November 2010 - tdwg-content

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 16 Nov '10

16 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

4 9

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)

3 2

[Re: [tdwg-tag] class design, generalization, L(O)D]
by Steve Baskauf 15 Nov '10

15 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

2 2

Re: [tdwg-content] Relation of GNA to TDWG vocabularies
by Kevin Richards 15 Nov '10

15 Nov '10

'Effective tools' to do X, Y & Z always seem to be on the agenda, but I'm not sure it is the tools that are the hold up. Unfortunately I think it boils down to funding... I'm sure if we had adequate funding to get people together for the required length of time, working on the right stuff etc, etc, then we would make fantastic progress. I'm thinking a really good session with a basic UML tool would be a big step forward. I have got hold of a UML tool and intend to have a go at a core tdwg model. I think it would be great then if we could organise a session on working on this model. Kevin Sent from my HTC ----- Reply message ----- From: "Lee Belbin" <leebelbin(a)gmail.com> Date: Sat, Nov 13, 2010 3:42 pm Subject: [tdwg-content] Relation of GNA to TDWG vocabularies To: "tdwg-content(a)lists.tdwg.org" <tdwg-content(a)lists.tdwg.org> Well stated Stan, but I'd add a third- 3. Effective tool/s for viewing (graph, sub-graph, tables, properties etc.), add/delete/modify with adaptable governance control (e.g., assigned management to sub-graph domains), annotate (with full logging of who did what, when and how...). This is in effect a collaboration tool. Until we have a tool (preferable to tools) that can be intuitive and effective for building, managing and deploying /exporting vocabs or ontologies, we will struggle with this socially and technically tough, but very necessary task. The social issues are the hardest, but an effective collaboration tool would be a big help. A tool that will be readily embraced by #2 (the domain specialists) seems far more important than the tools I've seen so far that are embraced by #1 (e.g. Protégé). That we don't have a TDWG ontology is an increasing worry. Lee Lee Belbin Geospatial Team Leader Atlas of Living Australia -----Original Message----- From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Blum, Stan Sent: Saturday, 13 November 2010 9:43 AM To: tdwg-content(a)lists.tdwg.org Subject: Re: [tdwg-content] Relation of GNA to TDWG vocabularies Progress on the TDWG ontology seems to require: 1) one or more people with good sense of what can be done with ontologies, both in the near-term and long-term; and 2) one or more people who understand the way information is partitioned in this domain and how it could fit together. I think we have a lot of #2, but not many of #1. FYI, we have seed money to bring these categories together. -Stan On 11/12/10 2:25 PM, "Bob Morris" <morris.bob(a)gmail.com> wrote: > On Fri, Nov 12, 2010 at 4:57 PM, Richard Pyle > <deepreef(a)bishopmuseum.org> > wrote: > >> [...] the current status of the TDWG-Ontology efforts. The Google >> Code website seems a bit anemic, > > Ooh, I love that line. I think I'll put it in the script of my next > animation, to be titled: "Alpha and Beta discuss the current status of > of the TDWG-Ontology efforts" > > Thanks for correcting the URL. > > Bob > > > 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) > _______________________________________________ > 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 ________________________________ Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

7 6

Background for the Individual class proposal. 3. Should an Individual also be a Collecting Unit?
by Steve Baskauf 15 Nov '10

