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Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad?
by Dmitry Mozzherin 19 Nov '10

19 Nov '10

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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)lists.tdwg.org > >>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content > >>>> > >>>> _______________________________________________ > >>>> tdwg-content mailing list > >>>> tdwg-content(a)lists.tdwg.org > >>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content > >>>> > >>> > >>> > >>> > >>> -- > >>> _________________ > >>> Jim Croft ~ jim.croft(a)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(a)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(a)bio.gla.ac.uk > >> Tel: +44 141 330 4778 > >> Fax: +44 141 330 2792 > >> AIM: rodpage1962(a)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(a)lists.tdwg.org > >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > _______________________________________________ > > tdwg-content mailing list > > tdwg-content(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > _______________________________________________ > > tdwg-content mailing list > > tdwg-content(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content >

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Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad?
by "Markus Döring (GBIF)" 19 Nov '10

19 Nov '10

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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)lists.tdwg.org >>>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >>>>> >>>>> _______________________________________________ >>>>> tdwg-content mailing list >>>>> tdwg-content(a)lists.tdwg.org >>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >>>>> >>>> >>>> >>>> >>>> -- >>>> _________________ >>>> Jim Croft ~ jim.croft(a)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(a)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(a)bio.gla.ac.uk >>> Tel: +44 141 330 4778 >>> Fax: +44 141 330 2792 >>> AIM: rodpage1962(a)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(a)lists.tdwg.org >>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content

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Re: [tdwg-content] [tdwg-tag] Inclusion of authorshipin DwC scientificName: good or bad?
by dipteryx＠freeler.nl 19 Nov '10

19 Nov '10

As I understand it both are allowed. However, it looks to me that putting the whole text string (if cultivars are allowed, these text strings can be lots more involved than discussed so far) in a field titled dwc:scientificName is not handy: it would make more sense to put the scientific name in a field with such a name. Paul van Rijckevorsel -----Oorspronkelijk bericht----- Van: John van Breda [mailto:john.vanbreda@specialfamilies.org] Verzonden: vr 19-11-2010 14:02 Aan: dipteryx(a)freeler.nl; tdwg-content(a)lists.tdwg.org Onderwerp: RE: [tdwg-content] [tdwg-tag] Inclusion of authorshipin DwC scientificName: good or bad? Not at all. I guess the question is whether DwC allows us to transmit a name as it was published/labelled etc, or only a correctly structured name according to the relevant code? From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of dipteryx(a)freeler.nl Sent: 19 November 2010 12:42 To: tdwg-content(a)lists.tdwg.org Subject: Re: [tdwg-content] [tdwg-tag] Inclusion of authorshipin DwC scientificName: good or bad? A botanical name consists of at most three parts (Art 24.1), so the name is Centaurea affinis affinis, although it may not be written so: the correct way to write this is Centaurea affinis var. affinis. Of course it is possible to write Centaurea affinis subsp. affinis var. affinis or to use any textstring whatsoever, but that is not its botanical name. Italics and parentheses are very much Code-specific. Sorry to barge in, Paul van Rijckevorsel Van: tdwg-content-bounces(a)lists.tdwg.org namens John van Breda Verzonden: vr 19-11-2010 13:06 Aan: 'David Remsen (GBIF)'; 'John van Breda' CC: tdwg-content(a)lists.tdwg.org; 'Jim Croft'; '"Markus Döring (GBIF)"' Onderwerp: Re: [tdwg-content] [tdwg-tag] Inclusion of authorshipin DwC scientificName: good or bad? 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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)lists.tdwg.org >>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >>>> >>>> _______________________________________________ >>>> tdwg-content mailing list >>>> tdwg-content(a)lists.tdwg.org >>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >>>> >>> >>> >>> >>> -- >>> _________________ >>> Jim Croft ~ jim.croft(a)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(a)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(a)bio.gla.ac.uk >> Tel: +44 141 330 4778 >> Fax: +44 141 330 2792 >> AIM: rodpage1962(a)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(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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Re: [tdwg-content] [tdwg-tag] Inclusion of authorshipin DwC scientificName: good or bad?
by dipteryx＠freeler.nl 19 Nov '10

