[tcs-lc] Demonstration Dataset

[Kennedy, Jessie]

>-----Original Message-----
>From: tcs-lc-admin at ecoinformatics.org
>[mailto:tcs-lc-admin at ecoinformatics.org]On Behalf Of Richard Pyle
>Sent: 04 March 2005 08:55
>To: tcs-lc at ecoinformatics.org
>Subject: [tcs-lc] Demonstration Dataset
>
>
>
>All:
>
>I spent this evening re-examining the TCS "Demonstration 
>Dataset" on the TCS
>Wiki:
>http://www.soc.napier.ac.uk/tdwg/index.php?pagename=TCSAndTheLi
>nneanCore
>
>To all the non-wiki folks on this list, I urge you to take a 
>look at this
>page, and in particular, download and review the "Timeline" 
>Powerpoint file
>(or re-review it if you've looked at it previously).  I would like to
>commend whoever created this file, as it very clearly and 
>graphically lays
>out a timeline of hypothetical nomenclatural changes, and serves as an
>excellent foundation for discussion, to help make sure we're 
>all on the same
>page.  Henceforth, I will (whenever possible) draw my 
>hypothetical examples
>from this file, rather than create them ad-hoc.
>
>I had looked at this file back when it was first announced, 
>but I didn't
>have time to scrutinize it.  I'm glad that I took the time 
>this evening to
>review it in more detail, as it helps me understand the TCS 
>perspective in a
>nomenclatural context.
>
>I have a couple of questions/comments about the PPT file, 
>which might help
>spark/focus additional discussion. My references to slide 
>numbers refer to
>actual slide numbers when viewed in Design mode -- not to 
>animation steps
>(often several per slide).
>
>Slide 1:
> - Probably trivial, but do the little symbols represent only those
>particular specimens examined by each "in" author -- or do 
>they represent
>the full scope of individual organisms (living, recently dead, and
>yet-to-be-born) on the planet that each author would have 
>included within
>each concept circumscription?  I'm assuming the latter, 
>because it is very
>unlikely that each author would have access to the same 
>particular set of
>specimens.  But then again, from the "Demo_v2.xml" file, it 
>looks like the
>symbols represent actual vouchered specimens. Like I said, 
>probably trivial,
>but I just want to make sure one way or the other.

You are right, the symbols "represent the full scope of individual organisms" in terms of the definition which could be given in TCS as vouchered specimens (and this implies the author had access to them all), relationships to other taxa, character description etc. So yes we know they are trying to define a concept that people can apply to living, dead or to-be-born organisms but in terms of comparing the definitions of the concepts we can only do so on the actual data i.e. the vouchered specimens, relationships to other taxa, character description etc. If no vouchered specimens or character description is given and only sya relationships to other taxa then that's all we have to compare then and we either trust the comparison or not as specified by the taxonomist.

>
>Slide 3:
>- Need to be really careful with the words "valid" and 
>"invalid" (side-box
>for Pyle 1990).  

Fair enough. We would hope that the taxonomist - botanical or zoological would use the correct relationship for their particular case.
We merely needed a simple example of a "purely nomenclatural change". Sorry if this created additional issues; hope they don't distract from what we are trying to show.

> Slide 4: [..] I'm 99% sure that you don't intend the actual 
> ID value to have embedded within it some sort of self-evident 
> link between an Original concept and its corresponding 
> Nominal concept [..]

You are right, the ids carry no information. If they seem to in the example it is only an aid to help the poor human who manually created the XML. 

>Slide 10: The Codes (at least the ICZN code) would not consider the
>gender-corrected "Aus beus" as a "replacement name" to "Aus 
>bea".  Indeed, I
>don't think any zoologist would think of these as different 
>"names" -- but
>rather as different spellings of the same "name". I don't 
>believe the Pyle
>1990 act of noting the corrected spelling would represent either an
>"Original" concept, or a "Nominal" concept.  More of a "usage" 
>instance.

we disagree here - if you are making this new name publicly available for people to use (in fact actually encouraging people to use it from now on...) then it should be a new concept - original because its the first usage of the name related to some either concept for its definition and of course a nominal concpet would be made for the undefined uise of that name.

>agree with this), but to me, what distinguishes an "Original" 
>concept from a
>"Nominal" concept is that the former has a specific implied concept
>circumscription, whereas the latter is purely nomenclatural.  
but the latter still has an implied concpet when it is used by someone in the future....
>Pyle 1990
>never made any assertions about concept circumscriptions for 
>either name,
>and therefore should not have an "Original" concept associated 
>with either
>(by my understanding, anyway).
>

but then it makes the name unusable if we agree it is meaningless to identify something to a name that has no concept.

>On the other hand, if Franz had discovered that Xus Pargiter 2003 was
>preoccupied by Xus Smith 1950 (thus Pargiter's "Xus" being a 
>junior homonym
>of Smith's "Xus"), then published the replacement name "Zus", 
>it *would* be
>appropriate to create a new "Original" concept and a new 
>"Nominal" concept.
we agree thiswould be correct but see hte previous example in the same way...

>But this is a special case, and there are botanical/zoological 
>differences
>here (with respect to basionym treatment).

yes - but when the name is use dit will be used with a meaning and deserves to have one....

