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.<div><br></div><div>Also demonstrating how the interoperate with related datasets.<br>
<div><br></div><div>- Pete<br><br><div class="gmail_quote">On Fri, Oct 22, 2010 at 12:03 AM, Cam Webb <span dir="ltr"><<a href="mailto:cwebb@oeb.harvard.edu">cwebb@oeb.harvard.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Kevin,<br>
<div class="im"><br>
> I can't help but feel we are getting into a much more complicated area<br>
> of biodiversity ( or any observation oriented field for that matter )<br>
> and that there must be other ontologies or models that we could follow<br>
> or reuse.<br>
<br>
</div>If you are referring specifically to adding depth to the observations of<br>
Individuals, I think one might look first at OBOE (OBOE: Extensible<br>
Observation Ontology) from the SEEK group at NCEAS:<br>
<br>
<a href="http://ecoinformatics.org/oboe/oboe.1.0/oboe.owl" target="_blank">http://ecoinformatics.org/oboe/oboe.1.0/oboe.owl</a><br>
<br>
In summary, this describes an Observation of an Entity, with the<br>
Observation comprising a Measurement of the Value for a Characteristic of<br>
the Entity:<br>
<br>
<br>
@prefix oboe: <<a href="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#" target="_blank">http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#</a>> .<br>
<br>
[] a oboe:Observation ;<br>
oboe:ofEntity [<br>
a oboe:Entity ;<br>
] ;<br>
oboe:hasMeasurement [<br>
a oboe:Measurement ;<br>
oboe:ofCharacteristic [<br>
a oboe:Characteristic ;<br>
] ;<br>
oboe:hasValue [<br>
a oboe:Entity ;<br>
] ;<br>
] .<br>
<br>
<br>
If we assert that a dwc:Occurrence is an instance of oboe:Entity, with<br>
dwc:basisOfRecord of "HumanObservation", with a dc:creator and dc:created<br>
(i.e., the space-time intersection of an Individual and a human observer),<br>
we can marry these two ontologies quite nicely. Please see Example 1,<br>
below, for a description of the fruit color of an individual plant.<br>
<br>
What's nice about the OBOE model is that it contains all three possible<br>
parts of an observation: the entity, the characteristic and the value.<br>
This allows direct mapping to the Prometheus Description Model (structure<br>
+ property + state = entity + characteristic + value; Pullan et al. 2005,<br>
Taxon 54:751-765), and indirect mapping to the popular EQ model (entity +<br>
quality, where quality = characteristic + value; Mabee et al. 2007,<br>
doi:10.1016/j.tree.2007.03.013). However, it doesn't map easily to the<br>
DELTA or SDD data models (character + character-state, where character =<br>
entity + characteristic and character-state = value).<br>
<br>
Because of the well-developed OBO ontologies, we can directly employ terms<br>
from, say, the Plant Ontology (po), for an oboe:Entity, and terms from<br>
PATO, the quality ontology, for a oboe:Measurement, combining<br>
characteristic and value into a quality. We need to assert that a<br>
pato:quality is equivalent to a oboe:Measurement and possibly that a<br>
po:PO_0000001 (top level `plant structure') is an oboe:Entity. We can<br>
also employ the OBO relational ontology (ro) to indicate that a fruit is<br>
ro:part_of the particular space-time Occurrence of an Individual (this<br>
might require a bit more discussion!).<br>
<br>
So, it seems that using only well-established vocabularies, we can make<br>
semantic statements about the characteristics of individuals originally<br>
defined primarily using DwC terms. Please see example 2, below for a<br>
fairly slim, usable model of a description of the fruit color of an<br>
individual plant. The image of the model is at:<br>
<br>
<a href="http://phylodiversity.net/cwebb/img/tdwg-obs.jpg" target="_blank">http://phylodiversity.net/cwebb/img/tdwg-obs.jpg</a><br>
<br>
<br>
Again, any comments on this model will be much appreciated. Are you aware<br>
of other attempts to join DwC Occurrence models with OBOE models?<br>
<br>
Best,<br>
<br>
Cam<br>
<br>
<br>
<br>
====================== Example 1 =======================================<br>
<br>
@prefix oboe: <<a href="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#" target="_blank">http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#</a>> .<br>
<div class="im">@prefix dwc: <<a href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a>> .<br>
</div><div class="im">@prefix dcterms: <<a href="http://purl.org/dc/terms/" target="_blank">http://purl.org/dc/terms/</a>> .<br>