19 Nov '10

A botanical name consists of at most three parts (Art 24.1), so the name is Centaurea affinis affinis, although it may not be written so: the correct way to write this is Centaurea affinis var. affinis. Of course it is possible to write Centaurea affinis subsp. affinis var. affinis or to use any textstring whatsoever, but that is not its botanical name. Italics and parentheses are very much Code-specific. Sorry to barge in, Paul van Rijckevorsel Van: tdwg-content-bounces(a)lists.tdwg.org namens John van Breda Verzonden: vr 19-11-2010 13:06 Aan: 'David Remsen (GBIF)'; 'John van Breda' CC: tdwg-content(a)lists.tdwg.org; 'Jim Croft'; '"Markus Döring (GBIF)"' Onderwerp: Re: [tdwg-content] [tdwg-tag] Inclusion of authorshipin DwC scientificName: good or bad? 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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)lists.tdwg.org >>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >>>> >>>> _______________________________________________ >>>> tdwg-content mailing list >>>> tdwg-content(a)lists.tdwg.org >>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >>>> >>> >>> >>> >>> -- >>> _________________ >>> Jim Croft ~ jim.croft(a)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(a)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(a)bio.gla.ac.uk >> Tel: +44 141 330 4778 >> Fax: +44 141 330 2792 >> AIM: rodpage1962(a)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(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad?
by David Remsen (GBIF) 19 Nov '10

19 Nov '10

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(a)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(a)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(a)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(a)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(a)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(a)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(a)lists.tdwg.org >>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >>>> >>>> _______________________________________________ >>>> tdwg-content mailing list >>>> tdwg-content(a)lists.tdwg.org >>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >>>> >>> >>> >>> >>> -- >>> _________________ >>> Jim Croft ~ jim.croft(a)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(a)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(a)bio.gla.ac.uk >> Tel: +44 141 330 4778 >> Fax: +44 141 330 2792 >> AIM: rodpage1962(a)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(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content >

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Re: [tdwg-content] [tdwg-tag] Inclusion of authorship in DwC scientificName: good or bad?
by David Remsen (GBIF) 19 Nov '10

19 Nov '10

Dear John, give it a try! http://gni.globalnames.org/parsers Best, David 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(a)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(a)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(a)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(a)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(a)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(a)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(a)lists.tdwg.org >>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >>>> >>>> _______________________________________________ >>>> tdwg-content mailing list >>>> tdwg-content(a)lists.tdwg.org >>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >>>> >>> >>> >>> >>> -- >>> _________________ >>> Jim Croft ~ jim.croft(a)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(a)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(a)bio.gla.ac.uk >> Tel: +44 141 330 4778 >> Fax: +44 141 330 2792 >> AIM: rodpage1962(a)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(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content >

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Use case for individuals
by Steve Baskauf 17 Nov '10

17 Nov '10

I received this information (unsolicited) from Bruce Kirchoff (with whom I have been collaborating for a number of years) regarding his collection of images from trees in the UNC Greensboro arboretum for use in visual keys: We have got 26 trees recorded with complete sets of images, and herbarium specimens collected in duplicate. One set of specimens will go to Chapel Hill, the other will stay here for teaching purposes. In this case, we have images, herbarium specimens duplicates in two institutions, and the living specimens in the arboretum (the foo that defines itself) that we want to organize under the banner of Individual. I will be archiving Bruce's images at Bioimages and elsewhere using HTTP URI guids. I will be representing the relationship among these resources in RDF. So expect to see functional examples using real resources in the near future. Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

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Why it matters what kind of things we include in the definition of Individual
by Steve Baskauf 17 Nov '10

