Looks like a you found an interesting bug John, I will take a look why the letter got changed!<div><br></div><div>Is it allowed to have capitalized 'var. part' of a name? I did not know that<br><div><br></div><div>
Dima<br><br><div class="gmail_quote">On Fri, Nov 19, 2010 at 7:06 AM, John van Breda <span dir="ltr"><<a href="mailto:john.vanbreda@specialfamilies.org">john.vanbreda@specialfamilies.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Thanks David. Interesting results though - if I run Centaurea affinis Friv.<br>
ssp. affinis var. Affinis then the canonical is returned as Centauzea<br>
affinis affinis - note the change of the letter r to z. It also seems to<br>
lose sight of the subspecies variant. It works well on Centaurea apiculata<br>
Ledeb. ssp. adpressa (Ledeb.) Dostál though.<br>
<br>
That looks like it will be a really useful service.<br>
<div class="im"><br>
John<br>
<br>
-----Original Message-----<br>
From: <a href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a><br>
</div><div class="im">[mailto:<a href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a>] On Behalf Of David Remsen<br>
(GBIF)<br>
</div><div><div></div><div class="h5">Sent: 19 November 2010 11:51<br>
To: John van Breda<br>
Cc: <a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>; '"Markus Döring (GBIF)"'; 'Jim Croft'<br>
Subject: Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC<br>
scientificName: good or bad?<br>
<br>
Correction<br>
<br>
<a href="http://gni.globalnames.org/parsers/new" target="_blank">http://gni.globalnames.org/parsers/new</a><br>
<br>
The URI I circulated a moment ago comes AFTER you run a list of names<br>
and doesn't seem friendly.<br>
<br>
DR<br>
<br>
On Nov 19, 2010, at 12:15 PM, John van Breda wrote:<br>
<br>
> I'm coming in a bit late on this conversation so I hope I am not<br>
> repeating<br>
> what has already been said, but botanical names can also have<br>
> authorship at<br>
> both specific and infraspecific levels, e.g.<br>
> Centaurea apiculata Ledeb. ssp. adpressa (Ledeb.) Dostál<br>
><br>
> And to make it even more complex, you can have subspecies variants,<br>
> so 2<br>
> infraspecific levels, e.g.<br>
> Centaurea affinis Friv. ssp. affinis var. Affinis<br>
><br>
> Atomising this properly could be quite complex but necessary to be<br>
> able to<br>
> present the name as it should be written with italics in the correct<br>
> place.<br>
> E.g. in the example above, the author string and rank strings are not<br>
> normally italiced, but the rest of the name is. Unless we can<br>
> include this<br>
> formatting information in dwc:scientificName?<br>
><br>
> Regards<br>
><br>
> John<br>
><br>
> -----Original Message-----<br>
> From: <a href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a><br>
> [mailto:<a href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a>] On Behalf Of "Markus<br>
> Döring<br>
> (GBIF)"<br>
> Sent: 19 November 2010 09:24<br>
> To: Roderic Page<br>
> Cc: <a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>; Jim Croft<br>
> Subject: Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC<br>
> scientificName: good or bad?<br>
><br>
> What Darwin Core offers right now are 2 ways of expressing the name:<br>
><br>
> A) the complete string as dwc:scientificName<br>
> B) the atomised parts:<br>
> genus, subgenus, specificEpithet, infraspecificEpithet,<br>
> verbatimTaxonRank (+taxonRank), scientificNameAuthorship<br>
><br>
> Those 2 options are there to satisfy the different needs we have<br>
> seen in<br>
> this thread - the consumers call for a simple input and the need to<br>
> express<br>
> complex names in their verbatim form.<br>
> Is there really anything we are missing?<br>
><br>
><br>
><br>
> When it comes to how its being used in the wild right now I agree<br>
> with Dima<br>
> that there is a lot of variety out there.<br>
> It would be very, very useful if everyone would always publish both<br>
