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Hi Pete (et al.):<br>
<br>
I can unfortunately only comment on some of this. One thing I'd
like to clarify, though perhaps not needed. -- There's a way in
which taxonomists sometimes say "different names, same concept".
Meaning: there's a synonymy relationship between two or more Latin
(species) names, but not a real disagreement about the underlying
circumscription of the taxon that's being referred to. I suppose
your "Felis concolor, Puma concolor and Puma conncolor" example fits
this situation.<br>
<br>
Now, that meaning of "sameness" ("same concept" as above) doesn't
strictly work in the taxon concept "world"; because concepts are in
the first instance distinguished by their LABELS, i.e. the Latin
name (name author) + sec. author/publication combo, as in Quercus
robur L. sec. Nixon 2003 (making this one up). So if you have
Quercus robur L. sec Linnaeus 1758 and Quercus robur L. sec. Nixon
2003; these are two different labels and thus two different concepts
in TCS speak, even if their meaning (referential extension) is "the
same". Sorry if this was obvious and thus missed the mark. The
problem is that there are at least two common meanings of "concept"
in the mix.<br>
<br>
The way I recall discussions as the TCS was designed, the role
for the DarwinCore was to allow data providers to include sufficient
information in the DC so that the vouchers/observations could be
identified to a suitably authoritative concept. In another realm of
the biodiversity informatics net, that concept would be represented
in more depth, and ideally have multiple relationships mapped and/or
inferred to relevant past, present, and future concepts.<br>
<br>
For what it's worth (really not much), I agree that the eBird
project is finding a (the?) pragmatic solution to expanding their
contributor base, and in all likelihood have a pretty good to
excellent taxonomy to work with already. Keep in mind that I study
weevils, with 65k species described and 220k species
(conservatively) estimated to exist, and a ~ 200 tribes mid-level
classifications based largely on Lacordaire's 1-2 external character
system established in 1863 (claws single, versus paired; virtually
none of these have any phylogenetic value). So experientially I come
from that part of the knowledge spectrum where we're likely
centuries away from a sufficiently stable naming system that
includes, say, more than 2/3 of the actual species diversity.<br>
<br>
I'm not opposed to pragmatic solutions for taxa where it makes
sense (again, as if anyone cared..). But, trying to foresee the very
substantive classificatory shifts that many other groups likely
still will experience 10, 20, 50, 100 years down the road from now,
I think just the same that there are solid grounds for working out
an admittedly non-pragmatic, but sematically maximally powerful
solution. I think it's not unreasonable to assume that from some
groups, classification in 250 years from now will look just as
different from today's system as Linnaeus' 1758 system looks to us
today. He recognized 2 weevil genera and about 90 species. Now we
have 5800 genera. We may end up with 15,000. <br>
<br>
The problem that at present only taxonomic experts can understand
how to retrace the meanings of concepts proposed in the history of
the field, and computers can't yet do this because the data are not
marked up and linked to each other precisely enough (as precisely as
an ontological representation would demand it), is not just going to
go away by some top-down adherence to a "consensus". Most
taxonomists jump into the field precisely because they come to
realize that the "consensus" has serious problems (read: "sucks").
So, as long as there is justified taxonomic research, there will be
reclassification. ]And no, IMO coming up with a synapomorphy-based
or node-pointing naming system will not miraculously allow us to
have a reliable system.]<br>
<br>
To the extent that there is a discussion here on the list as to
where the DC and a possible successor of the TCS is going, I think
that's a worthwhile discussion to have.<br>
<br>
Regards,<br>
<br>
Nico<br>
<br>
<br>
On 5/13/2011 4:41 PM, Peter DeVries wrote:
<blockquote
cite="mid:BANLkTineGxxtLs1hqYgeqjGNSBfKZzSqCQ@mail.gmail.com"
type="cite">Hi Nico,
<div><br>
</div>
<div>Thanks for posting this.</div>
<div><br>
</div>
<div>I have something in the concept model to indicate the basis
for the species concept.</div>
<div><br>
</div>
<div>For now I have three types. An individual species concept can
have a combination of one, two or all three</div>
<div><br>
</div>
<div>In the RDF they look like this</div>
<div><br>
</div>
<div><font class="Apple-style-span" face="'courier new',
monospace"><txn:speciesConceptBasedOn rdf:resource="<a
moz-do-not-send="true"
href="http://lod.taxonconcept.org/ontology/txn.owl#ObjectiveSpeciesModel">http://lod.taxonconcept.org/ontology/txn.owl#ObjectiveSpeciesModel</a>"/></font><br>
<br>
</div>
<div>The first is what I call the #ObjectiveSpeciesModel - this
indicates that it is a species concept because we say it is.</div>
<div><br>
</div>
<div>All the species concepts are at least
an #ObjectiveSpeciesModel</div>
<div><br>
</div>
<div>*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.</div>
<div><br>
</div>
<div>There are also tags for </div>
<div><br>
</div>
<div>
txn:PhylogeneticSpeciesModel</div>
<meta charset="utf-8">
<div>txn:BiologicalSpeciesModel</div>
<meta charset="utf-8">
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>I can think of a couple of different ways to handle the issue
of alternative species concepts.</div>
<div><br>
</div>
<div>* Note that the identifications as proposed by DarwinCore
don't seem to indicate what kind of model the identifications
were based on.</div>
<div> So it is not clear to me if a straight DarwinCore data set