17 Nov '10

What I think is getting lost in this attempt to define what is and what is not an Individual is that there is a clear and straightforward functional definition of Individual based on what it is intended to do: An Individual serves as a resource relationship node that connects Occurrences to Identifications. (This is stated explicitly in the comment I included with the term definition.) If you don't like the technical language, then look at the diagram: http://bioimages.vanderbilt.edu/pages/token-explicit.gif which shows that there is a many-to-one relationship between Occurrence and Individual, and a one-to-many relationship between Individual and Identification. If you prefer it in layman's language: an Individual can connect many Occurrences to many Identifications. If something that you want to call an Individual can't or doesn't do this, then it shouldn't be an Individual. The purpose why I have asked for this class to be added to DwC is to be able to accomplish the purpose listed above, not to see how many things we can think of for which we have philosophical reasons to think that they should be called an "individual". We gain three clear benefits from being able to create instances of the Individual class: Benefit 1. We can group Occurrences that document the same Individual over time (i.e. resampling). This is exactly the reason why the present term dwc:individualID exists (read the definition at http://rs.tdwg.org/dwc/terms/index.htm#individualID) That function is represented by the triangle on the left side of Individual in the diagram referenced above. Benefit 2. If there are multiple Identifications of an Individual, those identifications automatically are associated to all Occurrences that are associated with the Individual. That function is represented by the triangle on the right side of the diagram. If we connect several tokens to an Individual, those multiple Identifications are automatically associated with all of the tokens as well. Benefit 3. Individuals allow us to do semantic reasoning of a very primitive sort. If an Occurrence A and the token that acts as its evidence are associated with Individual A having Identification A, and if Occurrence B and the token that acts as its evidence are associated with Individual B having Identification B, then if we discover that Individual A is the same as Individual B then we know that Identification B also applies to Occurrence A (and its documenting token) and that Identification A applies to Occurrence B (and its documenting token). Writing it in this abstract way is a bit hard to follow, so I'll illustrate with two examples. In a previous post, I mentioned a living individual (possibly the only one) of Crataegus harbisonii. I have documented the Occurrence of this Individual on 2008-10-31T09:49:29 at 36.07° latitude, -86.88° longitude by the token http://bioimages.vanderbilt.edu/baskauf/70915 (an image) and have applied an Identification of Crataegus harbisonii to that Individual. Ron Lance has also recorded the Occurrence of the same Individual at the same location around 2000 and documented it by propagating it by a cutting which is now a living specimen in the North Carolina Arboretum. If someone examines that living specimen and and applies an Identification of Crataegus somethingelse to the Individual from which it was collected, then I can infer automatically that his/her Identification of Crataegus somethingelse applies to my 2008 Occurrence and its associated image. The person who looked at the living specimen would not need to look at my image for me to know that. Another example happened when a taxonomist was looking at several bark and leaf images for a particular species I had photographed. He wanted to know which flower images that I had taken came from the same tree as particular bark and leaf images. He knew logically that if he could identify the Individual by its flower that by inference that Identification would also apply to the bark image even if he couldn't do the actual identification based on the bark alone. A final application involves Identifications of "duplicates" found in different herbaria. A taxonomist is doing a revision of a genus and borrows specimens of that genus from several herbaria. Specimen A from herbarium A was identified as species A in the genus of interest. Specimen B from herbarium B was identified as species B in the same genus. By careful examination of the label records, the taxonomist is able to determine that the specimens are "duplicates" (i.e. they are from the same Individual). By inference, the taxonomist knows that the identifications of species A and species B apply to both specimen A and specimen B because they are both from the same Individual. In my original thinking about what should constitute an instance of the class Individual, I only allowed actual biological individuals, or small localized populations that were so tightly linked that a taxonomist collecting specimens from it would call them "duplicates". Under that definition of Individual, all three of the benefits listed above would apply. My qualms about applying the term Individual to the various buckets of dead homogeneous and heterogeneous mixtures of organisms stems from loss of benefit number 1 in those cases. Moving subsets of those dead organisms around and putting them into different jars has no aspect of resampling. Sorting and re-assigning individualIDs to the various jars still only involves a single Occurrence, the one in which the trawler collected the original bucket from the ocean. There are clever things we can do with multiple Identifications, but we've basically lost the triangle on the left side of Individual (no benefit #1). My qualms about applying the term Individual to cut up pieces of organisms involves the triangle on the right side of Individual (connecting Individuals to Identifications). If you chop up a fish into 100 pieces of organs, tissues, DNA samples, etc. and call all of those pieces Individuals, there is no point in assigning separate Identifications to all of them. Unless the original fish has had some kind of tricky human intervention like interspecific organ transplants, grafting, or creation of a chimera, it is a foregone conclusion that all of the parts of the individual fish have the same Identification. Assigning them all separate identifications would be a waste of time - no Benefit #2. Finally, applying the term Individual to containers that we know to contain biological individuals that probably differ at lower taxonomic levels causes problems with Benefit #3. Unless one has a way to specify that the Individual he is talking about is the kind of Individual that a taxonomist would take "duplicates" from (i.e. reliably a single taxon at a low level), it becomes difficult to be sure of the accuracy of the type of reasoning that I'd like us to be able to do based on Occurrences and tokens documenting a common Individual. So what I've tried to do here is to explain why I'm opposed to broadening the definition of Individual to include all of the things that people have suggested it should include. If the definition becomes so broad that we loose the benefits that were the reason for establishing the class Individual, then there is no point in having the class at all. I think that if we stick to the definition that I proposed, we can at least get Benefits #1 and #2. With the substitution of "taxon" for "species or lower...", I think to get benefit #3 we are going to need to also have the individualScope term that Rich proposed and it would need to include a value that indicated that the group of biological individuals were restricted to those that a taxonomist would call "duplicates". Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

