That’s an odd one indeed. It seems we have a random name generator at work!
No, you are correct, the var should not be capitalised. BUT, the point I am trying to make is that this is a real name attached to a real specimen, and as such I ought to be able to transmit this information. I agree, the parsers and the atomised versions of names cannot be expected to handle incorrect naming but I still think there is use for a true verbatim of the name.
And yes I am learning more than I expected about botanical names this afternoon ;)
John
From: dmozzherin@gmail.com [mailto:dmozzherin@gmail.com] On Behalf Of Dmitry Mozzherin
Sent: 19 November 2010 14:03
To: John van Breda
Cc: David Remsen (GBIF); John van Breda; tdwg-content@lists.tdwg.org; Jim Croft; "Markus Döring (GBIF)"
Subject: Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad?
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@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@lists.tdwg.org
[mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of David Remsen
(GBIF)
Sent: 19 November 2010 11:51
To: John van Breda
Cc: tdwg-content@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@lists.tdwg.org
> [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of "Markus
> Döring
> (GBIF)"
> Sent: 19 November 2010 09:24
> To: Roderic Page
> Cc: tdwg-content@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@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@mac.com]
>>>>> Sent: Friday, 19 November 2010 9:49 AM
>>>>> To: Rees, Tony (CMAR, Hobart); David Remsen
>>>>> Cc: tdwg-content@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@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@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@lists.tdwg.org
>>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>>>>
>>>> _______________________________________________
>>>> tdwg-content mailing list
>>>> tdwg-content@lists.tdwg.org
>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>>>>
>>>
>>>
>>>
>>> --
>>> _________________
>>> Jim Croft ~ jim.croft@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@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@bio.gla.ac.uk
>> Tel: +44 141 330 4778
>> Fax: +44 141 330 2792
>> AIM: rodpage1962@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
>> tdwg-content@lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>
> _______________________________________________
> tdwg-content mailing list
> tdwg-content@lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>
> _______________________________________________
> tdwg-content mailing list
> tdwg-content@lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>
_______________________________________________
tdwg-content mailing list
tdwg-content@lists.tdwg.org
http://lists.tdwg.org/mailman/listinfo/tdwg-content
_______________________________________________
tdwg-content mailing list
tdwg-content@lists.tdwg.org
http://lists.tdwg.org/mailman/listinfo/tdwg-content