[tdwg-content] Another example of non-overlapping concepts

Fri May 13 23:14:06 CEST 2011

Hi Peter,

Does your idea of #ObjectiveSpeciesModel correspond 1:1 with the TCS
standard's idea of a Nominal Concept (i.e., <TaxonConcept type="nominal">) ?
 Can you outline how your concept types differ from TCS concept types?

Thanks,
Matt

On Fri, May 13, 2011 at 12:41 PM, Peter DeVries <pete.devries at gmail.com>wrote:

> Hi Nico,
>
> Thanks for posting this.
>
> I have something in the concept model to indicate the basis for the species
> concept.
>
> For now I have three types. An individual species concept can have a
> combination of one, two or all three
>
> In the RDF they look like this
>
> <txn:speciesConceptBasedOn rdf:resource="
> http://lod.taxonconcept.org/ontology/txn.owl#ObjectiveSpeciesModel"/>
>
> The first is what I call the #ObjectiveSpeciesModel - this indicates that
> it is a species concept because we say it is.
>
> All the species concepts are at least an #ObjectiveSpeciesModel
>
> *This is in part a way to handle things like the domestic cat which you
> want to be seen as different from the African Wildcat.
>
> There are also tags for
>
> txn:PhylogeneticSpeciesModel
> txn:BiologicalSpeciesModel
>
> For now I don't have these other models set in the example data, but fields
> are in the database and the code for that an editor could state the basis
> for the model.
>
> I can think of a couple of different ways to handle the issue of
> alternative species concepts.
>
> * Note that the identifications as proposed by DarwinCore don't seem to
> indicate what kind of model the identifications were based on.
>   So it is not clear to me if a straight DarwinCore data set would allow
> the analysis above.
>
> Instead of having multiple different statements like
>
> *txn:occurrenceHasSpeciesConcept <> *in the record for each occurrence
>
> one could use different predicates to link to different kinds of species
> concepts.
>
> *txn:occurrenceHasUniprotConcept* => <
> http://purl.uniprot.org/taxonomy/9696>
>
> This would allow someone to query for the occurrences of <
> http://purl.uniprot.org/taxonomy/9696>
>
> That said, it is not clear to me what people mean by different
> identifications.
>
> Is the intent to have identifications with different homotypic synonyms to
> be an identification of the same thing or not?
>
> The way it works now in many data sets is that Felis concolor, Puma
> concolor and Puma conncolor are treated as identifications of different
> things.
>
> This is another way of saying* is the namestring the concept?*
> *
> *
> My understanding of the eBird project is that it allows citizen scientists
> to contribute their own observations. This creates a much larger data set
> for analysis etc.
>
> They have a created a curated list of species and a ~6 letter code for
> each. This serves as a guide for observers on how to encode their
> observations.
>
> I think their progress would be inhibited, the occurrence coding
> inconsistant, and contributors frustrated, if they have a list that included
> many overlapping species concepts.
>
> Thanks again for you comments,
>
> - Pete
>
> On Fri, May 13, 2011 at 3:05 AM, Nico Franz <nico.franz at upr.edu> wrote:
>
>>  Hello Pete (et al.):
>>
>>    For bird, Town Peterson at KU and colleagues have published these
>> papers showing how alternative bird taxonomies affect the ranking of
>> conservation priorities.
>>
>>
>> http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/PN_CB_1999.pdf
>>
>> http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/NP_BN_2004.pdf
>>
>> http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/P_BCI_2006.pdf
>>
>>    Here's the abstract of the 1999 paper:
>>
>> Analysis of geographic concentrations of endemic taxa is often used to
>> determine priorities for conservation
>> action; nevertheless, assumptions inherent in the taxonomic authority list
>> used as the basis for
>> analysis are not always considered. We analyzed foci of avian endemism in
>> Mexico under two alternate species
>> concepts. Under the biological species concept, 101 bird species are
>> endemic to Mexico and are concentrated
>> in the mountains of the western and southern portions of the country.
>> Under the phylogenetic species