> options<br>
> in a consistent way.<br>
><br>
> Right now the fulI name can be found in once of these combinations:<br>
> - scientificName<br>
> - scientificName & scientificNameAuthorship<br>
> - scientificName, taxonRank & scientificNameAuthorship<br>
> - scientificName, verbatimTaxonRank & scientificNameAuthorship<br>
> - genus, subgenus, specificEpithet, infraspecificEpithet, taxonRank,<br>
> scientificNameAuthorship<br>
> - genus, subgenus, specificEpithet, infraspecificEpithet,<br>
> verbatimTaxonRank, scientificNameAuthorship<br>
><br>
> To make matters worse the way the authorship is expressed is also<br>
> impressively rich of variants.<br>
> In particular the use of brackets is not always consistent. You find<br>
> things<br>
> like:<br>
><br>
> # regular botanical names with ex authors<br>
> Mycosphaerella eryngii (Fr. ex Duby) Johanson ex Oudem. 1897<br>
><br>
> # original name authors not in brackets, but year is<br>
> Lithobius chibenus Ishii & Tamura (1994)<br>
><br>
> # original name in brackets but year not<br>
> Zophosis persis (Chatanay), 1914<br>
><br>
> # names with imprint years cited<br>
> Ctenotus alacer Storr, 1970 ["1969"]<br>
> Anomalopus truncatus (Peters, 1876 ["1877"])<br>
> Deyeuxia coarctata Kunth, 1815 [1816]<br>
> Proasellus arnautovici (Remy 1932 1941)<br>
><br>
><br>
> On Nov 19, 2010, at 8:50, Roderic Page wrote:<br>
><br>
>> I'm with Jm. For the love of God let's keep things clean and simple.<br>
>> Have a field for the name without any extraneous junk (and by that I<br>
>> include authorship), and have a separate field for the name plus all<br>
>> the extra stuff. Having fields that atomise the name is also useful,<br>
>> but not at the expense of a field with just the name.<br>
>><br>
>> Please, please think of data consumers like me who have to parse this<br>
>> stuff. There is no excuse in this day and age for publishing data<br>
>> that<br>
>> users have to parse before they can do anything sensible with it.<br>
>><br>
>> Regards<br>
>><br>
>> Rod<br>
>><br>
>><br>
>> On 19 Nov 2010, at 07:06, Jim Croft wrote:<br>
>><br>
>>> Including the authors, dates and any thing else (with the<br>
>>> exception of<br>
>>> the infraspecific rank and teh hybrid symbol and in botany) as<br>
>>> part of<br>
>>> a thing called "the name" is an unholy abomination, a lexical<br>
>>> atrocity, an affront to logic and an insult the natural order of the<br>
>>> cosmos and any deity conceived by humankind.<br>
>>><br>
>>> In botany at least, the "name" (which I take to be the basic<br>
>>> communication handle for a taxon) is conventionally the genus plus<br>
>>> the<br>
>>> species epithet (plus the infraspecies rank and the infraspecies<br>
>>> name,<br>
>>> if present). All else is protologue and other metadata (e. s.l.<br>
>>> s.s,<br>
>>> taxonomic qualifiers) some of which may be essential for name<br>
>>> resolution, but metadata nevertheless. In much communication, the<br>
>>> name can and does travel in the absense of its metadata; that is not<br>
>>> to say it is a good or a bad thing, only that it happens. I am not<br>
>>> saying thi binominal approach is a good thing, in many respects<br>
>>> Linnaeus and the genus have a lot to answer for; but it what we have<br>
>>> been given to work with.<br>
>>><br>
>>> in zoology... well, who can say what evil lurks within... but if<br>
>>> what<br>
>>> you say below is right, at least they got it right with the<br>
>>> authorship... ;)<br>
>>><br>
>>> I think it is a really bad move to attempt to redefine "name" so<br>
>>> as to<br>
>>> include the name metadata to achieve some degree of name resolution<br>
>>> (basically the list of attributes does not end until you have<br>
>>> almost a<br>
>>> complete bibliographic citation - is author abbreviation enough? no,<br>
>>> add the full author surname? no, add the author initials? no, add<br>
