[Taxacom] A little more on Species Entities

[Peter DeVries]

The new DarwinCore has a field that allows this *taxonConceptID.*
I think this will help working taxonomists since it provides an open,
accessible repository for all that information that is currently to hard to
find.

I believe that it will also create a whole new funding stream to produce
well documented species descriptions that are open and accessible.

I think that funding agencies have been reluctant to fund another
non-machine interpretable narrowly specialized description that exists only
in an obscure journal that no one can get to. (*their perception not mine*)

Now those decision makers will think, *Hey they are acting like all the
other biologists and producing something that could be widely usable ... I
could see funding projects that follow this model**. **I guess taxonomist
are cool, not just name changers that frustrate all the other biologists.*
*
*
*I am on your side, and I think something like this will help the community.
We can argue all we want amongst ourselves about the perception problem and
whether it*
*is accurate or fair, but in the end we need to do something to address the
issue because it effects funding levels.*

*It is my opinion that something like this will improve:*

*1) productivity*
*2) widely held perceptions*
*3) funding*

*- Pete
*
On Thu, Oct 1, 2009 at 2:21 AM, Stephen Thorpe <s.thorpe at auckland.ac.nz>wrote:

> >Demonstrating the difference between a change in how these two species
> were seen vs. a simple mislabeling or misidentification
> In practice, a misidentification is a misidentification is a
> misidentification, whether or not it reflected current thinking at the time,
> or else was just the product of a rushed and sloppy identifier. From our
> point of view today, we don't need to know which. Perhaps you could start up
> a new discipline which studies old and defunct taxonomic concepts, but
> trying to add that into a database will just massively increase the
> complexity of the task for little or nothing of any use. Forgive the bad
> timing of this analogy, but think of taxonomy as like being on the crest of
> a wave - what we want to know is: are specimens correctly identified
> according to our CURRENT concepts? Seems to me that somehow the bioinfo
> people have lost sight of what the taxonomists actually do: when taxonomists
> see a published identification, they don't ask: what taxon concept is this
> talking about? Instead, and if they need to, they try to revisit the actual
> voucher specimens and see if they are correctly identified according to
> their present concept. In practice, this is the only way ...
> ________________________________________
> From: taxacom-bounces at mailman.nhm.ku.edu [
> taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Peter DeVries [
> pete.devries at gmail.com]
> Sent: Thursday, 1 October 2009 7:59 p.m.
> To: taxacom at mailman.nhm.ku.edu
> Subject: [Taxacom] A little more on Species Entities
>
> The species entities can have many scientific names. These names are not
> concepts just the literal string.
>
> Don't assume that a given name can't be linked to several different species
> entities.
>
> The names list just says, *what are the various legitimate names that this
> species entity has had overtime.*
>
> It makes no assumptions that other species entities have not legitimately
> used that same name string.
>
> Here is a very hypothetical (incorrect) example:
>
> http://lod.taxonconcept.org/ses/v6n7p now called *Puma concolor (Linnaeus,
> 1771))*
>         => http://lod.taxonconcept.org/scinames/v6n7p_1001 => gni:505310
>         => http://lod.taxonconcept.org/scinames/v6n7p_1002 => gni:12104361
>
> http://lod.taxonconcept.org/ses/kKOIv now called *Panthera leo* (Linnaeus,
> 1758)
>         => http://lod.taxonconcept.org/scinames/kKOIv_1001 => gni:20753654
>         => http://lod.taxonconcept.org/scinames/kKOIv_1002 => gni:12104361
>
> This would be the case where at one time it was thought that all large cats
> were one species called Felis concolor
>
> What this hypothetical example shows is that at one time these two
> different
> species were known by the
> same literal name *Felis concolor* Linnaeus, 1771 (gni:12104361)
>
> Demonstrating the difference between a change in how these two species were
> seen vs. a simple mislabeling or misidentification.
>
> An old specimen might be labeled Felis concolor, but someone "Joe" may
> choose to tag it in their own database as
>
> Label name "Felis concolor" interpreted by JoeSchmoe to be an instance
> of *Panthera
> leo* se:kKOIv
>
> What if someone decides that the Lion really should be in its own genus
> (Leothera), but believes that all the specimens of Panthera leo are still
> one species?
>
> Then *Panthera leo* se:kKOIv  => *Leothera leo* se:kKOIv
>
> Now the idea "this is a species"  is cleanly separated from the idea that
> "this is a species in a particular genus".
>
> In my opinion, this is how it should have been done in the first place.
>
> 1) This is a species
> 2) This species has this particular position in the tree of life
>
> Clearly two separate issues.
>
> Also:
>
> Need to know what the characters, definitive specimens, DNA barcodes etc,
> are for a given species entity?
>
> Puma concolor se:v6n7p <http://lod.taxonconcept.org/ses/v6n7p.xhtml>
> *
> *
> Then click on namespaced version of the species entity URI in the line
> above.
>
> - Pete
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>
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>
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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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