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

"Markus Döring (GBIF)" mdoering at gbif.org
Fri Nov 19 14:54:53 CET 2010 

We maintain another java based parser at GBIF for public use:
http://tools.gbif.org/nameparser/

Try it:
Centaurea affinis Friv. ssp. affinis var. affinis
Centaurea apiculata Ledeb. ssp. adpressa (Ledeb.) Dostál
Mycosphaerella eryngii (Fr. ex Duby) Johanson ex Oudem. 1897
Zophosis persis (Chatanay), 1914
Lithobius chibenus Ishii & Tamura (1994)
Ctenotus alacer Storr, 1970 ["1969"]
Anomalopus truncatus (Peters, 1876 ["1877"])


Even though 4 parted names are common in botany, only 3 parted names are covered by the code:
http://ibot.sav.sk/icbn/frameset/0028Ch3Sec5a024.htm

This is why our parsers and darwin core atomises to genus, species & infraspecific only and use a single authorship for the lowest combination.

Markus


On Nov 19, 2010, at 13:06, John van Breda 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
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>>>> 
>>> 
>>> ---------------------------------------------------------
>>> 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
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
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>>> tdwg-content at lists.tdwg.org
>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
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