>> concept, however, total endemic species rises to 249, which are
>> concentrated in the mountains and lowlands
>> of western Mexico. Twenty-four narrow endemic biological species are
>> concentrated on offshore islands, but
>> 97 narrow endemic phylogenetic species show a concentration in the
>> Transvolcanic Belt of the mainland and
>> on several offshore islands. Our study demonstrates that conservation
>> priorities based on concentrations of
>> endemic taxa depend critically on the particular taxonomic authority
>> employed and that biodiversity evaluations
>> need to be developed in collaboration or consultation with practicing
>> systematic specialists.
>>
>>    There was a debate recently on Taxacom that was started and
>> subsequently neatly summarized by Fabian Haas. The topic was "let's
>> summarize reasons why 'donors' seem to not fund taxonomy". One point from
>> the summary was this:
>>
>> 3) Taxonomy is over-accurate for most applications
>>
>> Most (not all) decisions in e.g. modelling and conservation are done and
>> can be done without complete knowledge of taxa. As it is, decisions for
>> conservation areas are often based on flagship species (e.g. elephants), on
>> taxa which have an excellent research background, e.g. birds (IBAs), on
>> availability of land (e.g. land with a high Tsetse burden), importance as
>> corridor and other factors, but never on a complete view on an all
>> biodiversity in a specific area. Even if an inventory existed, it would be
>> an illusion that we could collect data on ecological requirements and
>> population dynamics for most of the species necessary for informed
>> decisions. A complete inventory does not seem to provide an advantage for
>> conservation.
>>    I personally think there's some truth to that. I also think that, while
>> it's understandable that an accurate representation of the (sometimes)
>> fleetingness of taxonomic consensus it not a priority for applied ecological
>> projects, if taxonomists themselves don't find better ways to document and
>> link these alternatives perspectives, then it's not the best science we can
>> do. That would be fine too if adopted outright as a pragmatic stance.
>>
>> Regards,
>>
>> Nico
>>
>>
>>
>> On 5/13/2011 1:08 AM, Peter DeVries wrote:
>>
>> I thought that I would also mention that in addition to The Plants List,
>> the eBird project also uses on overlapping concepts in its bird list (it
>> does have concepts for common hybrids)
>>
>>  What is clear to me is that you cannot create graphs like these if every
>> observation can have X number of species (especially those that overlapping
>> ) without any indication which is is the most appropriate one.
>>
>>  eBird Occurrence Maps Northern Cardinal
>> http://ebird.org/content/ebird/about/occurrence-maps/northern-cardinal
>>
>>  NCBI is also similar.
>>
>>  Perhaps a member of the consensus committee can comment?
>>
>> -- Pete
>>
>> ------------------------------------------------------------------------------------
>> Pete DeVries
>> Department of Entomology
>> University of Wisconsin - Madison
>> 445 Russell Laboratories
>> 1630 Linden Drive
>> Madison, WI 53706
>> Email: pdevries at wisc.edu
>> TaxonConcept <http://www.taxonconcept.org/>  &  GeoSpecies<http://about.geospecies.org/> Knowledge
>> Bases
>> A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
>>
>> --------------------------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> tdwg-content mailing listtdwg-content at lists.tdwg.orghttp://lists.tdwg.org/mailman/listinfo/tdwg-content
>>
>>
>>
>> _______________________________________________
>> tdwg-content mailing list
>> tdwg-content at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>>
>>
>
>
> --
>
> ------------------------------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> Email: pdevries at wisc.edu
> TaxonConcept <http://www.taxonconcept.org/>  &  GeoSpecies<http://about.geospecies.org/> Knowledge
> Bases
> A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
>
> --------------------------------------------------------------------------------------
>
> _______________________________________________
> tdwg-content mailing list
> tdwg-content at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.tdwg.org/pipermail/tdwg-content/attachments/20110513/4911c253/attachment.html 