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class design, generalization, L(O)D
by Bob Morris 16 Nov '10

16 Nov '10

I sent this to tdwg-tag instead of this more appropriate list. My apologies to those who see it twice, along with any replies to it. Jonathan Reese, an employee of the Science Commons and TDWG member (and who knows way more about semantic web than I do) recently sent me this. I copy it here with his permission. Each of the paragraphs seems to me to be germane in different ways to the discussions about what should be an Individual. For those not deep into RDF, for the word "axiom", you could loosely understand "rule", although that term also has technical meaning that is sometimes a little different. Jonathan raises an important use case in the second paragraph, which is data quality control. That's a topic of interest to many, but especially those following the new Annotation Interest Group. Originally, this was part of a discussion we had about my favorite hobby horse, rdfs:domain. He is not on my side. When people who know more than I do about something are skeptical of my arguments about it, I usually suspend disbelief and temporarily adopt their position. Jonathan's first point is pretty much what Paul Murray observed yesterday in response to a question of Kevin Richards. "(a) subclassing is the way in RDFS or OWL you would connect the more specific to the less specific, so that you can apply general theorems to a more specific entity. That is, a well-documented data set would be rendered using classes and properties that were very specific so as to not lose information, and then could be merged with a badly-documented data set by relaxing to more general classes and properties using subclass and subproperty knowledge. (b) axioms (i.e. specificity) are valuable not only for expressing operational and inferential semantics, but also for "sanity checking" e.g. consistency, satisfiability, Clark/Parsia integrity checks ( http://clarkparsia.com/pellet/icv/ ), and similar. Being able to detect ill-formed inputs is incredibly valuable. People talk past one another because there are many distinct use cases for RDF and assumptions are rarely surfaced. For L(O)D, you're interested in making lots of links with little effort. Semantics is the enemy because it drives up costs. For semantic web, on the other hand, you're interested in semantics, i.e. understanding and documenting the import of what's asserted and making a best effort to only assert things that are true, even in the presence of open world assumption and data set extensibility. Semantics is expensive because it requires real thought and often a lot of reverse engineering. People coming from these two places will never be able to get along." ---Jonathan Rees in email to Bob Morris ================ Bob Morris -- -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: morris.bob(a)gmail.com web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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[Re: [tdwg-tag] class design, generalization, L(O)D]
by Steve Baskauf 16 Nov '10