>>> the<br>
>>> first name? no, add the transferring author? no, add the year of the<br>
>>> publication? no, add the journal? no, add the article title? no, add<br>
>>> the type specimen? no, add the... )<br>
>>><br>
>>> That is not to say these strings of the name and selected metadata<br>
>>> are<br>
>>> not useful, perhaps even essential, in certain contexts; only that<br>
>>> we<br>
>>> should not pretend or declare they are the "name". They are<br>
>>> something<br>
>>> else and we should find another "name" for them. "Scientific<br>
>>> name" is<br>
>>> not good enough as a normal person would interpret this as the latin<br>
>>> name<br>
>>><br>
>>> Fortunately I think nearly every modern application keeps all the<br>
>>> bits<br>
>>> of the name and publication metadata separate in some form, so it is<br>
>>> just a matter of geekery to glue them together in whatever<br>
>>> combination<br>
>>> we might require...<br>
>>><br>
>>> jim<br>
>>><br>
>>> On Fri, Nov 19, 2010 at 9:57 AM, <Tony.Rees@csiro.au> wrote:<br>
>>>> Well, that sounds fine to me, however you may note that the ICZN<br>
>>>> Code at least expressly states that authorship is *not* part of the<br>
>>>> scientific name:<br>
>>>><br>
>>>> "Article 51. Citation of names of authors.<br>
>>>><br>
>>>> 51.1. Optional use of names of authors. The name of the author does<br>
>>>> not form part of the name of a taxon and its citation is optional,<br>
>>>> although customary and often advisable."<br>
>>>><br>
>>>> I vaguely remember this has been discussed before - would anyone<br>
>>>> care to comment further?<br>
>>>><br>
>>>> Cheers - Tony<br>
>>>><br>
>>>><br>
>>>>> -----Original Message-----<br>
>>>>> From: Markus Döring [mailto:<a href="mailto:m.doering@mac.com">m.doering@mac.com</a>]<br>
>>>>> Sent: Friday, 19 November 2010 9:49 AM<br>
>>>>> To: Rees, Tony (CMAR, Hobart); David Remsen<br>
>>>>> Cc: <a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a> List<br>
>>>>> Subject: Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in<br>
>>>>> DwC<br>
>>>>> scientificName: good or bad?<br>
>>>>><br>
>>>>> Sorry if I wasnt clear, but definitely b)<br>
>>>>> Not all names can be easily reassembled with just the atoms.<br>
>>>>> Autonyms need<br>
>>>>> a bit of caution, hybrid formulas surely wont fit into the atoms<br>
>>>>> and<br>
>>>>> things like Inula L. (s.str.) or Valeriana officinalis s. str.<br>
>>>>> wont be<br>
>>>>> possible either. dwc:scientificName should be the most complete<br>
>>>>> representation of the full name. The (redundant) atomised parts<br>
>>>>> are a<br>
>>>>> recommended nice to have to avoid any name parsing.<br>
>>>>><br>
>>>>> As a consumer this leads to trouble as there is no guarantee that<br>
>>>>> all<br>
>>>>> terms exist. But the same problem exists with all of the ID terms<br>
>>>>> and<br>
>>>>> their verbatim counterpart. Only additional best practice<br>
>>>>> guidelines can<br>
>>>>> make sure we have the most important terms such as taxonRank or<br>
>>>>> taxonomicStatus available.<br>
>>>>><br>
>>>>> Markus<br>
>>>>><br>
>>>>><br>
>>>>> On Nov 18, 2010, at 23:26, Tony.Rees@csiro.au wrote:<br>
>>>>><br>
>>>>>> Just re-sending the message below because it bounced the first<br>
>>>>>> time.<br>
>>>>>><br>
>>>>>><br>
>>>>>> Markus/all,<br>
>>>>>><br>
>>>>>> I guess my point is that (as I understand it) scientificName is a<br>
>>>>> required field in DwC, so the question is what it should be<br>
>>>>> populated<br>
>>>>> with. If it is (e.g.) genus + species epithet + authority, then is<br>
>>>>> it<br>
>>>>> beneficial to supply these fields individually / atomised as well,<br>
>>>>> maybe<br>
>>>>> with other qualifiers as needed?<br>
>>>>>><br>
>>>>>> Just looking for an example "best practice" here - or maybe it<br>
>>>>>> exists<br>
>>>>> somewhere and you can just point to it.<br>
>>>>>> in other words:<br>