</div><div class="im">@prefix sernec: <<a href="http://bioimages.vanderbilt.edu/rdf/terms#" target="_blank">http://bioimages.vanderbilt.edu/rdf/terms#</a>> .<br>
@prefix geo: <<a href="http://www.w3.org/2003/01/geo/wgs84_pos#" target="_blank">http://www.w3.org/2003/01/geo/wgs84_pos#</a>> .<br>
</div>@prefix : <#> .<br>
<div class="im"><br>
<<a href="http://phylodiversity.net/xmalesia/indiv/9" target="_blank">http://phylodiversity.net/xmalesia/indiv/9</a>><br>
a sernec:Individual ;<br>
</div> sernec:derivativeOccurrence _:blank1 .<br>
<br>
_:blank1<br>
# The Occurrence of the Individual...<br>
a dwc:Occurrence ;<br>
# ... at a position in space-time...<br>
<div class="im"> dcterms:created "2008-01-01" ;<br>
</div> dcterms:spatial [<br>
<div class="im"> a dcterms:Location ;<br>
geo:lon "109.95371" ;<br>
geo:lat "-1.25530" ;<br>
</div> dwc:coordinateUncertaintyInMeters "100" ;<br>
] ;<br>
# is a recordable OBOE Entity<br>
a oboe:Entity ;<br>
# as recorded by a human<br>
dcterms:creator "Cam Webb" ;<br>
dwc:basisOfRecord "HumanObservation" .<br>
<br>
# The details of the observation:<br>
[] a oboe:Observation ;<br>
oboe:ofEntity [<br>
# The observed entity is actually *part of* the occurrence<br>
# of the Individual at a particular Space and Time<br>
a :Fruit ;<br>
:partOf _:blank1 ;<br>
] ;<br>
oboe:hasMeasurement [<br>
oboe:ofCharacteristic :Color ;<br>
oboe:hasValue :Green ;<br>
] .<br>
<br>
:Fruit a oboe:Entity .<br>
:Color a oboe:Characteristic .<br>
:Green a oboe:Entity .<br>
<br>
========================================================================<br>
<br>
<br>
====================== Example 2 =======================================<br>
<br>
@prefix oboe: <<a href="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#" target="_blank">http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#</a>> .<br>
<div class="im">@prefix dwc: <<a href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a>> .<br>
</div><div class="im">@prefix dcterms: <<a href="http://purl.org/dc/terms/" target="_blank">http://purl.org/dc/terms/</a>> .<br>
</div><div class="im">@prefix sernec: <<a href="http://bioimages.vanderbilt.edu/rdf/terms#" target="_blank">http://bioimages.vanderbilt.edu/rdf/terms#</a>> .<br>
@prefix geo: <<a href="http://www.w3.org/2003/01/geo/wgs84_pos#" target="_blank">http://www.w3.org/2003/01/geo/wgs84_pos#</a>> .<br>
</div>@prefix ro: <<a href="http://www.obofoundry.org/ro/ro.owl#" target="_blank">http://www.obofoundry.org/ro/ro.owl#</a>> .<br>
@prefix pato: <<a href="http://purl.org/obo/owl/PATO#" target="_blank">http://purl.org/obo/owl/PATO#</a>> .<br>
@prefix po: <<a href="http://purl.org/obo/owl/PO#" target="_blank">http://purl.org/obo/owl/PO#</a>> .<br>
@prefix rdfs: <<a href="http://www.w3.org/2000/01/rdf-schema#" target="_blank">http://www.w3.org/2000/01/rdf-schema#</a>> .<br>
<div class="im"><br>
<<a href="http://phylodiversity.net/xmalesia/indiv/9" target="_blank">http://phylodiversity.net/xmalesia/indiv/9</a>><br>
</div> sernec:derivativeOccurrence _:blank1 .<br>
<br>
_:blank1<br>
a dwc:Occurrence ;<br>
<div class="im"> dcterms:created "2008-01-01" ;<br>
</div> dcterms:spatial [<br>
<div class="im"> geo:lon "109.95371" ;<br>
geo:lat "-1.25530" ;<br>
</div> dwc:coordinateUncertaintyInMeters "100" ;<br>
] ;<br>
dcterms:creator "Cam Webb" ;<br>
dwc:basisOfRecord "HumanObservation" .<br>
<br>
# The details of the observation:<br>
[] a oboe:Observation ;<br>
oboe:ofEntity [<br>
ro:part_of _:blank1 ;<br>
a po:PO_0009001 ; # Fruit<br>
] ;<br>
oboe:hasMeasurement pato:PATO_0000320 . # Green color<br>
<br>
po:PO_0009001 rdfs:label "fruit" .<br>
pato:PATO_0000320 rdfs:label "green" .<br>
<br>
========================================================================<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>----------------------------------------------------------------<br>Pete DeVries<br>Department of Entomology<br>University of Wisconsin - Madison<br>445 Russell Laboratories<br>
1630 Linden Drive<br>Madison, WI 53706<br><a href="http://www.taxonconcept.org/" target="_blank">TaxonConcept Knowledge Base</a> / <a href="http://lod.geospecies.org/" target="_blank">GeoSpecies Knowledge Base</a><br><a href="http://about.geospecies.org/" target="_blank">About the GeoSpecies Knowledge Base</a><br>
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