[tdwg-content] practical details of recording a determination What is an Occurrence?

Peter DeVries pete.devries at gmail.com
Fri Oct 22 08:30:50 CEST 2010


For example, here is a sparql query that will show the occurrences that are
tagged to the concept for the American Toad.

PREFIX txn:            <http://lod.taxonconcept.org/ontology/txn.owl#>
PREFIX american_toad:  <http://lod.taxonconcept.org/ses/kQmp4#Species>

DESCRIBE ?x WHERE {
  ?x txn:occurrenceHasSpeciesConcept american_toad:.
}

This bit.ly link will take you to my endpoint which will display these on a
map. (Need to change the Visualization to GoogleMaps)

http://bit.ly/aHOECG

These should also work on anyone else's endpoint, and on the LOD endpoint
when the set is crawled.





On Fri, Oct 22, 2010 at 12:59 AM, Bob Morris <morris.bob at gmail.com> wrote:

> I am convenor of a group charged with recommending positions about
> Knowledge Organization Systems (KOS) to GBIF. Among the things that
> will be in our report will be a survey important vocabularies and
> ontologies for biodiversity Knowledge Organization. Not only will OBOE
> be among those discussed, but one of its architects, Mark Schildauer,
> is a member of the work group. Similarly re: the OBO ontologies. When
> our report is drafted, it will be opened for public comment both as to
> what we recommend and what we may have missed.  Meanwhile, there is a
> survey at http://surveymonkey.com/GBIFKOSurvey to which all are
> invited to participate if you haven't already.  If you have favorite
> KOS resources, there is good opportunity to list them there.
>
> Also, the TDWG 2010 Thursday sessions on Observations will, I believe,
> soon have their notes on the TDWG website (if not there already).
>
> Bob Morris
>
> On Fri, Oct 22, 2010 at 1:03 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" .
> >
> > ========================================================================
> > _______________________________________________
> > tdwg-content mailing list
> > tdwg-content at lists.tdwg.org
> > http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >
>
>
>
> --
> Robert A. Morris
> Emeritus Professor  of Computer Science
> UMASS-Boston
> 100 Morrissey Blvd
> Boston, MA 02125-3390
> Associate, Harvard University Herbaria
> email: morris.bob at gmail.com
> web: http://bdei.cs.umb.edu/
> web: http://etaxonomy.org/mw/FilteredPush
> http://www.cs.umb.edu/~ram
> phone (+1) 857 222 7992 (mobile)
> _______________________________________________
> tdwg-content mailing list
> tdwg-content at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>



-- 
----------------------------------------------------------------
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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