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

Mon Nov 22 15:30:12 CET 2010

>> 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/800e92ea-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_Treatment,_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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