Re: Species Concept Mapping RDF fixes and question, should the species be represented as a class? Class SpeciesConcept => Class Species Cougar

Hi Leigh,

It is my understanding that Bob will be busy until the 20th, so his comments
might come later.

One of the issues that got me started on this was how to deal with data sets
where the same species is listed under different names.

For instance: Ochlerotatus triseriatus / Aedes triseriatus

I needed some sort of identifier that would be used to track the species,
not a human hypothesis of a particular species phylogeny.

In this case, the name change was the result of an elevation of the subgenus
Ochlerotatus to genus status, not a change in what specimens
were examples of the species.

Looking at the new TDWG example, these species concept classes seem to have
the original problem in that Ochlerotatus triseriatus and
Aedes triseriatus are different things with different superclasses?

Also I was under the impression it it best to avoid extensive hierarchies of
classes and subclasses?

I suspect that the TDWG hierarchies and the NCBI hierarchies will be
different.

In the GeoSpecies representation I used inFamily, inOrder, etc. to link a
species concept to the higher clades.

In this case the higher clades are "tag"s applied to a species and can be
ignored or tagged in your own way if needed.

It is not clear to me how to handle this in the taxonconcept.orgrepresentations.

Maybe there will be even more representations of species

It looks to me as if TDWG really wants to model species as a fully
phylogenetic representation, but ecologists and epidemiologists need a
representation that separates the idea that there is a species from the idea
that that species is it's current ephemeral phylogenetic hypothesis.

Maybe someone of the list has some ideas as to which representations are
best for these different use cases.

This has left me a bit puzzled. :-)

Thanks!

- Pete


On Tue, Dec 15, 2009 at 7:19 AM, Leigh Dodds <leigh.dodds@talis.com> wrote:

> Hi Bob,
>
> 2009/12/4 Bob Morris <morris.bob@gmail.com>:
> > On Tue, Dec 1, 2009 at 10:14 PM, Peter DeVries <pete.devries@gmail.com>
> wrote:
> > ...
> > In the end, for ecological observations, it is likely that it will be
> > necessary to be able to talk about several species at once; e.g. when
> > it is important to determine if there were two particular species
> > observed at the same time and place. To me, this alone suggests that
> > important applications will need a merged ontology at least as to the
> > species (concepts).  There is fair concensus that the number of known
> > species is roughly 1.8M---so concepts perhaps 2-3 times that (???).
> > Also, it is well and often pointed out that for even simple reasoning,
> > one may have to align the species concepts, not the names, to decide
> > whether occurrences reported in different data sets are really talking
> > about the same kind of thingie---which is why you and TDWG model
> > concepts.  So from that I deduce that for interests of people who
> > study communities and their interactions, rather than those who study
> > taxonomic groups, making a species (concept) be a class instead of (or
> > in addition to)  an instance will lead to as many as several millions
> > of classes (or several hundreds of million if we find the other 28M
> > species before we destroy them all....). So I guess I believe that
> > modeling species (concepts) as classes is not scalable.
>
> Isn't this what the TWDG ontology does though?
>
> Looking at the definition of a TaxonConcept [1] I see that its a
> defined as a Class. This is confirmed by this example [2] which shows
> the concept for Puma concolor as being a sub-class of TaxonConcept,
> and the Puma concolor concept is itself a class.
>
> I did some digging around and found that:
>
> * Dbpedia and Uniprot model taxa as instances, as does the RDF data
> coming from the Ubio LSID resolver
> * The ETHAN ontology, and the TWDG TaxonConcept model (AIUI), both
> model taxa as Classes
> * Peter's species concept examples use skos:Concepts which are
> themselves instances rather than classes.
> * OpenCyc uses Collections which seem to be a little of both :)
>
> Obviously there's no right answer here, but just wanted to get some
> clarification on your comments.
>
> [1]. http://rs.tdwg.org/ontology/voc/TaxonConcept
> [2].
> http://code.google.com/p/tdwg-ontology/source/browse/trunk/docs/publishing_taxa/full_example.rdf
> [3]. http://spire.umbc.edu/ont/ethan.php
>
> Cheers,
>
> L.
>
> --
> Leigh Dodds
> Programme Manager, Talis Platform
> Talis
> leigh.dodds@talis.com
> http://www.talis.com
>



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Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
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