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

20 Oct 2010


      Dear Steve and Rich,
Encouraged by your discussion of models of Occurrences and Individuals, 
and by Steve's related Biodiv. Informatics paper, I have modeled a real 
example of an individual plant and some of its various occurrences in RDF, 
using Steve's sernec terms to provide the predicates that are missing from 
DwC.  As I did so, a number of questions came up relating to choices of 
terms, and I would greatly appreciate your input on these choices.  The 
following includes all the choices considered, and so may not be 
semantically correct.  The questions (Q1-9) are interspersed with the RDF 
(serialized as Turtle).
@prefix dwc: http://rs.tdwg.org/dwc/terms/ .
@prefix dwcvoc: http://rs.tdwg.org/ontology/voc/ .
@prefix dcterms: http://purl.org/dc/terms/ .
@prefix geo: http://www.w3.org/2003/01/geo/wgs84_pos# .
@prefix sernec: http://bioimages.vanderbilt.edu/rdf/terms# .
http://phylodiversity.net/xmalesia/indiv/9
     a sernec:Individual ;  # Q1 - Is this an Individual ...
     a dwc:individualID ;   # Q1 - ... or an individualID (Baskauf 2010 app'x)?
# Specimen
     sernec:derivativeOccurrence [
         # Q2 : Use generic Occurrence from dwc:Occurrence ...
         a dwc:Occurrence ;
         dwc:basisOfRecord "PreservedSpecimen" ;
         dwc:recordNumber "Webb 5008" ;
         dwc:recordedBy "Cam Webb" ;
         # Q2 : ... or treat directly as a Specimen?
         a dwcvoc:Specimen ;
         dwcvoc:collectorsFieldNumber "5008" ;
         dwcvoc:collector "Cam Webb" ;
         # Q3 : Add the dwc:eventDate here as suggested by Baskauf?
         dwc:eventDate "2008-01-01" ;
         # Q4 : Treat occurrence as generic resource, using dc metadata?
         dcterms:creator "Cam Webb" ;
         dcterms:created "2008-01-01" ;
         # Q5 : Add dwc location data for Occurrence...
         dwc:coordinateUncertaintyInMeters "100" ;
         dwc:decimalLatitude "-1.25530" ;
         dwc:decimalLongitude "109.95371" ;
         dwc:geodeticDatum "WGS84" ;
         dwc:locality "Sukadana" ;
         # Q5 : ... or a Location.
         dcterms:spatial _:blank1 ;
         ] ;
# Photo:
     sernec:derivativeOccurrence [
         # Q6 : a dwc:Occurrence...
         a dwc:Occurrence ;
         # Q6 : ... or a dwcvoc:TaxonOccurrence. Which is better?
         a dwcvoc:TaxonOccurrence ;
         # Q7 : Again, use dwc terms...
         dwc:occurrenceID
                 http://phylodiversity.net/xmalimg/cw_28617.400px.jpg ;
         dwc:basisOfRecord "DigitalStillImage" ;
         dwc:recordedBy "Cam Webb" ;
         dwc:eventDate "2008-01-01" ;
         # Q7 : or cd terms?
         dcterms:identifier
                 http://phylodiversity.net/xmalimg/cw_28617.400px.jpg ;
         dcterms:creator "Cam Webb" ;
         dcterms:created "2008-01-01" ;
         dcterms:type http://purl.org/dc/dcmitype/StillImage ;
         # Q8 : Spatial data, same issue as above
         dcterms:spatial _:blank1 ;
         ] .
# Determination
[]  a dwc:Identification ;
     sernec:identifiesIndividual http://phylodiversity.net/xmalesia/indiv/9 ;
     dwc:identifiedBy "Ferry Slik" ;
     dwc:taxonConceptID urn:lsid:ubio.org:namebank:5963772 ;
     dwc:dateIdentified "2009-02-22" ;
     # Q9 : Use dwc:identificationReferences or...
     dwc:identificationReferences
          http://phylodiversity.net/xmalimg/cw_28617.400px.jpg ;
     # Q9 : ... sernec:basedOnOccurrence ?
     sernec:basedOnOccurrence
          http://phylodiversity.net/xmalimg/cw_28617.400px.jpg .
# Location data for photo and specimen
_:blank1
     a dcterms:Location ;
     geo:lon "109.95371" ;
     geo:lat "-1.25530" ;
     dwc:locality "Sukadana, on Tanah Merah road to beach" ;
     dwc:coordinateUncertaintyInMeters "100" .
I realize that for LOD applications the blank nodes should eventually have 
GUIDs.  Now, here is a slimmed down version of the above with my own 
choices. In general, I went with dcterms over dwc, where appropriate. 
You can also see the network (via dot) at: 
http://phylodiversity.net/cwebb/img/indiv9-slim.jpg or 
http://linkeddata.uriburner.com/ode/?uri=http://phylodiversity.net/cwebb/tmp...
@prefix dwc: http://rs.tdwg.org/dwc/terms/ .
@prefix dwcvoc: http://rs.tdwg.org/ontology/voc/ .
@prefix dcterms: http://purl.org/dc/terms/ .
@prefix geo: http://www.w3.org/2003/01/geo/wgs84_pos# .
@prefix sernec: http://bioimages.vanderbilt.edu/rdf/terms# .
http://phylodiversity.net/xmalesia/indiv/9
     a sernec:Individual ;
     sernec:derivativeOccurrence [  # Specimen
         a dwc:Occurrence ;
         dwc:basisOfRecord "PreservedSpecimen" ;
         dcterms:identifier "Webb 5008" ;
         dcterms:creator "Cam Webb" ;
         dcterms:created "2008-01-01" ;
         dcterms:spatial _:blank1 ;
         ] ;
     sernec:derivativeOccurrence [  # Photo
         a dwc:Occurrence ;
         dwc:basisOfRecord "DigitalStillImage" ;
     	dcterms:identifier
                 http://phylodiversity.net/xmalimg/cw_28617.400px.jpg ;
         dcterms:creator "Cam Webb" ;
         dcterms:created "2008-01-01" ;
         dcterms:spatial _:blank1 ;
         ] .
[]  a dwc:Identification ;
     sernec:identifiesIndividual http://phylodiversity.net/xmalesia/indiv/9 ;
    dwc:identifiedBy "Ferry Slik" ;
    dwc:taxonConceptID urn:lsid:ubio.org:namebank:5963772 ;
     dwc:dateIdentified "2009-02-22" ;
     sernec:basedOnOccurrence
          http://phylodiversity.net/xmalimg/cw_28617.400px.jpg .
_:blank1
     a dcterms:Location ;
     geo:lon "109.95371" ;
     geo:lat "-1.25530" ;
     dwc:locality "Sukadana, on Tanah Merah road to beach" ;
     dwc:coordinateUncertaintyInMeters "100" .
I didn't think this could be done without creating new terms, so I'm very 
pleased be getting closer to my goal of a LOD representation of our data
that maintains the Individuals as base entities.
Many thanks in advance for any thoughts.
Best,
Cam