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@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@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
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@wisc.edu
TaxonConcept  &  GeoSpecies Knowledge Bases
A Semantic Web, Linked Open Data  Project
--------------------------------------------------------------------------------------

_______________________________________________
tdwg-content mailing list
tdwg-content@lists.tdwg.org
http://lists.tdwg.org/mailman/listinfo/tdwg-content


_______________________________________________
tdwg-content mailing list
tdwg-content@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@wisc.edu
TaxonConcept  &  GeoSpecies Knowledge Bases
A Semantic Web, Linked Open Data  Project
--------------------------------------------------------------------------------------

_______________________________________________
tdwg-content mailing list
tdwg-content@lists.tdwg.org
http://lists.tdwg.org/mailman/listinfo/tdwg-content