16 Nov '10

I hit reply-all and my response also went to the wrong list. Because I am an RDF/OWL novice, I will not say much about how I think Jonathan/Bob's comments apply to the discussion about the scope of Individual. But I think that the suggestion that there may be stricter and broader uses of an Individual class probably describes the root of the disagreement pretty well. I have a particular, narrow use-case in mind (facilitating resampling and inferring duplicates using some kind of taxonomically homogeneous entity). Rich wants a broader interpretation based on ideas of what an individual means in various contexts. I think this difference in outlook is reflected in this statement from Rich's last response: 'We can argue about the properties and tokens later; first we need to nail down the "essence" of an Individual.' I actually disagree strongly with this statement. I have tried to stay out of the current thread about the future course of the TDWG ontology because it isn't my something that I know much about. But I think I am leaning to the side of those who suggest that we create use cases first and then see how the ontology can be developed to facilitate those use cases. I am actively using the class Individual in RDF way I have defined it in my proposal. I know of at least one other person who plans to do so as well. It is not clear to me what the use case is for doing what Rich wants: combining what I've called the "token" aspect of individuals with the "resampling" aspect. It may be that there is such a use, but I'd like to see how it will work - in particular how it will work in RDF without "breaking" the use that I need for the Individual class. If it is possible to combine the two aspects of individuals, perhaps that might be done in a "lax" definition (using Paul's term) that reflects the "essence" of an individual. Unfortunately, figuring out what the "essence" is of an individual is more difficult than showing how one plans to use the term. Steve Bob Morris wrote: > Jonathan Reese, an employee of the Science Commons and TDWG member > (and who knows way more about semantic web than I do) recently sent me > this. I copy it here with his permission. Each of the paragraphs seems > to me to be germane in different ways to the discussions about what > should be an Individual. For those not deep into RDF, for the word > "axiom", you could loosely understand "rule", although that term also > has technical meaning that is sometimes a little different. Jonathan > raises an important use case in the second paragraph, which is data > quality control. That's a topic of interest to many, but especially > those following the new Annotation Interest Group. Originally, this > was part of a discussion we had about my favorite hobby horse, > rdfs:domain. He is not on my side. When people who know more than I > do about something are skeptical of my arguments about it, I usually > suspend disbelief and temporarily adopt their position. > > Jonathan's first point is pretty much what Paul Murray observed > yesterday in response to a question of Kevin Richards. > > > "(a) subclassing is the way in RDFS or OWL you would connect the more > specific to the less specific, so that you can apply general theorems > to a more specific entity. That is, a well-documented data set would > be rendered using classes and properties that were very specific so as > to not lose information, and then could be merged with a > badly-documented data set by relaxing to more general classes and > properties using subclass and subproperty knowledge. > > (b) axioms (i.e. specificity) are valuable not only for expressing > operational and inferential semantics, but also for "sanity checking" > e.g. consistency, satisfiability, Clark/Parsia integrity checks ( > http://clarkparsia.com/pellet/icv/ ), and similar. Being able to > detect ill-formed inputs is incredibly valuable. > > People talk past one another because there are many distinct use cases > for RDF and assumptions are rarely surfaced. For L(O)D, you're > interested in making lots of links with little effort. Semantics is > the enemy because it drives up costs. For semantic web, on the other > hand, you're interested in semantics, i.e. understanding and > documenting the import of what's asserted and making a best effort to > only assert things that are true, even in the presence of open world > assumption and data set extensibility. Semantics is expensive because > it requires real thought and often a lot of reverse engineering. > People coming from these two places will never be able to get along." > ---Jonathan Rees in email to Bob Morris > ================ > > > Bob Morris > > -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu _______________________________________________ tdwg-tag mailing list tdwg-tag(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tag . -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

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