15 Nov '10

In the first and second installment of this series, I have tried to show that the class Individual as I have proposed it is a central part of a fully denormalized Darwin Core model. It's connective role allows for one-to-many relationships between itself and both the Occurrence and Identification classes (see http://bioimages.vanderbilt.edu/pages/full-model.jpg). I have also pointed out that in that role, it has very few properties. The reason for this is described in detail on p.26 of my Biodiversity Informatics paper (https://journals.ku.edu/index.php/jbi/article/view/3664), but in summary the only way we can actually find out anything about an individual organism is through some kind of observation or collection, which is exactly what happens in an Occurrence. Thus things that we "know" about Individuals generally are directly or indirectly associated with Occurrences, not with the instances of Individual themselves. Rich has suggested that we should consider whether some properties that are currently properties of Occurrence should be moved into the proposed Individual class. It is good to think about this, because we do want to have an economy of classes and terms (no point in having two classes for something when one would do), and because the mental image that we have about an individual organism does include aspects of both the proposed Individual class and the part of the ASC diagram called "Collecting Unit". There are a number of ways of approaching this problem. The first approach, which is the way the discussion developed on the email list, is to just try moving terms from Occurrence to the proposed Individual class and to see whether that would "work" or not. As the discussion progressed, I began to feel increasingly uncomfortable with this process, but wasn't sure why. After I went back to the ASC diagram, it became clear to me what was the problem was. I believe that the question is really being framed incorrectly. What I have proposed for the class Individual is precisely what I have described in the previous posts: for it to serve as a node connecting Occurrences to Identificaitons. What I think Rich wants to recognize is the section of the ASC model called Collecting Unit and the boxes below it: Unsorted Lot, Lot, Specimen, and Specimen Component (I'm not sure exactly what "Derived Object" is - maybe things like images of specimens?). If I am correct in understanding what Rich wants, then the question boils down to: can or should my proposed class be the same as (or possibly include) the section on the ASC diagram called Collecting Unit. I think that I have a pretty clear idea in my mind what Individual as I have defined it means, so my task has been to try to understand what exactly is a CollectingUnit and what properties should it have. The I can approach the question of congruence with "my" Individual. If all things that we would want to fold within CollectingUnit share properties that can be placed within the Individual class, then they are congruent and should be the same thing. If some or most properties that we want to fit within CollectingUnit don't fit the defined purpose of the Individual class, then they should be two separate classes. Because the ASC model was developed by the museum community, I think that its creators were primarily concerned with handling dead specimens. However, as Rich has correctly pointed out, the distinction between dead and living CollectingUnits is probably artificial. Rather, both living and preserved specimens may be instances of the same class which have a different value for some "live/dead" property (see http://code.google.com/p/darwincore/issues/detail?id=91). So for the moment, I'm assuming that a CollectingUnit can be either living or preserved. The case of preserved specimens is fairly straightforward. The have their origin in a single Occurrence that happens at a single Event (what I called a "resource creation event" in my Biodiversity Informatics paper). Living specimens are more complex. They may originate when the whole organism is collected from the wild and moved to a zoo or botanical garden (John's wildebeest calf). In that case there is a clear "resource creation event" if we call the living specimen a resource that is distinct from the organism when it was in the wild. In some cases, the living specimen is born in captivity, grown from a seed, or propagated vegetatively from a cutting. In that case, there is also a definable event when the living specimen originated. What was really driving me crazy was this: http://bioimages.vanderbilt.edu/vanderbilt/7-314 The Bicentennial oak is a tree that is growing in Vanderbilt's arboretum. It seemed to me that it was a living specimen because it is now a part of a collection of trees (the arboretum). But it is over 230 years old and Vanderbilt itself is only 137 years old. So clearly nobody captured, moved, or planted it to make it a part of the arboretum. For a while I tried to define it out of being a living specimen, but then I realized that the thing that made it different from other old trees that are standing around Nashville is that it has been accessioned. In other words, when the tree was claimed as a part of the arboretum, assigned an identifier (7-314), and added to the arboretum database, it became a living specimen in addition to being just a normal tree. The event of calling the tree a part of the arboretum, assigning it an identifier, and adding it to the arboreutm database is the Occurrence that marks the creation of the thing "living specimen". At that point it can have any attribute that other Occurrences have and it is then capable of serving as evidence for the Occurrence because anybody can examine