[tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad?

Mon Nov 22 19:35:17 CET 2010

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 at lists.tdwg.org 
> [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of 
> Markus Döring
> Sent: Monday, November 22, 2010 4:30 AM
> To: Tony.Rees at csiro.au
> Cc: tdwg-content at lists.tdwg.org; dmozzherin at 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 at mac.com]
> > Sent: Monday, 22 November 2010 10:03 PM
> > To: Rees, Tony (CMAR, Hobart)
> > Cc: nico.franz at upr.edu; tdwg-content at lists.tdwg.org; 
> > dmozzherin at 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 at 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
> >> 
> >> _______________________________________________
> >> tdwg-content mailing list
> >> tdwg-content at lists.tdwg.org
> >> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> 
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