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

Fri Nov 19 15:03:11 CET 2010

Looks like a you found an interesting bug John, I will take a look why the
letter got changed!

Is it allowed to have capitalized 'var. part' of a name? I did not know that

Dima

On Fri, Nov 19, 2010 at 7:06 AM, John van Breda <
john.vanbreda at specialfamilies.org> wrote:

> Thanks David. Interesting results though - if I run Centaurea affinis Friv.
> ssp. affinis var. Affinis then the canonical is returned as Centauzea
> affinis affinis - note the change of the letter r to z. It also seems to
> lose sight of the subspecies variant. It works well on Centaurea apiculata
> Ledeb. ssp. adpressa (Ledeb.) Dostál though.
>
> That looks like it will be a really useful service.
>
> John
>
> -----Original Message-----
> From: tdwg-content-bounces at lists.tdwg.org
> [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of David Remsen
> (GBIF)
> Sent: 19 November 2010 11:51
> To: John van Breda
> Cc: tdwg-content at lists.tdwg.org; '"Markus Döring (GBIF)"'; 'Jim Croft'
> Subject: Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC
> scientificName: good or bad?
>
> Correction
>
> http://gni.globalnames.org/parsers/new
>
> The URI I circulated a moment ago comes AFTER you run a list of names
> and doesn't seem friendly.
>
> DR
>
> On Nov 19, 2010, at 12:15 PM, John van Breda wrote:
>
> > I'm coming in a bit late on this conversation so I hope I am not
> > repeating
> > what has already been said, but botanical names can also have
> > authorship at
> > both specific and infraspecific levels, e.g.
> > Centaurea apiculata Ledeb. ssp. adpressa (Ledeb.) Dostál
> >
> > And to make it even more complex, you can have subspecies variants,
> > so 2
> > infraspecific levels, e.g.
> > Centaurea affinis Friv. ssp. affinis var. Affinis
> >
> > Atomising this properly could be quite complex but necessary to be
> > able to
> > present the name as it should be written with italics in the correct
> > place.
> > E.g. in the example above, the author string and rank strings are not
> > normally italiced, but the rest of the name is. Unless we can
> > include this
> > formatting information in dwc:scientificName?
> >
> > Regards
> >
> > John
> >
> > -----Original Message-----
> > From: tdwg-content-bounces at lists.tdwg.org
> > [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of "Markus
> > Döring
> > (GBIF)"
> > Sent: 19 November 2010 09:24
> > To: Roderic Page
> > Cc: tdwg-content at lists.tdwg.org; Jim Croft
> > Subject: Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC
> > scientificName: good or bad?
> >
> > What Darwin Core offers right now are 2 ways of expressing the name:
> >
> > A) the complete string as dwc:scientificName
> > B) the atomised parts:
> >    genus, subgenus, specificEpithet, infraspecificEpithet,
> > verbatimTaxonRank (+taxonRank), scientificNameAuthorship
> >
> > Those 2 options are there to satisfy the different needs we have
> > seen in
> > this thread - the consumers call for a simple input and the need to
> > express
> > complex names in their verbatim form.
> > Is there really anything we are missing?
> >
> >
> >
> > When it comes to how its being used in the wild right now I agree
> > with Dima
> > that there is a lot of variety out there.
> > It would be very, very useful if everyone would always publish both
> > options
> > in a consistent way.
> >
> > Right now the fulI name can be found in once of these combinations:
> > - scientificName
> > - scientificName & scientificNameAuthorship
> > - scientificName, taxonRank & scientificNameAuthorship
> > - scientificName, verbatimTaxonRank & scientificNameAuthorship
> > - genus, subgenus, specificEpithet, infraspecificEpithet, taxonRank,
> > scientificNameAuthorship
> > - genus, subgenus, specificEpithet, infraspecificEpithet,
> > verbatimTaxonRank, scientificNameAuthorship
> >
> > To make matters worse the way the authorship is expressed is also
> > impressively rich of variants.
> > In particular the use of brackets is not always consistent. You find
> > things
> > like:
> >
> > # regular botanical names with ex authors
> > Mycosphaerella eryngii (Fr. ex Duby) Johanson ex Oudem. 1897
> >
> > # original name authors not in brackets, but year is
> > Lithobius chibenus Ishii & Tamura (1994)
> >
> > # original name in brackets but year not
> > Zophosis persis (Chatanay), 1914
> >
> > # names with imprint years cited
> > Ctenotus alacer Storr, 1970 ["1969"]
> > Anomalopus truncatus (Peters, 1876 ["1877"])
