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

Mon Nov 22 20:44:24 CET 2010

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 at bishopmuseum.org]
Sent: Tuesday, 23 November 2010 5:35 AM
To: 'Markus Döring'; Rees, Tony (CMAR, Hobart)
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?

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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