it at will. The "claimed as a part of the arboretum" part is important, because I can go out into the woods and collect information about a tree there, assign it an identifier, and add it to my database, but that doesn't make it a living specimen because I don't assert that I have any control over it or that I can guarantee anyone that I can verify its status at will. If I band a bird and release it, I have assigned it an identifier and hopefully will be able to track it over time, but I can't claim it is a living specimen because I don't claim to exert control over it. That's different from John's wildebeest calf which is in a pen and be observed at will. It is similar to a maize plant in a field in Iowa which was cultivated by a human, but has no curator who is making sure that it can be found again and that it won't be harvested and ground up into wildebeest food without his or her knowledge. If I think about all of the kinds of things that I would like to put into the spot on the ASC diagram labeled "Collecting Unit" (including things like the Bicentennial Oak that was never "collected" by anybody), the one thing that they all seem to have in common is this aspect of being "accessioned". So I would assert that in a general model, "AccessionedUnit" would be a better name than "CollectingUnit". Some of the terms that I think should come out of Occurrence (such as preparations and disposition) could apply to any AccessionedUnit. So that brings me back to the question of whether this thing that I'm calling AccessionedUnit (which is sitting in the spot on the ASC diagram where Collecting Unit was originally) can or should be considered the same as what I have proposed to be the class dwc:Individual. The decision on this should not be made based on what we "think" an Individual should be, but rather on what we need it to be to fulfill the role that we have assigned it in our model. With that in mind, it might be better for the moment to change the name dwc:Individual to dwc:ResamplingUnitHavingDetermination because that is what it needs to do according to its current definition and location in the model diagram (I'm considering resampling to be the documentation of multiple Occurrences). The question them becomes: should AccessionedUnit be considered the same as ResamplingUnitHavingDetermination because they share the same properties (i.e. are described by the same terms)? To me the answer is clearly "no". It is very likely that an AccessionedUnit will never be associated with more than one Occurrence (i.e. be resampled), particuarly if it is dead and has been put in a museum collection. It is possible that the thing referred to by an AccessionedUnit might be documented by multiple Occurrences if it is alive (like the Bicentennial Oak), but that is not an intrinsic property of an AccessionedUnit in the same way that preparations or disposition would be. On the other hand it is also quite clear that many "ResamplingUnitHavingDetermination"s will never become accessioned. That would include the banded bird, a tree photographed in the forest, or a whale observed swimming in the ocean. The longer I think about this, the more convinced I am that making a distinction between AccessionedUnit and ResamplingUnitHavingDetermination is the best course of action. Having made a decision about this based on functional need and shared properties, it is still helpful for me to try to develop a mental image of what these two things are. In my mind, I imagine the ResamplingUnitHavingDetermination (which I will henceforth return to calling dwc:Individual) to be an entity having a homogeneous taxonomic identity. It has some moment when it came into existance as a living thing (by being born, planted, or founded) although we will never know when that moment was unless an Occurrence happens that allows us to document that Event. The Individual remains an entity as long as it has the potential to be documented as an Occurrence. That doesn't necessarily means that it must be alive. But if it decomposes, or is preserved and put into a collection, it no longer is capable of being resampled (i.e. documented by an Occurrence). Thus a fossil that is dead for a million years and is sitting in some stratum still fits my mental image of an Individual. If it gets chipped out of the rock and put in a museum, there would no longer be any point in documenting another Occurrence for it since there would be no useful Location or GeologicalContext information to be gained from that. A roadside population of herbaceous plants having homogenous taxonomic identity would be an Individual from the first time it was capable of being sampled (when it was founded) and would end being an Individual when it was extirpated by some road construction crew and was no longer capable of being documented by an Occurrence. A wolf pack would be a similar case. My mental image of AccessionedUnit is an entity that comes into existence when some human person or institution takes control of it, assigns it an identifier, and keeps records of it. I think I would never see it as coming to an end. Even if it is lost or destroyed, it would continue to exist as long as the person or institution maintains its record. It would just have dwc:disposition "lost" or "destroyed". It could be a dead, preserved specimen in a jar or glued to a sheet of paper, a living wildebeest calf in a zoo, or even a field sampling plot in a park as long as the park exerts control and ownership over it and maintains records about it. It could not be any wild, free-ranging animal or plant. It could not be roadkill left on the side of the road to decompose. It could not be a photograph of a wildebeest calf in the zoo, or the sound recording