Hi Rich, thanks for the suggestion.
"unininomial" would equal "canonicalName" for ranks subgenus and above, but not for species and below, while canonicalName (or scientificNameCanonical if you prefer) covers all cases, which is why I thik it is preferable, especially as the majority of names in circulation are at species level and below I think...
Atomising further i.e. a binomial or poynomial into genus, species, infaspecies is actually a separate activity with its own rationale, I would say.
Just my personal view, of course...
Regards - Tony
________________________________________ From: Richard Pyle [deepreef@bishopmuseum.org] Sent: Tuesday, 23 November 2010 5:35 AM To: 'Markus Döring'; Rees, Tony (CMAR, Hobart) Cc: tdwg-content@lists.tdwg.org; dmozzherin@eol.org Subject: RE: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad?
TCS includes the element "Uninomial" (under the "CanonicalName" node), to address all names consisting of a single "part" (=single "NameElement" in GNUB-speak); including names at the rank of genus. I don't rememeber exactly whether names at the rank of genus are supposed to be represented in both "Uninomial" and "Genus", but I guess it doesn't really matter.
The addition of "Uninomial" to DwC would effectively solve the problem of representing names not among the "main" ranks.
Rich
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Markus Döring Sent: Monday, November 22, 2010 4:30 AM To: Tony.Rees@csiro.au Cc: tdwg-content@lists.tdwg.org; dmozzherin@eol.org Subject: Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad?
Im not sure if I correctly understand. dwc:scientificName
is used for
ANY rank, not only infrageneric ones. You dont have to use
the higher
taxon terms at all if you already use the adjacency format
via DwC:parentNameUsageID.
What I was saying was that e.g.
dwc:scientifcName=Pinus abies L. dwc:rank=species dwc:genus=Picea dwc:specificEpithet=abies
may work alright as an alternative to the suggested canonicalName,
however the following has no workaround:
dwc:scientificName=Crustacea Brünnich, 1772 dwc:rank=subphylum would then need: //dwc:subphylum=Crustacea// under this
model, but it
does not exist
(same for most other intermediate ranks)
Ah, perfectly right of course!
Assuming we would add canonicalName and we use genus for the classification - is there any purpose left for specific- and infraspecificEpithet?
i.e. there is no dwc pre-formatted element for intermediate
ranks between kingdom/phylum/class/order/family/genus, but there would be plenty of canonical names at these ranks.
Regards - Tony
From: Markus Döring [m.doering@mac.com] Sent: Monday, 22 November 2010 10:03 PM To: Rees, Tony (CMAR, Hobart) Cc: nico.franz@upr.edu; tdwg-content@lists.tdwg.org; dmozzherin@eol.org Subject: Re: [tdwg-content] [tdwg-tag] Inclusion of
authorship in DwC scientificName: good or bad?
Thanks Tony for bringing this back. I think I tend to support the idea of a new canonicalName
term, see below.
On Nov 22, 2010, at 3:50, Tony.Rees@csiro.au wrote:
Correct - and returning to my original question, there
appear to be 2 contrasting views:
(1) Include authority and other strictly "non canonical
name" info in DwC:scientificName as available (as exemplified by Markus, Rich Pyle, also present DwC specification) - however now the canonical elements must be obtained by re-parsing the supplied scientificName content, or supplied separately in DwC:genus, DwC:specificEpithet, etc.
(2) Omit authority and other strictly "non canonical name"
info from DwC:scientificName since this can be supplied elsewhere e.g. in DwC: scientificNameAuthorship, and makes the strictly canonical name information available directly rather than having to re-parse the DwC:scientificName element (Rod, Hilmar, Catalogue of Life format, Dmitry (?), also my practice for the last 8+ years although possibly not correct).
Yes, thats the current choice one has with dwc. Problems with #2 when dealing with not only simple
binomials I think I have stressed before.
Another confusion that should need clarification is
actually the role of the higher taxon terms in dwc - you touch on it below too.
In case of synonyms does dwc:genus actually hold the genus
of the synonym name or is it the accepted genus the synonym is classified to?
If you look at the term definition it says: "The full
scientific name of the genus in which the taxon is classified." This is consistent with all other higher taxon terms in darwin core that represent the taxonomic hierarchy. A quick example:
dwc:scientifcName=Pinus abies L. dwc:genus=Picea dwc:taxonomicStatus=homotypic synonym dwc:acceptedNameUsage=Picea abies (L.) H.Karst
If we accept this view, then there really is no way to
express the canonical name and I would indeed vote for having a new dwc:canonicalName term. With no doubt the canonical form of a name is the most important string when first dealing with a name and trying to align it with names from other sources. And we surely shouldnt require a name parser to be used for this very frequent use case.
