December 2013 - tdwg-content

Re: [tdwg-content] If you need something for referring to a population, then it is probably best to do it as a related class
by Nico Franz 05 Jun '25

05 Jun '25

Hello all: I have a few inserted comments, hopefully with some clarifying effect: On 5/4/2011 10:54 AM, Peter DeVries wrote: > Hi Steve, > > I may have overloaded the term specimen to make the explanation easier > to follow. > > A specimen could be an individual or it could be part of an individual. > > To some extent you need to think about how these models will be used. > > If you subscribe to the model that a species is whatever a taxonomists > says it is then it is difficult to make statements like. > > X% of the world's species will be extinct by 2050. > > If you mean a species as defined by the concept documented at this URI > which is supported by these specimens, images, and DNA then you are on > firmer ground. > > Species in the natural world do a pretty good job recognizing those > individuals that are appropriate mates. In other words members of > their own species. > > Are we modeling species or variations in human conceptualizations of > species? > >> Assuming that there was only one individual organism identified >> there is really one one species (or hybrid). > Aaaaaaaaaaaaaah! Please Nico C., don't take this one up! > > > I stick with this. Assuming you don't have a hybrid individual. That > individual is one species. The fact that human may disagree on what > species it is a human issue. > > Again, Are we modeling species or variations in human > conceptualizations of species? NMF: I believe there is a history of biodiversity database engineering that actually led some people, initially in Australia (Greg Whitbread?) and Europe (Berendsohn's group) to place more emphasis on modeling human conceptualizations of taxa. I understand this happened in the late 80s / early 90s. The motivation was, apparently, that no long-term consensus seemed available to model a single and sufficiently widely accepted taxonomy of, say, Central European vascular plant species or mosses. I believe that projects such as the Euro + Med PlantBase (http://www.emplantbase.org/home.html) are examples of the persistence (success?) of this 20+ year old practice. I think this is the kind of background that Steve is referring to. > > Which of these is of primary importance to decision makers and > non-taxonomist biologists? > Part of the problem with various publications relating to ontologies > and taxonomy is that their species models entail a specific > phylogenetic hypothesis. > > In the real world taxa are not as clean as some would like to make > them out to be. > > Each individual is a unique combination of thousands of separate gene > lineages which often do not follow clean monophyletic paths. > > I would argue that most of those who work with species related data > see them as useful typological constructs which in general follow the > biological species model. NMF: The solution of how to properly model things such as species in RDF, OWL (etc.) should ideally accommodate all "species concepts" (BCS, ESC, PSC, GSC, there's dozens), i.e. it should be neutral towards this issue. The examples below are too simple, ignoring for example cases such as pro parte synonymy, or a concept ("species") that appears unique and monophyletic to one author but (vastly) polyphyletic to another. To do an accurate mapping in that latter case (which is not super-common but it's real), I think one would have to come down on saying we're modeling human conceptualizations. They are not just that, so really it's not a strict dichotomy, meaning that by modeling conceptualizations we do not have to say "the species only exist on our heads", or "well, then anything goes". I agree (sheepishly) that it does come down to what the input data look like, and what the expectations are towards just accommodating the user community versus pushing them in a particular direction. Some of this also on p. 47 of this PDF: https://journals.ku.edu/index.php/jbi/article/view/3927/3852 > > /Aedes triseriatus/ owl:sameAs /Ochlerotatus triseriatus/ > > Others seem to see them as phylogenetic end nodes which entail a > specific phylogenetic history. > > /Aedes triseriatus/ distinctFrom /Ochlerotatus triseriatus/ > / > / > If you are primarily interested in understanding issues of ecology, > disease, diversity and conservation the former model is more > appropriate than the later. > > Respectfully, > > - Pete Regards, Nico Nico M. Franz, Ph.D. Assistant Professor Director, UPRM Invertebrate Collection Department of Biology University of Puerto Rico Call Box 9000 Mayagüez, PR 00681-9000 Phone: (787) 832-4040, ext. 3005 Fax: (787) 834-3673 E-mail: nico.franz(a)upr.edu Laboratory website: http://academic.uprm.edu/~franz/ UPRM-INVCOL: http://uprm-invcol-project.tumblr.com/

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New Term Request - typifiedName
by John Wieczorek 14 Jan '14

