This is sounding scarily close to my Organism Concept idea I had a while back. ;-)
From: Peter DeVries [mailto:pete.devries@gmail.com]
Sent: Friday, 11 June 2010 11:34 a.m.
To: Richard Pyle
Cc: Jerry Cooper; Kevin Richards; tdwg-content@lists.tdwg.org
Subject: Re: [tdwg-content] Name is species concept thinking
Richard and Jerry are getting at something that we need to think about.
There will be differences in what people think is an ideal species concept model.
Depending on the needs of different groups they may need some different conceptualization.
I recognize the utility in documenting the different conceptualizations over time.
There are however a lot of people who are more interested in these kinds of relationships.
<SnowShoeHare> <preyItemOf> <NorthAmericanLynx>
<Ochlerotatus_triseriatus> <documentedVectorOf> <LaCrosseEncephalitis>
A number of the records that have been submitted to GBIF etc are from groups that are primarily thinking about species concepts in this way.
In fact traditional taxonomy does not have much information that helps separate those individuals that can be vectors or pathogens and those that cannot.
For these kinds of users it might be more useful to have an open machine interpretable document that can be used to determine the criteria for what species concepts are good matches for a specimen and what species concepts are not good
matches.
In this sense it is a way to agree on what are the characteristics (and the variability in those characteristics) that assign specimen x most closely with species concept Y.
I think that the species concepts that you describe in GNUB will allow you to capture the variations in conscriptions you are talking about.
I also think that the general things that Dima and I are working through will also help either directly though the TaxonConcept concepts or figuring out the best way to get the GNUB concepts working as you describe in a triplestore. I think
they maybe thinking that the TaxonConcept concepts might help them determine how best to RDF the GNUB concepts if they will be different.
What proportion of currently described taxa have these types of overlapping conscriptions? I know of several insects like this, but what about mammals like the Cougar?
I hope that people are willing to accept that there maybe different types of species concepts depending on how they are intended to be used.
We may not be able to agree on what a species is but I think we might be able get to the point where it is clearer when we state that identifer X means instances with these somewhat variable set of characteristics.
Frankly I think it would be an improvement if we could get maps etc that combine Aedes triseriatus / Ochlerotatus triseriatus into one map and Felis concolor and Puma concolor into a different single map. :-)
Respectfully,
- Pete
On Thu, Jun 10, 2010 at 5:15 PM, Richard Pyle <deepreef@bishopmuseum.org> wrote:
Warning to Tim: Go get your cup of tea before reading....
Hi Jerry,
I believe what you describe:
> I think we do need an agreed way for identifying a 'set of
> name/article pointers' that define a useful grouping (which I
> would hesitate to call a concept). I don't think an
> open-ended linked data chain does provide that defined grouping.
...is already built into the GNUB data model.
Starting with a particular TaxonNameUsageID instance, we can directly get a
set of Protonyms that are asserted in the Usage to be included within the
taxon. From these Protonyms, we can explode out as far as you want to go.
The limitation, however, is that GNUB only includes the explict facts, not
the interpreted meanings. In other words, we may know that Smith 1955
regarded Aus cus, Aus dus, and Aus eus as synonyms of Aus bus; but if he
never mentioned Aus xus (either as another synonym, or as a distinct
species) we can't know whether his circumscription of Aus bus would have
included the type and implied other members of Aus xus. So, the facts alone
don't cut it.
So if Smith treated Aus bus as follows (synonym indended below asserted
valid name):
Aus bus L.
- Aus bus L.
- Aus cus Jones
- Aus dus Brown
- Aus eus Lamarck
And Pyle treated Aus bus as
Aus bus L.
- Aus bus L.
- Aus cus Jones
- Aus dus Brown
- Aus eus Lamarck
- Aus xus Cooper
[without any mention of Smith's treatment of Aus bus]
...then we need a third party to assert whether or not "Aus bus sec. Smith"
and "Aus bus sec. Pyle" are congruent.
With our new GNUB data model, we *could* represent these third-party
assertions; but my gut feeling is that the third-party assertions should be
external to the core GNUB model. But this is, of course, open for
discussion.
> Pete's point about the two different name/article
> intersections referring to the same 'concept' is resolved by
> the fact they are based on the same type, and that issue I
> prefer to see resolved at the nomenclatural level by
> protologue & type-collection pointers (as in the GNUB model).
Types don't do it for us. Using my example above, suppose we have DeVries'
treatment of the Aus bus complex as follows.
Aus bus L.
- Aus bus L.
- Aus cus Jones
- Aus dus Brown
Aus eus Lamarck
- Aus xus Cooper
That is, he treated Aus bus and Aus eus as valid species, and included Aus
xus as a synonym of the latter.
In all three treatements of Aus bus (Smith, Pyle, DeVries), the name "Aus
bus" shares the same type -- but that doesn't mean that all three had the
same taxon concept (circumscription).
So, in my mind, the real question is:
Do we need a separate "taxonConceptID" (as in the TDWG version of DwC) that
we can use to brand the abstract Concept? Or are we able to assemble the
same results from individual usage-instance mappings?
So, let's say that we are confident that Smith and Pyle both had the same
idea for the taxon concept/circumscription of Aus bus (it's just that Smith
forgot to list Aus xus in his synonymy). Do we need a single taxonConceptID
to express the fact that they are the same taxon concept? Or can we derive
that easily enough from a third-party assertion of the congruency of the
concepts represented by the two usage-instances? Presumably we would also
have separate taxonConceptID's for "Aus bus sec. DeVries", and for "Aus eus
sec. DeVries".
> I think it would help if we took a step back from using the
> term 'taxon concept' and agreed on what we are trying to
> achieve by linking/grouping the various constructs, and then
> arrive at a more precisely defined vocabulary for
> name/article intersections, and the open-ended universe of
> related stuff.
AGREED!!!
> I suspect we will find that different end-user groups (e.g.
> hard core nomenclaturalists, nomenclaturally savvy
> taxonomists, most taxonomists, and the most important group
> ... non taxonomic savvy end-users of taxonomic services) all
> have differing and overlapping requirements, and a different
> understanding of the words being used.
NO DOUBT!
> Despite my peripheral involvement in taxon concept space for
> many years I suspect the above comments reflect a deep seated
> blinkered view that stops me seeing how it should work given
> the existing vocabulary!
ME TOO! :-)
Rich
--
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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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