[SEEK-Taxon] Re: Comment on Napier Taxonomic Transfer Schema

Nozomi Ytow nozomi at biol.tsukuba.ac.jp
Thu May 27 10:22:18 PDT 2004


(It seems that some trouble happend on mail transaction except to
 gbif-dadi at roles.circa.gbif.net, so I'm re-sending this mail.
 If you received it twice or more, please ignore muliplications)
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(I'm not confident to whom I should send this mail.  I picked
 addresses from Roberts' and Donald's mail with removing
 included in GBIF-DADI or SEEK-Taxon, and two addition.
 If you find someone missing from To: or Cc: fields,
 please let me know.)
 
Dear Jessie and Robert,

In trying to map the Nomencurator data structure to the exchange 
schema, I have the following difficulties, including issues raised at
the Edinburgh meeting.  Could you clarify these points, please?
I hope they don't reflect fundamental problems with the schema.

1.  Ambiregnal issue (again).  Suppose a publication describes a new 
unicellular eukaryote species with two valid names, one under ICBN and 
the other under ICZN (such things are not rare).  Although Jessie said 
they are two taxon concepts having different name at the meeting, it is 
obvious that the author(s) composed a single taxon concept that 
required two valid names.  Counting it as a single taxon concept would 
be helpful if we assign a GUID to the taxon concept.  If the
TaxonConcept element in the schema is a wrapper rather than the taxon
concept object, however, two taxon concept wrappers are reasonable.
I suggest reconsidering the element name to indicate that it is a
wrapper.  It also eliminates the odd combination "vernacular taxon
concept".  Note: those two valid names can't be synonyms in the
nomenclatural sense because both are valid names under different
Codes.  In the same sense, vernacular names can't be synonyms of valid
scientific names because they are not part of the same nomenclatural
code.

If TaxonConcepts are actual objects, rather than wrappers, and are 
assigned GUIDs, then how do you avoid the inflationary problem that 
Walter described in his 1995 potential taxon concept paper?

2.  I have another difficulty in mapping Nomencurator data to the 
schema. We have two elements of a Name (or TaxonConcept) that would map 
to 'AccordingTo', i.e. sensu and secundum.  These two are necessary to 
capture different name usages in a single revisional work comparing two 
or more concepts in previous works.  Jessie suggested that it may be 
captured by the relationship between concepts, but it is impossible to 
be sure that the later author's understanding of the earlier concept is 
directly equivalent to that of the earlier author (cf. 
http://www.nomencurator.org/Taxonomists.html ). Such equivalence may be 
assumed safely if and only if both the authors used the same specimen 
set and the taxon concept is explicitly defined by those specimens. 
Such model would be feasible for botanical taxonomic work, but unlikely 
to be so for soft-bodied invertebrates.  Therefore, I propose replacing 
'AccordingTo' with 'Secundum' to capture the source of the name usage 
in the later work (the author of the revision), and adding 'Sensu' to 
refer to the earlier author using a Name (or TaxonConcept).  This 
modification is partially relevant to the directed graph issue raised 
by Walter with the ABC-triangle.

3. There can be cases where linkage to the higher taxon is required
instead of lower taxa linkages to compose a taxonomic hierarchy
containing the taxon.  Since the current exchange schema contains only 
linkages to lower taxa as TaxonConceptCircumscription, users need to
compose a query as 'give TaxonConcept(s) having this TaxonConcept as its
(their) TaxonConceptCircumscription' even if the backend database has
the higher taxon concept as an attribute of the taxon concept data.
Therefore, I suggest adding a 'HigherTaxonConcept' element to the
'TaxonConcept' element in order to reduce query and data transfer.  

4. Minor suggestion: add DOI element to Publication element

Finally, a simple question: is there a source of the publication type 
list?

James
---
Dr. Nozomi "James" Ytow
Institute of Biological Sciences / Gene research center
University of Tsukuba
Tsukuba, Ibaraki 305-8572
Japan



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