For example, here is a sparql query that will show the occurrences that are tagged to the concept for the American Toad.<div><br></div><div><div><font class="Apple-style-span" face="tahoma, sans-serif">PREFIX txn: <<a href="http://lod.taxonconcept.org/ontology/txn.owl#">http://lod.taxonconcept.org/ontology/txn.owl#</a>></font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif">PREFIX american_toad: <<a href="http://lod.taxonconcept.org/ses/kQmp4#Species">http://lod.taxonconcept.org/ses/kQmp4#Species</a>></font></div><div><font class="Apple-style-span" face="tahoma, sans-serif"><br>
</font></div><div><font class="Apple-style-span" face="tahoma, sans-serif">DESCRIBE ?x WHERE { </font></div><div><font class="Apple-style-span" face="tahoma, sans-serif"> ?x txn:occurrenceHasSpeciesConcept american_toad:.</font></div>
<div><font class="Apple-style-span" face="tahoma, sans-serif">} </font></div><div><br></div><div>This <a href="http://bit.ly">bit.ly</a> link will take you to my endpoint which will display these on a map. (Need to change the Visualization to GoogleMaps)</div>
<div><br></div><div><a href="http://bit.ly/aHOECG">http://bit.ly/aHOECG</a><br></div><div><br></div><div>These should also work on anyone else's endpoint, and on the LOD endpoint when the set is crawled.</div><div><br>
</div><div><br></div><div><br></div><div><br></div><br><div class="gmail_quote">On Fri, Oct 22, 2010 at 12:59 AM, Bob Morris <span dir="ltr"><<a href="mailto:morris.bob@gmail.com">morris.bob@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">I am convenor of a group charged with recommending positions about<br>
Knowledge Organization Systems (KOS) to GBIF. Among the things that<br>
will be in our report will be a survey important vocabularies and<br>
ontologies for biodiversity Knowledge Organization. Not only will OBOE<br>
be among those discussed, but one of its architects, Mark Schildauer,<br>
is a member of the work group. Similarly re: the OBO ontologies. When<br>
our report is drafted, it will be opened for public comment both as to<br>
what we recommend and what we may have missed. Meanwhile, there is a<br>
survey at <a href="http://surveymonkey.com/GBIFKOSurvey" target="_blank">http://surveymonkey.com/GBIFKOSurvey</a> to which all are<br>
invited to participate if you haven't already. If you have favorite<br>
KOS resources, there is good opportunity to list them there.<br>
<br>
Also, the TDWG 2010 Thursday sessions on Observations will, I believe,<br>
soon have their notes on the TDWG website (if not there already).<br>
<font color="#888888"><br>
Bob Morris<br>
</font><div><div></div><div class="h5"><br>
On Fri, Oct 22, 2010 at 1:03 AM, Cam Webb <<a href="mailto:cwebb@oeb.harvard.edu">cwebb@oeb.harvard.edu</a>> wrote:<br>
> Hi Kevin,<br>
><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>
> 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>
> @prefix dwc: <<a href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a>> .<br>
> @prefix dcterms: <<a href="http://purl.org/dc/terms/" target="_blank">http://purl.org/dc/terms/</a>> .<br>
> @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>
> @prefix : <#> .<br>
><br>
> <<a href="http://phylodiversity.net/xmalesia/indiv/9" target="_blank">http://phylodiversity.net/xmalesia/indiv/9</a>><br>
> a sernec:Individual ;<br>
> sernec:derivativeOccurrence _:blank1 .<br>
><br>
> _:blank1<br>
> # The Occurrence of the Individual...<br>
> a dwc:Occurrence ;<br>
> # ... at a position in space-time...<br>
> dcterms:created "2008-01-01" ;<br>
> dcterms:spatial [<br>
> a dcterms:Location ;<br>
> geo:lon "109.95371" ;<br>
> geo:lat "-1.25530" ;<br>
> 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>
> @prefix dwc: <<a href="http://rs.tdwg.org/dwc/terms/" target="_blank">http://rs.tdwg.org/dwc/terms/</a>> .<br>
> @prefix dcterms: <<a href="http://purl.org/dc/terms/" target="_blank">http://purl.org/dc/terms/</a>> .<br>
> @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>
> @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>
><br>
> <<a href="http://phylodiversity.net/xmalesia/indiv/9" target="_blank">http://phylodiversity.net/xmalesia/indiv/9</a>><br>
> sernec:derivativeOccurrence _:blank1 .<br>
><br>
> _:blank1<br>
> a dwc:Occurrence ;<br>
> dcterms:created "2008-01-01" ;<br>
> dcterms:spatial [<br>
> geo:lon "109.95371" ;<br>
> geo:lat "-1.25530" ;<br>
> 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>
> _______________________________________________<br>
> tdwg-content mailing list<br>
> <a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
> <a href="http://lists.tdwg.org/mailman/listinfo/tdwg-content" target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><br>
><br>
<br>
<br>
<br>
</div></div>--<br>
<div class="im">Robert A. Morris<br>
Emeritus Professor of Computer Science<br>
UMASS-Boston<br>
100 Morrissey Blvd<br>
Boston, MA 02125-3390<br>
Associate, Harvard University Herbaria<br>
email: <a href="mailto:morris.bob@gmail.com">morris.bob@gmail.com</a><br>
web: <a href="http://bdei.cs.umb.edu/" target="_blank">http://bdei.cs.umb.edu/</a><br>
web: <a href="http://etaxonomy.org/mw/FilteredPush" target="_blank">http://etaxonomy.org/mw/FilteredPush</a><br>
<a href="http://www.cs.umb.edu/~ram" target="_blank">http://www.cs.umb.edu/~ram</a><br>
phone (+1) 857 222 7992 (mobile)<br>
</div><div><div></div><div class="h5">_______________________________________________<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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