That leads me to another question. Does the canonical name
string for an infraspecific taxon include the rank marker? Ideally I think it shouldnt as the main point for having a canonical name string is to have a string that is highly similar across different sources. Removing the rank marker not only avoids spelling variations, but also zoologists pretty much only deal with subspecies and there dont have to use a rank marker.
Zoological example: http://www.marinespecies.org/aphia.php?p=taxdetails&id=293570
dwc:scientifcName=Clupea pallasii marisalbi Berg, 1923 dwc:taxonRank=subspecies dwc:canonicalName=Clupea pallasii
marisalbi
dwc:scientifcNameAuthorship=Berg, 1923
Botanic example:
http://wp6-cichorieae.e-taxonomy.eu/portal/?q=cdm_dataportal/taxon/800
e92ea-496b-4368-abf9-9ae12f7f40d1/synonymy
dwc:scientifcName=Lactuca macrophylla subsp. uralensis (Rouy) N. Kilian & Greuter dwc:taxonRank=subspecies dwc:canonicalName=Lactuca macrophylla uralensis dwc:scientifcNameAuthorship=(Rouy) N. Kilian & Greuter
dwc:scientifcName=Mulgedium macrophyllum var. hispidum
(Ledeb.) Korsh.
dwc:taxonRank=variety dwc:canonicalName=Mulgedium macrophyllum hispidum dwc:scientifcNameAuthorship=(Ledeb.) Korsh. dwc:taxonomicStatus=heterotypic synonym
dwc:acceptedNameUsage=Lactuca
macrophylla subsp. uralensis (Rouy) N. Kilian & Greuter
In my initial email my thought was that (1) would be an
acceptable solution provided that the canonical information was supplied in (e.g. at species level) DwC:genus and DwC:specificEpithet. However I now realise that this solution will not scale, as per the following use case:
Currently I am preparing around 1.9 million records for
export as DwCA format. E.g. my record for Philander opossum Linnaeus, 1758 (the previous cited worked example taxon from http://code.google.com/p/darwincore/wiki/Examples#Taxonomic_Tr eatment,_normalised) reads as follows (paraphrased from the relevant row in my csv file):
DwC:taxonId=mam10000822 DwC:scientificName=Philander opossum DwC:scientificNameAuthorship=Linnaeus, 1758 DwC:taxonRank=species DwC:taxonomicStatus=accepted DwC:nomenclaturalStatus=available DwC:nameAccordingTo=CoL2006/ITS DwC:originalNameUsageID= DwC:namePublishedIn= DwC:acceptedNameUsageID=mam10000822 DwC:parentNameUsage=Philander DwC:parentNameUsageID=mam1001153 DwC:taxonRemarks= dc:modified=21-09-2006 DwC:nomenclaturalCode=ICZN
This follows model (2) above.
Initially I thought that in order to convert into model (1) as recommended, all I would have to do would be to add 2 elements,
DwC:genus=Philander DwC:specificEpithet=opossum
and concatenate (add in) the authority into the
DwC:scientificName element. However this is not the total solution, since my file also includes other ranks i.e. genus (not an issue), family, order, class, phylum and kingdom, each of which would then be required to be populated for an entry of that rank, but will basically be blank for entries of all other ranks (since the hierarchy is available by traversing DwC:parentNameUsageID and following that trail upwards). This means that my "table" of currently 1.9m rows x 15 columns then becomes 1.9m rows x 22 columns, quite an overhead for data transfer and subsequent ingestion/parsing into another system. Of course if I had additional ranks too e.g. subgenus, subfamily, infraorder and the rest the size blows out even more - and in any case, with the exception of subgenus, there are no Darwin core elements for other intermediate ranks as far as I can see.
Im not sure if I correctly understand. dwc:scientificName
is used for ANY rank, not only infrageneric ones. You dont have to use the higher taxon terms at all if you already use the adjacency format via DwC:parentNameUsageID.
So, I am now beginning to think that the case for a new
element DwC:canonicalName or equivalent is strengthened - all I would need is to put the scientific name without authority into that element, the scientific name with authority into DwC:scientificName and the problem is solved in the most efficient manner; also serving the needs of both arguments for either interpretation (1) or interpretation (2) above.
If others agree, is there then a case for going this
route, and adding the relevant additional element to DwC?
Tony, I do agree and also think this solves all problems
discussed here so far!
As a recommendation both scientificName and canonicalName
Regards - Tony
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