
      a dwc:Occurrence ;
      # ... at a position in space-time...
      dcterms:created "2008-01-01" ;
      dcterms:spatial [
          a dcterms:Location ;
          geo:lon "109.95371" ;
          geo:lat "-1.25530" ;
          dwc:coordinateUncertaintyInMeters "100" ;
          ] ;
      # is a recordable OBOE Entity
  	a oboe:Entity ;
      # as recorded by a human
      dcterms:creator "Cam Webb" ;
      dwc:basisOfRecord "HumanObservation" .

# The details of the observation:
[]  a oboe:Observation ;
      oboe:ofEntity [
          # The observed entity is actually *part of* the occurrence
          #   of the Individual at a particular Space and Time
          a :Fruit ;
          :partOf _:blank1 ;
          ] ;
      oboe:hasMeasurement [
          oboe:ofCharacteristic :Color ;
          oboe:hasValue :Green ;
          ] .

:Fruit a oboe:Entity .
:Color a oboe:Characteristic .
:Green a oboe:Entity .

---

I was interested at the time (and still am) in exploring the capabilities 
and limits of Darwin Core, so I represented the above in DwC as:
---
dcterms:creator					Cam Webb
dcterms:created					2008-01-01
geo:lon						109.95371
geo:lat						-1.25530
dwc:coordinateUncertaintyInMeters		100
dwc:individualID 				http://phylodiversity.net/xmalesia/indiv/9
dwc:basisOfRecord				HumanObservation

dwc:measurementType				fruit colour
dwc:measurementValue				green
---

In other words, Darwin Core, as it exists, can be used to represent EQ 
modeling. It would seem easy to extend it to accomodate OBOE modeling 
also, e.g.

dwc:measurementEntity				fruit
dwc:measurementCharacteristic			colour
dwc:measurementValue				green

As Cam pointed out, either of these approaches would make it easy to 
incorporate OBO ontologies such as PATO into Darwin Core records. It seems 
to me that how the model is serialized (flat, nested, etc.) doesn't really 
alter its semantics.

Looking back at the the obs-archives, I see that, conversly, Darwin Core 
occurrence records can be expressed via OBOE.

What do you think of the idea of using this year's TDWG field event (if 
there is one) to explore capturing and reasoning over observational data?

All the best -
Joel.
---

1. http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001736.html




On Wed, 5 Jan 2011, Matt Jones wrote:

> Hi Joel and Gregor,
>
> This is exactly the type of issue being addressed by observation models in
> the SONet and TDWG Observations groups.  Existing observations models (e.g.,
> OBOE, O+M, etc) do provide the ability to use terms from OWL vocabularies
> for the entity being measured and the measured characteristics as well as
> for units, value space domains, and a variety of other salient components of
> the observations.  I think there's a lot of potential for crosswalking these
> with characters described in EQ and SDD.  If you're interested in the
> observations work, you might be interested in the slides and some of the
> background material that we prepared about the ways in which different
> observational data models work and how they serialize observational data,
> which are listed on the agenda from the last TDWG Observations meeting:
>  https://sonet.ecoinformatics.org/workshops/tdwg-2010-meeting
>
> These models address exactly the case described, but they don't try to put
> complex, multidimensional data relations into a single flat structure as is
> proposed using the subscripts shown here.
>
> Observational data modeling work is discussed on the open mailing list '
> obs at ecoinformatics.org' if you want to join in the discussion (subscribe at
> http://lists.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/obs).
>
> Cheers,
> Matt
>
> On Wed, Jan 5, 2011 at 12:22 PM, Gregor Hagedorn <g.m.hagedorn at gmail.com>wrote:
>
>>> Couldn't this be addressed using subscripts? E.g.
>>> MeasurementID_1="tail length"
>>> MeasurementID_2="brain volume"
>>> MeasurementUnit_1="cm"
>>> MeasurementUnit_2="cubic cm"
>>> MeasurementValue_1="9"
>>> MeasurementValue_2="8"
>>
>> I have no problems with pragmatism, but why are the characters not RDF
>> concepts itself? I believe they should be rdf vocabularies for those
>> who want to reason on them.
>>
>> One more problem: the states can be polymorphic, as in
>>
>>> MeasurementID_1="flower color"
>>> MeasurementValue_1="red"
>>> MeasurementValue_1="orange"
>>
>> Gregor
>> _______________________________________________
>> tdwg-content mailing list
>> tdwg-content at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>>
>