>>>>>><br>
>>>>>> (a)<br>
>>>>>> <scientificName>Homo sapiens</scientificName><br>
>>>>>> <scientificNameAuthorship>Linnaeus, 1758</a><br>
>>>>>><br>
>>>>>> or (b):<br>
>>>>>> <scientificName>Homo sapiens Linnaeus, 1758</scientificName><br>
>>>>>> <genus>Homo</genus><br>
>>>>>> <specificEpithet>sapiens</specificEpithet><br>
>>>>>> <scientificNameAuthorship>Linnaeus, 1758</a><br>
>>>>>><br>
>>>>>> if you get my drift...<br>
>>>>>><br>
>>>>>> Regards - Tony<br>
>>>>>><br>
>>>>>> Tony Rees<br>
>>>>>> Manager, Divisional Data Centre,<br>
>>>>>> CSIRO Marine and Atmospheric Research,<br>
>>>>>> GPO Box 1538,<br>
>>>>>> Hobart, Tasmania 7001, Australia<br>
>>>>>> Ph: 0362 325318 (Int: +61 362 325318)<br>
>>>>>> Fax: 0362 325000 (Int: +61 362 325000)<br>
>>>>>> e-mail: Tony.Rees@csiro.au<br>
>>>>>> Manager, OBIS Australia regional node, <a href="http://www.obis.org.au/" target="_blank">http://www.obis.org.au/</a><br>
>>>>>> Biodiversity informatics research activities:<br>
>>>>> <a href="http://www.cmar.csiro.au/datacentre/biodiversity.htm" target="_blank">http://www.cmar.csiro.au/datacentre/biodiversity.htm</a><br>
>>>>>> Personal info:<br>
>>>>> <a href="http://www.fishbase.org/collaborators/collaboratorsummary.cfm" target="_blank">http://www.fishbase.org/collaborators/collaboratorsummary.cfm</a>?<br>
>>>>> id=1566<br>
>>>>>><br>
>>>>>> _______________________________________________<br>
>>>>>> tdwg-content mailing list<br>
>>>>>> <a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
>>>>>> <a href="http://lists.tdwg.org/mailman/listinfo/tdwg-content" target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><br>
>>>><br>
>>>> _______________________________________________<br>
>>>> tdwg-content mailing list<br>
>>>> <a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
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>>>><br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>> _________________<br>
>>> Jim Croft ~ <a href="mailto:jim.croft@gmail.com">jim.croft@gmail.com</a> ~ +61-2-62509499 ~<br>
>>> <a href="http://www.google.com/profiles/jim.croft" target="_blank">http://www.google.com/profiles/jim.croft</a><br>
>>> 'A civilized society is one which tolerates eccentricity to the<br>
>>> point<br>
>>> of doubtful sanity.'<br>
>>> - Robert Frost, poet (1874-1963)<br>
>>><br>
>>> Please send URIs, not attachments:<br>
>>> <a href="http://www.gnu.org/philosophy/no-word-attachments.html" target="_blank">http://www.gnu.org/philosophy/no-word-attachments.html</a><br>
>>> _______________________________________________<br>
>>> tdwg-content mailing list<br>
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>>><br>
>><br>
>> ---------------------------------------------------------<br>
>> Roderic Page<br>
>> Professor of Taxonomy<br>
>> Institute of Biodiversity, Animal Health and Comparative Medicine<br>
>> College of Medical, Veterinary and Life Sciences<br>
>> Graham Kerr Building<br>
>> University of Glasgow<br>
>> Glasgow G12 8QQ, UK<br>
>><br>
>> Email: <a href="mailto:r.page@bio.gla.ac.uk">r.page@bio.gla.ac.uk</a><br>
>> Tel: +44 141 330 4778<br>
>> Fax: +44 141 330 2792<br>
>> AIM: <a href="mailto:rodpage1962@aim.com">rodpage1962@aim.com</a><br>
>> Facebook: <a href="http://www.facebook.com/profile.php?id=1112517192" target="_blank">http://www.facebook.com/profile.php?id=1112517192</a><br>
>> Twitter: <a href="http://twitter.com/rdmpage" target="_blank">http://twitter.com/rdmpage</a><br>
>> Blog: <a href="http://iphylo.blogspot.com" target="_blank">http://iphylo.blogspot.com</a><br>
>> Home page: <a href="http://taxonomy.zoology.gla.ac.uk/rod/rod.html" target="_blank">http://taxonomy.zoology.gla.ac.uk/rod/rod.html</a><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> _______________________________________________<br>
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</div></div></blockquote></div><br></div></div>