would allow the analysis above.</div>
<div><br>
</div>
<div>Instead of having multiple different statements like </div>
<div><br>
</div>
<div><b>txn:occurrenceHasSpeciesConcept <> </b>in the
record for each occurrence</div>
<div><br>
</div>
<div>one could use different predicates to link to different kinds
of species concepts.</div>
<div><br>
</div>
<div>
<meta charset="utf-8">
<b>txn:occurrenceHasUniprotConcept</b> => <<a
moz-do-not-send="true"
href="http://purl.uniprot.org/taxonomy/9696">http://purl.uniprot.org/taxonomy/9696</a>></div>
<div><br>
</div>
<div>This would allow someone to query for the occurrences of <<a
moz-do-not-send="true"
href="http://purl.uniprot.org/taxonomy/9696">http://purl.uniprot.org/taxonomy/9696</a>></div>
<div><br>
</div>
<div>That said, it is not clear to me what people mean by
different identifications.</div>
<meta charset="utf-8">
<div><br>
</div>
<div>Is the intent to have identifications with different
homotypic synonyms to be an identification of the same thing or
not?</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>This is another way of saying<i> is the namestring the
concept?</i></div>
<div><i><br>
</i></div>
<div>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.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Thanks again for you comments,</div>
<div><br>
</div>
<div>- Pete</div>
<div> <br>
<div class="gmail_quote">On Fri, May 13, 2011 at 3:05 AM, Nico
Franz <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:nico.franz@upr.edu">nico.franz@upr.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"> Hello Pete (et al.):<br>
<br>
For birds, Town Peterson at KU and colleagues have
published these papers showing how alternative bird
taxonomies affect the ranking of conservation priorities.<br>
<br>
<a moz-do-not-send="true"
href="http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/PN_CB_1999.pdf"
target="_blank">http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/PN_CB_1999.pdf</a><br>
<a moz-do-not-send="true"
href="http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/NP_BN_2004.pdf"
target="_blank">http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/NP_BN_2004.pdf</a><br>
<a moz-do-not-send="true"
href="http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/P_BCI_2006.pdf"
target="_blank">http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/P_BCI_2006.pdf</a><br>
<br>
Here's the abstract of the 1999 paper:<br>
<br>
Analysis of geographic concentrations of endemic taxa is
often used to determine priorities for conservation<br>
action; nevertheless, assumptions inherent in the
taxonomic authority list used as the basis for<br>
analysis are not always considered. We analyzed foci of
avian endemism in Mexico under two alternate species<br>
concepts. Under the biological species concept, 101 bird
species are endemic to Mexico and are concentrated<br>
in the mountains of the western and southern portions of
the country. Under the phylogenetic species<br>
concept, however, total endemic species rises to 249,
which are concentrated in the mountains and lowlands<br>
of western Mexico. Twenty-four narrow endemic biological
species are concentrated on offshore islands, but<br>
97 narrow endemic phylogenetic species show a
concentration in the Transvolcanic Belt of the mainland
and<br>
on several offshore islands. Our study demonstrates that
conservation priorities based on concentrations of<br>
endemic taxa depend critically on the particular taxonomic
authority employed and that biodiversity evaluations<br>
need to be developed in collaboration or consultation with
practicing systematic specialists.<br>
<br>
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:<br>
<p class="MsoNormal">3) Taxonomy is over-accurate for most
applications <br>
</p>
<p class="MsoNormal">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.</p>
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.<br>
<br>
Regards,<br>
<br>
Nico
<div>
<div class="h5"><br>
<br>
<br>
On 5/13/2011 1:08 AM, Peter DeVries wrote: </div>
</div>
<blockquote type="cite">
<div>
<div class="h5">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)
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>eBird Occurrence Maps Northern Cardinal</div>
<div><a moz-do-not-send="true"
href="http://ebird.org/content/ebird/about/occurrence-maps/northern-cardinal"
target="_blank">http://ebird.org/content/ebird/about/occurrence-maps/northern-cardinal</a><br
clear="all">
<br>
</div>
<div>NCBI is also similar.</div>
<div><br>
</div>
<div>Perhaps a member of the consensus committee can
comment?</div>
<div><br>
-- Pete<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>
Email: <a moz-do-not-send="true"
href="mailto:pdevries@wisc.edu" target="_blank">pdevries@wisc.edu</a><br>
<a moz-do-not-send="true"
href="http://www.taxonconcept.org/"
target="_blank">TaxonConcept</a> & <a
moz-do-not-send="true"
href="http://about.geospecies.org/"
target="_blank">GeoSpecies</a> Knowledge Bases<br>
A Semantic Web, <a moz-do-not-send="true"
href="http://linkeddata.org/" target="_blank">Linked
Open Data</a> Project<br>
--------------------------------------------------------------------------------------<br>
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</div>
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<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>
Email: <a moz-do-not-send="true" href="mailto:pdevries@wisc.edu"
target="_blank">pdevries@wisc.edu</a><br>
<a moz-do-not-send="true" href="http://www.taxonconcept.org/"
target="_blank">TaxonConcept</a> & <a
moz-do-not-send="true" href="http://about.geospecies.org/"
target="_blank">GeoSpecies</a> Knowledge Bases<br>
A Semantic Web, <a moz-do-not-send="true"
href="http://linkeddata.org/" target="_blank">Linked Open Data</a> Project<br>
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