[tdwg-content] Fwd: [Fwd: Re: If you need something for referring to a population, then it is probably best to do it as a related class]

Thu May 5 03:07:11 CEST 2011

Hi Rich,

Some of this depends on if the bulk of data associated with C. flavicauda
are under than name or recorded as C. fisheri.

You can always merge two concepts using owl:sameAs, so if someone considered
them one species they could download them and run a sameAs.

The problem with keeping them separate is that you might have data sets that
are really about C. flavicauda, but were recorded as C. fisheri.

There was a similar example involving birds that David Remsen mentioned but
I looked around and all the major records were with the entities as separate
species, so I kept them separate.

In the case of subspecies, and in the absence of a more elegant solution, I
would record them as instances of a species concept *in the form of Genus
epithet subspecific epithet.*
*
*
That way you capture the full intent, without causing additional problem.

The example I use is this. Two Cougar cubs are born on a mountain.

One of the cubs is seen on the North side of the mountain and recorded by
scientist A as *Puma concolor couguar*, the other is seen on the South side
of the mountain and recorded by scientist B as* Puma concolor.*

**Since every instance of a true subspecies is also an instance of the
species it is safe to say that both are occurrences of the species concept
for the Cougar.

However when treated as separate strings, as they are in many systems, these
are later interpreted as instances of two different things. e.g. two ITIS
numbers.

Also, I thought I might restate what I mean by the individual is one kind of
thing.

Think of it this way.

An all omniscient being that could see all that individuals DNA, lineage and
extent of reproductive isolation could in most cases be able to determine
what kind of thing it is and what other individuals are also  instances of
that kind.
She would also be able to recognize what individuals are not instances of
that kind of thing.

We as humans can only hypothesize what the things are and also make
assertions about what individuals are instances of that thing.

So Nico and I are not really that far apart I just think that for some types
of queries and questions it would be best to consider the observation of a
specimen, or individual to be one of type of thing at a time.

That does not mean that you can't model it in a way that states we are
treating this as this type of thing, but others believe it is a different
kind of thing.

I also don't seem to understand why if someone can find some missing utility
in existing vocabularies, and mints one starting with txn, it is seen by
some as an act of heresy, while the minting a new vocabulary starting with
dsw is not.

Heretical enough to be written out of the sacred scrolls?

Respectfully,

- Pete

On Wed, May 4, 2011 at 6:03 PM, Richard Pyle <deepreef at bishopmuseum.org>wrote:

> Hi Pete,
>
>
>
> Yes, I know – and you are among the MANY people to whom I owe some
> follow-up work (my inbox of unanswered email has crept up past the 8,000
> mark).  But I entered this fray in part to re-kindle that conversation we
> had started months ago.  That notwithstanding, I don’t remember an answer to
> the question I posed just now, concerning taxonconcept.org as a concept
> store.  I had been under the impression that it would establish C. fisheri
> s.s. and C. fisheri s.l. as two distinct Concepts, with two distinct GUIDs,
> and a mapping of relationships between them and with other entities (e.g.,
> cross-referencing specimens, nomenclature, TaxonNameUsage instances, etc.)
> The thing that caught my attention in your recent email was the notion that
> one would need to leave taxonconcept.org to see alternative concept
> definitions.
>
>
>
> Aloha,
>
> Rich
>
>
>
> *From:* Peter DeVries [mailto:pete.devries at gmail.com]
> *Sent:* Wednesday, May 04, 2011 12:25 PM
> *To:* Richard Pyle
> *Cc:* Nico Cellinese; tdwg-content at lists.tdwg.org
> *Subject:* Re: [tdwg-content] Fwd: [Fwd: Re: If you need something for
> referring to a population, then it is probably best to do it as a related
> class]
>
>
>
> Hi RIch,
>
>
>
> These were the very issue that we had talked about modeling last fall and I
> thought we were planning to work on after the holidays.
>
>
>
> Check your old email I have your prototype fish list.
>
>
>
> Perhaps SKOS:narrower?
>
>
>
> http://lod.taxonconcept.org/Pomacanthidae.html
>
>
>
> Respectfully,
>
>
>
> - Pete
>
> On Wed, May 4, 2011 at 4:46 PM, Richard Pyle <deepreef at bishopmuseum.org>
> wrote:
>
> Alas, I don't have time to dive-in to this conversation in full (I still
> owe
> too many things to too many people), though I have been very tempted!
>
> Very quickly:
>
>
> > The model supports links to alternative concepts. The uniprot and
> bio2rdf,
> and DBpedia
> > URI's can be considered closely related concepts.
> > The way this works ideally is that the identifier of this insect (from
> TDWG) makes the assertion that
> > this
> observation
> http://ocs.taxonconcept.org/ocs/0da685c9-9cdc-4dff-baf3-38d1bdbc
> 6552.html<http://ocs.taxonconcept.org/ocs/0da685c9-9cdc-4dff-baf3-38d1bdbc%0d%0a6552.html>
>
> > represents an instance of this
>
> concept http://lod.taxonconcept.org/ses/z9oqP#Species
>
> But if I understand you correctly, alternate concepts don't exist within
> taxonconcept.org; but only as links to other repositories of concepts,
> that
> may or may not be congruent with those represented in taxonconcept.org.
>  If
> that's the case, then what happens when the person who identifies the
> observation
> [http://ocs.taxonconcept.org/ocs/0da685c9-9cdc-4dff-baf3-38d1bdbc6552.html
> ]
> doesn't agree with the concept represented in
> [http://lod.taxonconcept.org/ses/z9oqP#Species] -- or any other concept
> represented in taxonconcept.org?  Do they have to hunt around through the
> other repositories to find the right one?
>
> Let me give an example.  The type specimen of Centropyge fisheri  was
> collected in Hawaii (e.g.,
> http://pbs.bishopmuseum.org/images/JER/detail.asp?ID=-1377454029 ). The
> type
> specimen of C. flavicauda  was collected in the South China Sea, and is
> known throughout the rest of the tropical Pacific (e.g.,
> http://pbs.bishopmuseum.org/images/JER/detail.asp?ID=-1339602635).
>
> Many taxonomists have treated these two species as distinct and valid; and
> hence two separate taxon concepts representing populations in Hawaii, and
> in
> the broader Pacific, respectively.  Other taxonomists have considered them
> to be conspecific, and thus only one species throughout the tropical
> Pacific, including Hawaii.  The name "fisheri" has priority, so the concept
> labeled as "Centropyge fisheri, sensu stricto" refers to the species
> concept
> consisting of individuals from Hawaii, and the concept labeled as
> "Centropyge fisheri, sensu lato" refers to the species concept consisting
> of
> individuals throughout the tropical Pacific (including Hawaii).
>
> If I understand you correctly, there would be only one of these two
> concepts
> represented in taxonconcept.org.  For the sake of argument, let's say it
> was
> the sensu lato concept (which is the more modern interpretation, lumping
> the
> two historically distinct species).  What if someone made an observation in
> Johnston Atoll, and they are a splitter (i.e. recognizing Hawaii C. fisheri
> as a distinct species from Pacific C. flavicauda), and wanted to identify
> their specimen to the concept that *excludes* the Hawaii population (i.e.,
> C. flavicauda)?  Would they be able to do so?  Or would they have to look
> through uniprot and bio2rdf, DBpedia, etc. to find a species-level concept
> that matches the one they want to represent the observation as?
>
> Apologies if I have completely misunderstood this conversation...but at the
> very least, perhaps a concrete example (with pictures!) might help to
> disambiguate some of this thread.
>
> Aloha,
> Rich
>
>
>
>
>
> --
>
> ------------------------------------------------------------------------------------
> 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
>
> --------------------------------------------------------------------------------------
>

-- 
------------------------------------------------------------------------------------
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
--------------------------------------------------------------------------------------
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