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
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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
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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
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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@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
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Actually, yes, in botany a specific or infraspecific epithet may be capitalized. These days it is rarely done and very likely it will disallowed within a few decades. It is very unusual to capitalize an epithet such as affinis; capitalization is reserved for nouns and names. So, in a publication dedicated to Sijfert Koorders one may find names such as Millettia Koordersii, deliberately capitalized. Paul -----Oorspronkelijk bericht----- Van: tdwg-content-bounces@lists.tdwg.org namens Dmitry Mozzherin Verzonden: vr 19-11-2010 15:03
Is it allowed to have capitalized 'var. part' of a name? I did not know that
Dima
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dipteryx＠freeler.nl -
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John van Breda