> > Deyeuxia coarctata Kunth, 1815 [1816]
> > Proasellus arnautovici (Remy 1932 1941)
> >
> >
> > On Nov 19, 2010, at 8:50, Roderic Page wrote:
> >
> >> I'm with Jm. For the love of God let's keep things clean and simple.
> >> Have a field for the name without any extraneous junk (and by that I
> >> include authorship), and have a separate field for the name plus all
> >> the extra stuff. Having fields that atomise the name is also useful,
> >> but not at the expense of a field with just the name.
> >>
> >> Please, please think of data consumers like me who have to parse this
> >> stuff. There is no excuse in this day and age for publishing data
> >> that
> >> users have to parse before they can do anything sensible with it.
> >>
> >> Regards
> >>
> >> Rod
> >>
> >>
> >> On 19 Nov 2010, at 07:06, Jim Croft wrote:
> >>
> >>> Including the authors, dates and any thing else (with the
> >>> exception of
> >>> the infraspecific rank and teh hybrid symbol and in botany) as
> >>> part of
> >>> a thing called "the name" is an unholy abomination, a lexical
> >>> atrocity, an affront to logic and an insult the natural order of the
> >>> cosmos and any deity conceived by humankind.
> >>>
> >>> In botany at least, the "name" (which I take to be the basic
> >>> communication handle for a taxon) is conventionally the genus plus
> >>> the
> >>> species epithet (plus the infraspecies rank and the infraspecies
> >>> name,
> >>> if present).  All else is protologue and other metadata (e. s.l.
> >>> s.s,
> >>> taxonomic qualifiers) some of which may be essential for name
> >>> resolution, but metadata nevertheless.  In much communication, the
> >>> name can and does travel in the absense of its metadata; that is not
> >>> to say it is a good or a bad thing, only that it happens.  I am not
> >>> saying thi binominal approach is a good thing, in many respects
> >>> Linnaeus and the genus have a lot to answer for; but it what we have
> >>> been given to work with.
> >>>
> >>> in zoology... well, who can say what evil lurks within... but if
> >>> what
> >>> you say below is right, at least they got it right with the
> >>> authorship... ;)
> >>>
> >>> I think it is a really bad move to attempt to redefine "name" so
> >>> as to
> >>> include the name metadata to achieve some degree of name resolution
> >>> (basically the list of attributes does not end until you have
> >>> almost a
> >>> complete bibliographic citation - is author abbreviation enough? no,
> >>> add the full author surname? no, add the author initials? no, add
> >>> the
> >>> first name? no, add the transferring author? no, add the year of the
> >>> publication? no, add the journal? no, add the article title? no, add
> >>> the type specimen? no, add the... )
> >>>
> >>> That is not to say these strings of the name and selected metadata
> >>> are
> >>> not useful, perhaps even essential, in certain contexts; only that
> >>> we
> >>> should not pretend or declare they are the "name".  They are
> >>> something
> >>> else and we should find another "name" for them.  "Scientific
> >>> name" is
> >>> not good enough as a normal person would interpret this as the latin
> >>> name
> >>>
> >>> Fortunately I think nearly every modern application keeps all the
> >>> bits
> >>> of the name and publication metadata separate in some form, so it is
> >>> just a matter of geekery to glue them together in whatever
> >>> combination
> >>> we might require...
> >>>
> >>> jim
> >>>
> >>> On Fri, Nov 19, 2010 at 9:57 AM,  <Tony.Rees at csiro.au> wrote:
> >>>> Well, that sounds fine to me, however you may note that the ICZN
> >>>> Code at least expressly states that authorship is *not* part of the
> >>>> scientific name:
> >>>>
> >>>> "Article 51. Citation of names of authors.
> >>>>
> >>>> 51.1. Optional use of names of authors. The name of the author does
> >>>> not form part of the name of a taxon and its citation is optional,
> >>>> although customary and often advisable."
> >>>>
> >>>> I vaguely remember this has been discussed before - would anyone
> >>>> care to comment further?
> >>>>
> >>>> Cheers - Tony
> >>>>
> >>>>
> >>>>> -----Original Message-----
> >>>>> From: Markus Döring [mailto:m.doering at mac.com]
> >>>>> Sent: Friday, 19 November 2010 9:49 AM
> >>>>> To: Rees, Tony (CMAR, Hobart); David Remsen
> >>>>> Cc: tdwg-content at lists.tdwg.org List
> >>>>> Subject: Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in
> >>>>> DwC
> >>>>> scientificName: good or bad?
> >>>>>
