[tdwg-content] practical details of recording a determination What is an Occurrence?
Peter DeVries
pete.devries at gmail.com
Fri Oct 22 08:00:02 CEST 2010
People should be marking up these vocabularies with real data and
demonstrating how they can be used to make useful queries in a viewable
sparql endpoint or the LOD cloud endpoint.
Also demonstrating how the interoperate with related datasets.
- Pete
On Fri, Oct 22, 2010 at 12:03 AM, Cam Webb <cwebb at oeb.harvard.edu> wrote:
> Hi Kevin,
>
> > I can't help but feel we are getting into a much more complicated area
> > of biodiversity ( or any observation oriented field for that matter )
> > and that there must be other ontologies or models that we could follow
> > or reuse.
>
> If you are referring specifically to adding depth to the observations of
> Individuals, I think one might look first at OBOE (OBOE: Extensible
> Observation Ontology) from the SEEK group at NCEAS:
>
> http://ecoinformatics.org/oboe/oboe.1.0/oboe.owl
>
> In summary, this describes an Observation of an Entity, with the
> Observation comprising a Measurement of the Value for a Characteristic of
> the Entity:
>
>
> @prefix oboe: <http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#> .
>
> [] a oboe:Observation ;
> oboe:ofEntity [
> a oboe:Entity ;
> ] ;
> oboe:hasMeasurement [
> a oboe:Measurement ;
> oboe:ofCharacteristic [
> a oboe:Characteristic ;
> ] ;
> oboe:hasValue [
> a oboe:Entity ;
> ] ;
> ] .
>
>
> If we assert that a dwc:Occurrence is an instance of oboe:Entity, with
> dwc:basisOfRecord of "HumanObservation", with a dc:creator and dc:created
> (i.e., the space-time intersection of an Individual and a human observer),
> we can marry these two ontologies quite nicely. Please see Example 1,
> below, for a description of the fruit color of an individual plant.
>
> What's nice about the OBOE model is that it contains all three possible
> parts of an observation: the entity, the characteristic and the value.
> This allows direct mapping to the Prometheus Description Model (structure
> + property + state = entity + characteristic + value; Pullan et al. 2005,
> Taxon 54:751-765), and indirect mapping to the popular EQ model (entity +
> quality, where quality = characteristic + value; Mabee et al. 2007,
> doi:10.1016/j.tree.2007.03.013). However, it doesn't map easily to the
> DELTA or SDD data models (character + character-state, where character =
> entity + characteristic and character-state = value).
>
> Because of the well-developed OBO ontologies, we can directly employ terms
> from, say, the Plant Ontology (po), for an oboe:Entity, and terms from
> PATO, the quality ontology, for a oboe:Measurement, combining
> characteristic and value into a quality. We need to assert that a
> pato:quality is equivalent to a oboe:Measurement and possibly that a
> po:PO_0000001 (top level `plant structure') is an oboe:Entity. We can
> also employ the OBO relational ontology (ro) to indicate that a fruit is
> ro:part_of the particular space-time Occurrence of an Individual (this
> might require a bit more discussion!).
>
> So, it seems that using only well-established vocabularies, we can make
> semantic statements about the characteristics of individuals originally
> defined primarily using DwC terms. Please see example 2, below for a
> fairly slim, usable model of a description of the fruit color of an
> individual plant. The image of the model is at:
>
> http://phylodiversity.net/cwebb/img/tdwg-obs.jpg
>
>
> Again, any comments on this model will be much appreciated. Are you aware
> of other attempts to join DwC Occurrence models with OBOE models?
>
> Best,
>
> Cam
>
>
>
> ====================== Example 1 =======================================
>
> @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 .
>
> ========================================================================
>
>
> ====================== Example 2 =======================================
>
> @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 ro: <http://www.obofoundry.org/ro/ro.owl#> .
> @prefix pato: <http://purl.org/obo/owl/PATO#> .
> @prefix po: <http://purl.org/obo/owl/PO#> .
> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
>
> <http://phylodiversity.net/xmalesia/indiv/9>
> sernec:derivativeOccurrence _:blank1 .
>
> _:blank1
> a dwc:Occurrence ;
> dcterms:created "2008-01-01" ;
> dcterms:spatial [
> geo:lon "109.95371" ;
> geo:lat "-1.25530" ;
> dwc:coordinateUncertaintyInMeters "100" ;
> ] ;
> dcterms:creator "Cam Webb" ;
> dwc:basisOfRecord "HumanObservation" .
>
> # The details of the observation:
> [] a oboe:Observation ;
> oboe:ofEntity [
> ro:part_of _:blank1 ;
> a po:PO_0009001 ; # Fruit
> ] ;
> oboe:hasMeasurement pato:PATO_0000320 . # Green color
>
> po:PO_0009001 rdfs:label "fruit" .
> pato:PATO_0000320 rdfs:label "green" .
>
> ========================================================================
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>
--
----------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies
Knowledge Base <http://lod.geospecies.org/>
About the GeoSpecies Knowledge Base <http://about.geospecies.org/>
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