>
>Slide 12: You illustrate "Xus beus" as having a new "Original" 
>concept and
>new "Nominal" concept.  This the botanical perspective, but not the
>zoological perspective.  There's been a general assumption that the
>Zoological perspective would change to accommodate the botanical
>perspective, but I think it depends ultimately on how the names data is
>ultimately modeled within TCS (i.e., as attributes of Concepts, or as
>objects to themselves).  Needs more discussion.

ok we are trying to be consisten in the modelling approach the actual 
relationships (i.e. what they are called - still to be agreed on but good list for starters by Nico) can capture these semantic differences between the codes.

>
>Slide 14: I had been under the impression that "Original" concept was
>restricted to Basionyms, true "replacement names", and *perhaps* new
>combinations (if the botanists win) -- but not alternate 
>spellings. However,
>I get the impression that here a new "Original" concept is 
>created whenever
>there is a novel "NameString" (specific string of characters).
  
yes they are created for all novel Namestrings - but only new strings that are in a taxon definition or a nomenclatural act (if that's what its called), not just some usage in say the New York Times..... ;-)

>Also, I
>thought they were created only in cases where an actual concept
>(circumscription of specimens) was asserted -- not for purely 
>nomenclatural
>acts (without any concept implications).
no

>
>Slide 15: Because Pyle never made any statements about the
>shape/size/position of the concept circumscriptions associated 
>with the two
>names he was correcting, I don't see why there should be any "SEC Pyle"
>instances.

because the corrected the name - deosn't he deserve a SEC. for this?
>
>- Also, I think there is an error in the box for TCrev19 -- 
>shouldn't that
>be "Aus cea Fry 1989", instead of "Aus cea Archer 1965"? 
yes there is a mistake sorry it should be "Aus cea BFry 1989"  
>Also, 
>what's with
>the "BFry"?  Is that a botanical author code?
>
it was just to show that the author Fry could also  be abreviated as BFry (Linnaeus, L. Linn. etc) i.e. differently in the name and in the publication.
There were a couple of other little typos on that slide....The lower TCori14 should've been TCori16 and "Aus ceus Archer 1965" should be "Aus ceus BFry 1989"
just like in real life ;-)
>
>Regarding the "Demo_v2.xml" file:
>
>- Why don't any of the Species-rank names have Relationships?  
>Are there no
>reciprocal "is type of" or "is child of" relationships?
>

we represetned the XML to match the scenario and the genera were defined in terms of the species as in this example this is what we said the taxonomists did. You can back-track the speciifed relationships if you want - but we don't represent explicitly.

>- Does <Relationship type="has type"> mean "Has type 
>species."?  If so, I
>understand why cl1 has this relationship, but why is it 
>repeated for ca1,
>cf1, ct1, etc.  Is this only because these are "Revision" 
>concepts, and in
>each case the author re-affirmed the type species of the 
>genus? 
yes htat's how we interpretted it.
> Or will
>*all* concept instances of Aus L. 1758 contain a copy of this 
>connection
>with the type species? 
not if in the definition it doesn't reaffirm it.
> This is an example of something that 
>is a property
>of the *name* "Aus", not of every single Concept instances of "Aus".
>
This could also be inferred  by navigating to the orignal concept.

>- For TaxonConcept cp5 (original concept of "Xus beus (Archer 
>1965) Pargiter
>2003"), there are "Relationships" with ct2 and cf3.  Does their
>representation here (instead of as a RelationshipAssertion)?  Is this
>because relationships stated by Pargiter 2003 himself about 
>his own concepts
>belong within his TaxonConcept instance, and 
>RelationshipAssertions are for

yes
>"third-party" relationship assertions? (Is this effectively 
>the definition
>distinction between Relationships and RelationshipAssertions? 
>I.e., between
>intra- and inter-publication relationship statements?)
>
yes

>
>General question about "Original" vs. "Nominal" concept:
>Intuitively, it makes sense to me that if you're going to go 
>to the trouble
>of automatically creating a Nominal Concept for every Original 
>Concept, then
>the Nomenclatural information should be embedded within the "Nominal"
>version, and that should be the unit of exchange for 
>nomenclators. 
well that gives some definition to it ansdwe're trying ot say use hte nominal concept where you don't know what the name means.

> It seems
>intuitive to me that a "Nominal" concept would be a container 
>for "all the
>name stuff".  I think an "Original Concept" should be used for a true
>concept -- the concept that was asserted by the Author(s) of 
>the original
>description of the name.
we've discussed this before I think and are saying that an original concept will always hold the nomenclautraul information ralted to that name.

>
>Also, we need more discussion about what sorts of "name changes" should
>warrant the creation of a new "Original" concept and/or 
>"Nominal" concept.
>
yes - see earlier discussion - any name that has a published definition and any name change that is intended to be followed and therefore has an implied definition.
There is clearly a role here for the likes of ITIS who say what species exist - if a nomencalturist publishes a name correction (which if he/she doesn't say to which concepts it applies and then we can assume there is a correction to the original concept), then ITIS might assert the definition of that name by relating it to an existing defined concept - this would in effect be a concept wiht the new name SEC. ITIS.
 
>If the TCS group would find it useful, I could offer a 
>real-world set of
>examples in fishes that offer a set of particularly thorny 
>nomenclatural
>issues.  I would begin with a PPT file similar to the abstract one in
>"TimeLine", except I would replace it with real values. Would that be
>worthwhile?
>
yes we were always asking for real data .......
we can always see if how you would do it would be how we thought it could be done.


Jessie and Robert