[tdwg-content] DwC for the semantic web

Mikel Egaña Aranguren megana at fi.upm.es
Thu Apr 28 16:35:18 CEST 2011


On og., 2011.eko apiren 28a 15:41, Steve Baskauf wrote:
> Mikel,
> Thanks for your suggestion.  There was quite a bit of discussion last 
> October and November about how to handle groups of organisms above the 
> level of an individual organism.  I won't repeat it here because it's 
> referenced in the DSW wiki pages, particularly 
> http://code.google.com/p/darwin-sw/wiki/ClassIndividual .  As a point 
> of clarification, the class dsw:IndividualOrganism as we have defined 
> it in DSW does not specify that an instance of the class must actually 
> be an individual organism.  It should be understood to be a 
> taxonomically homogeneous entity which can be assigned zero to many 
> dwc:Identification instances, be recorded by zero to many 
> dwc:Occurrence instances, and be documented by zero to many dsw:Token 
> instances .  So really anything that meets those criteria could be 
> considered a dsw:IndividualOrganism,  including clonal organisms, 
> colonial organisms, small populations, and I suppose also parts of 
> organisms (such as tissue cultures) if one wanted.  At one point we 
> considered using the name TaxonomicallyHomogeneousEntity, but that 
> seemed unwieldy.
> So I guess my response would be to say that a population could be 
> considered an instance of dsw:IndividualOrganism.  It would need to be 
> well-defined enough that it could be potentially documented as a 
> dwc:Occurrence, but since dwc:Event and dcterms:Location (which are 
> associated with a dwc:Occurrence) can potentially have a very broad 
> scope, I think that there would not be a problem with classing a 
> population as a dsw:IndividualOrganism .  Certainly entities such as a 
> stable animal herd or immobile plant population could be handled by it 
> and maybe other things as well.
> I should also note that the page 
> http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity 
> presents the topic of how to model taxonomically heterogeneous groups 
> of organisms, which was the topic of an extended discussion in 
> November.  We did not include a class to handle such groups in our 
> basic ontology, mostly because we didn't know how to do it.  However, 
> the wiki page just mentioned suggests a possible approach and perhaps 
> people with more skill in defining OWL ontologies than Cam and I have 
> could suggest an approach that would actually be able to handle that 
> more complex situation.

I see, so dsw:IndividualOrganism should do for populations. I'm asking 
cause I have some biodiversity data that perhaps I will publish as 
Linked Data (Depending on the funding :-) and the data always follow the 
taxon-population pattern, having for each taxon many populations. I 
would like to use dsw as vocabulary, most probably extending it to 
accomodate further concepts like Situation (At risk, etc.)

> I did not state in my first email that DSW is essentially a draft 
> intended to foster discussion (such as this).  We make no claims that 
> it is or should be "THE" ontology.  Cam and I needed something 
> functional for our projects, so we just made DSW to serve that purpose.
> Thanks again for the comment/suggestion!

Have you considered including this ontology in Open Biological and 
Biomedical Ontologies (http://www.obofoundry.org/)?


> Steve
> Mikel Egaña Aranguren wrote:
>> Hi;
>> Perhaps this has been discussed before, but I think there should be a
>> class for population.
>> Different populations of the same taxon are located in different places,
>> each population with its own circumstances (e.g. some will be at risk
>> and some not).
>> Cheers
>> On og., 2011.eko apiren 28a 04:01, Steve Baskauf wrote:
>>> Dear colleagues,
>>> With the exciting development of Semantic Web technologies, many of us already need a way to consistently express DwC in RDF.  In particular, we need it to meet the requirements for GUID resolution (as expressed in the TDWG applicability guide) and to be able to share and aggregate diverse kinds of biodiversity metadata in the Linked Open Data world.
>>> After several months of development, stimulated by the tdwg-content discussions of last Fall, we would like to offer an
>>> ontology for consideration, based on Darwin Core terms:
>>>      Darwin-SW:
>>>        General site:http://code.google.com/p/darwin-sw/
>>>        Using namespace dsw ="http://purl.org/dsw/"
>>> It is a candidate for general usage, but we do not claim it is _the_ solution, and greatly respect the efforts by others to develop similar ontologies, from which we have learned much. However, for DSW, we wanted to use existing DwC terms for classes and data properties whenever possible and only create new terms when there were no existing terms that would do the job.  We did feel that there was a need for clarity in how resources should be typed (i.e. rdf:type property) and for object properties that expressed the relationships among classes unambiguously. Please see the Rationale, DesignPrinciples and ClassesAndTypes wiki pages at the above address.
>>> In the ontology, we sought to embody relationships among classes based on our perception of the community consensus of what the classes represent and how they are related to each other, as expressed in posts to the tdwg-content list.  Thus each class is documented carefully on the wiki with hyperlinked references to specific tdwg-content posts. We also sought
>>> to clarify or resolve issues that were raised in the list discussion, most notably the relationship among Occurrences and the evidence that documents them (i.e. tokens), and the role of "individuals".  See wiki pages for the Token, Occurrence, and IndividualOrganism classes.
>>> The ontology is now in use athttp://bioimages.vanderbilt.edu/, and we intend to use it more widely.  We would value your opinions on the fitness of this ontology as a general solution for consistently expressing DwC concepts in RDF.
>>> Sincerely,
>>> Steve Baskauf and Cam Webb
>>> steve.baskauf at Vanderbilt.Edu
>>> cwebb at oeb.harvard.edu
>>> _______________________________________________
>>> tdwg-content mailing list
>>> tdwg-content at lists.tdwg.org
>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> -- 
> Steven J. Baskauf, Ph.D., Senior Lecturer
> Vanderbilt University Dept. of Biological Sciences
> postal mail address:
> VU Station B 351634
> Nashville, TN  37235-1634,  U.S.A.
> delivery address:
> 2125 Stevenson Center
> 1161 21st Ave., S.
> Nashville, TN 37235
> office: 2128 Stevenson Center
> phone: (615) 343-4582,  fax: (615) 343-6707
> http://bioimages.vanderbilt.edu

Mikel Egaña Aranguren, PhD

Marie Curie post-doc at Ontology Engineering Group, UPM

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