of the wildebeest calf's grunt. It COULD be a tissue sample from the wildebeest calf or from the roadkill. The critical thing is that it is a physical artifact originating from a living thing that has been cataloged and placed under human control. I think this is the kind of thing that Rich wanted to be able to define when he wanted to broaden the definition of Individual. For any entity having an origin as a living thing (in my mental image), its status as an Individual is independent of its status as an AccessionedUnit. If the entity is removed and preserved in its entirety (fish killed and put in a jar of formaldehyde), it ceases to exist as a dwc:Individual and begins to exist as an AccessionedUnit. If a branch is removed from a tree or one plant pulled from a roadside population to become specimens, the removed part becomes an AccessionedUnit while the dwc:Individual continues to exist. In the case of the Bicentennial Oak or a permanent sampling plot, the entity simultaneously exists as both an AccessionedUnit and a dwc:Individual. In terms of metadata records, the establishment of any AccessionedUnit is an Occurrence (grouped under the Individual) having a property of recordedBy. Whether or not subsequent Occurrences are possible for the Individual depends on whether the act of creating the AccessionedUnit has rendered subsequent sampling irrelevant. I agree with the point that was made previously that no specific taxonomic level should be placed in the definition of Individual. That would allow for the possibility that Individuals could contain several different lower level taxa as long as the Individual is homogeneous at the taxonomic level at with the determination is applied. I am open to suggestion for how this could be accomplished. Somehow there needs to be a value for a term like "individualScope" that allows one to make the kind of inferences about duplicates that I described previously. Maybe one controlled value for "individualScope" should be "DuplicateLevel" meaning that the Individual is homogeneous in taxonomic identity to the level at which a taxonomist would collect multiple specimens and call them duplicates. That would get us out of the problem of deciding whether the several grass stems we collect and send off to different herbaria are actually the same biological individual or clones connected by underground stems. Other possible levels could be "BiologicalIndividual" for things known to be single biological individuals, and "Heterogeneous" for things that are know or suspect to be mixtures of lower level taxa but for which it is convenient to assign a determination at a higher taxonomic level at which we know the mixture to be homogeneous. For AccessionedUnit, I think there should also be an accessionedUnitScope term. I defer to the museum people on this, but the boxes in the ASC diagram (unsorted lot, lot (presumably homogeneous), specimen (presumably one biological individual), and specimen component) could be a starting point. The "partOf" and "hasPart" properties could be used to related AccessionedUnits that are related to each other. Relating these various levels of AccessionedUnits to levels of Individual above "DuplicateLevel" is going to be tricky, but if people want to do this, I'm sure there is a way to represent the relationships in RDF. THE BOTTOM LINE I believe that the proposed definition for the DwC class Individual should stand as it is (i.e. as a node to connect multiple Occurrences to multiple Identifications). To allow Identifications for Individuals that are homogeneous at higher taxonomic levels, we also need a term like dwc:individualScope. I believe that there needs to be a separate class that represents what I've described here as "AccessionedUnit" which also has some kind of scope property. I am not going to propose a name for this thing or propose what properties belong with it. Rich and the herbarium/museum/botanical garden/zoo people need to decide and propose that. AccessionedUnit then becomes one of several types of evidence that can be used to support an Occurrence, with dctype:StillImage, dctype:Sound, dctype:Text as other possibilities. Darwin Core does not need to define their properties and types since others (MRTG, DCMI) have already done so. We then need two more terms: one to relate the evidence to the Occurrence and one to relate the Occurrence to the evidence (I would suggest "hasEvidence" and "isEvidenceFor" as possibilities). If we can do these things, I think we could say that a general (i.e. denormalized enough to satisfy everyone who is dissatisfied at the present moment) Darwin Core model is "complete" to the "left" of Identification on the http://bioimages.vanderbilt.edu/pages/full-model.jpg diagram. I'm not going to touch the Taxon side right now. Whether or not action is taken on creating a class for what I'm calling "AccessionedUnit", there is no reason to hold up action on my Individual class proposal if people agree with the points I've made here. 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

5 13

Ontology
by Lee Belbin 14 Nov '10

14 Nov '10

Re (0) - fair point Roger, but as I said (implied maybe) in my last post, surely the most significant use case is the harmonization of old and new TDWG standards?! Your 'stool' analogy is currently missing at least one leg. Lee Lee Belbin Geospatial Team Leader Atlas of Living Australia

3 2

Relation of GNA to TDWG vocabularies
by Bob Morris 13 Nov '10

13 Nov '10

What will be the relationship of the GNA to the TDWG ontologies now managed at http://code.google.com/p/tdwg-ontology/source/ (or at least to those parts concerned with names) ? Thanks Bob -- 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)

5 8