> >>>>> Sorry if I wasnt clear, but definitely b)
> >>>>> Not all names can be easily reassembled with just the atoms.
> >>>>> Autonyms need
> >>>>> a bit of caution, hybrid formulas surely wont fit into the atoms
> >>>>> and
> >>>>> things like Inula L. (s.str.) or Valeriana officinalis s. str.
> >>>>> wont be
> >>>>> possible either. dwc:scientificName should be the most complete
> >>>>> representation of the full name. The (redundant) atomised parts
> >>>>> are a
> >>>>> recommended nice to have to avoid any name parsing.
> >>>>>
> >>>>> As a consumer this leads to trouble as there is no guarantee that
> >>>>> all
> >>>>> terms exist. But the same problem exists with all of the ID terms
> >>>>> and
> >>>>> their verbatim counterpart. Only additional best practice
> >>>>> guidelines can
> >>>>> make sure we have the most important terms such as taxonRank or
> >>>>> taxonomicStatus available.
> >>>>>
> >>>>> Markus
> >>>>>
> >>>>>
> >>>>> On Nov 18, 2010, at 23:26, Tony.Rees at csiro.au wrote:
> >>>>>
> >>>>>> Just re-sending the message below because it bounced the first
> >>>>>> time.
> >>>>>>
> >>>>>>
> >>>>>> Markus/all,
> >>>>>>
> >>>>>> I guess my point is that (as I understand it) scientificName is a
> >>>>> required field in DwC, so the question is what it should be
> >>>>> populated
> >>>>> with. If it is (e.g.) genus + species epithet + authority, then is
> >>>>> it
> >>>>> beneficial to supply these fields individually / atomised as well,
> >>>>> maybe
> >>>>> with other qualifiers as needed?
> >>>>>>
> >>>>>> Just looking for an example "best practice" here - or maybe it
> >>>>>> exists
> >>>>> somewhere and you can just point to it.
> >>>>>> in other words:
> >>>>>>
> >>>>>> (a)
> >>>>>> <scientificName>Homo sapiens</scientificName>
> >>>>>> <scientificNameAuthorship>Linnaeus, 1758</a>
> >>>>>>
> >>>>>> or (b):
> >>>>>> <scientificName>Homo sapiens Linnaeus, 1758</scientificName>
> >>>>>> <genus>Homo</genus>
> >>>>>> <specificEpithet>sapiens</specificEpithet>
> >>>>>> <scientificNameAuthorship>Linnaeus, 1758</a>
> >>>>>>
> >>>>>> if you get my drift...
> >>>>>>
> >>>>>> Regards  - Tony
> >>>>>>
> >>>>>> Tony Rees
> >>>>>> Manager, Divisional Data Centre,
> >>>>>> CSIRO Marine and Atmospheric Research,
> >>>>>> GPO Box 1538,
> >>>>>> Hobart, Tasmania 7001, Australia
> >>>>>> Ph: 0362 325318 (Int: +61 362 325318)
> >>>>>> Fax: 0362 325000 (Int: +61 362 325000)
> >>>>>> e-mail: Tony.Rees at csiro.au
> >>>>>> Manager, OBIS Australia regional node, http://www.obis.org.au/
> >>>>>> Biodiversity informatics research activities:
> >>>>> http://www.cmar.csiro.au/datacentre/biodiversity.htm
> >>>>>> Personal info:
> >>>>> http://www.fishbase.org/collaborators/collaboratorsummary.cfm?
> >>>>> id=1566
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> tdwg-content mailing list
> >>>>>> tdwg-content at lists.tdwg.org
> >>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >>>>
> >>>> _______________________________________________
> >>>> tdwg-content mailing list
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> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> _________________
> >>> Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~
> >>> http://www.google.com/profiles/jim.croft
> >>> 'A civilized society is one which tolerates eccentricity to the
> >>> point
> >>> of doubtful sanity.'
> >>> - Robert Frost, poet (1874-1963)
> >>>
> >>> Please send URIs, not attachments:
> >>> http://www.gnu.org/philosophy/no-word-attachments.html
> >>> _______________________________________________
> >>> tdwg-content mailing list
> >>> tdwg-content at lists.tdwg.org
> >>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >>>
> >>
> >> ---------------------------------------------------------
> >> Roderic Page
> >> Professor of Taxonomy
> >> Institute of Biodiversity, Animal Health and Comparative Medicine
> >> College of Medical, Veterinary and Life Sciences
> >> Graham Kerr Building
> >> University of Glasgow
> >> Glasgow G12 8QQ, UK
> >>
> >> Email: r.page at bio.gla.ac.uk
> >> Tel: +44 141 330 4778
> >> Fax: +44 141 330 2792
> >> AIM: rodpage1962 at aim.com
> >> Facebook: http://www.facebook.com/profile.php?id=1112517192
> >> Twitter: http://twitter.com/rdmpage
> >> Blog: http://iphylo.blogspot.com
> >> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> tdwg-content mailing list
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> >
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>
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