14 Jan '14

Dear all, This message is to open public commentary on a request for a new term, typifiedName, submitted by Markus Döring to the Darwin Core issue tracker at https://code.google.com/p/darwincore/issues/detail?id=197. The justification given for inclusion of the term is: "Clear separation of the type status and the typified scientific name that is typified by a type specimen, the subject. Looking at how dwc:typeStatus has been used in all of GBIFs specimen data one can see there is the need to express this, but it should better be handled with a term on its own and leave typeStatus for the status of the type only. The term name itself is also used by ABCD: http://wiki.tdwg.org/twiki/bin/view/ABCD/AbcdConcept0603." The proposal is as follows: Definition: The scientific name that is based on the type specimen. Comment: It is recommended to also indicate the typeStatus of the specimen. Refines: Has Domain: Has Range: Replaces: ABCD 2.06: DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignations/NomenclaturalTypeDesignation/TypifiedName

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dcterms:rights, dcterms:accessRights, and dcterms:license in Darwin Core
by John Wieczorek 29 Dec '13

29 Dec '13

Dear all, Bob Morris recently submitted an issue [1] to the Darwin Core code site showing a potential ambiguity in the inclusion from Dublin Core of both dcterms:rights and dcterms:accessRights in the Simple Darwin Core schema [2]. The ambiguity arises from the fact that dcterms:accessRights is actually a subclass of dcterms:rights. Looking at the Darwin Core documentation about the use of these terms, I noticed that dcterms:rights [3] suggests a license ("http://creativecommons.org/licenses/by-sa/3.0/") as an example. I think this example is an inappropriate use for the term and instead is an example of a dcterms:license. I think it would be a good idea to add dcterms:license to the list of terms promoted by Darwin Core, especially after reading Peter Desmet's blog posts [4, 5]. If license was indeed the intent for including dcterms:rights in the first place, then perhaps it can be deprecated, leaving only its subtype dcterms:accessRights. Discussion welcome, so that I know whether to submit an issue for these changes to the Darwin Core. Thanks, John [1] https://code.google.com/p/darwincore/issues/detail?id=196 [2] https://darwincore.googlecode.com/svn/trunk/xsd/tdwg_dwc_simple.xsd [3] http://rs.tdwg.org/dwc/terms/index.htm#dcterms:rights [4] http://peterdesmet.com/posts/illegal-bullfrogs.html [5] http://www.canadensys.net/2012/why-we-should-publish-our-data-under-cc0

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Re: [tdwg-content] New Term Request - typifiedName
by Richard Pyle 04 Dec '13

04 Dec '13

Yes, I understand that as I mentioned. But what about my question regarding the same specimen being used to typify multiple taxa? Rich From: Gregor Hagedorn [mailto:gregor.hagedorn@mfn-berlin.de] Sent: Wednesday, December 04, 2013 7:16 PM To: Richard Pyle Cc: John R. Wieczorek; TDWG Content Mailing List Subject: Re: [tdwg-content] New Term Request - typifiedName I endorse Markus proposal enthusiastically. What Rich writes is appropriate if you use DwC in a structured way, with Identification instances that support a 1:n relation between specimen and identification instances. However, this cannot be assumed for all uses of DwC. Gregor On 4 December 2013 11:51, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Hmmm..... This is the reason that typeStatus was included in the Identification class -- so that it always is associated with both a specimen (manifest as an occurrence), and to a taxon (name) -- to which the specimen is Identified. This is in keeping with what the concept of a "type specimen" really is -- that is, a specimen is not a type inherently, but rather a specimen is *designated* as a type by someone at some time, via an Identification instance. Of course, because DwC classes are not really intended to be used in an ontological sense, and because most Museums put their "typeStatus" field in their specimen table (rather than in an Identification table), I can certainly understand the need for this proposed new term. I guess my main concern/question is: how to deal with specimens that represent types of more than one name? (not common, but not necessarily an Edge-case either) Aloha, Rich > -----Original Message----- > From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content- > bounces(a)lists.tdwg.org] On Behalf Of John Wieczorek > Sent: Wednesday, December 04, 2013 4:13 AM > To: TDWG Content Mailing List > Subject: [tdwg-content] New Term Request - typifiedName > > Dear all, > > This message is to open public commentary on a request for a new term, > typifiedName, submitted by Markus Döring to the Darwin Core issue tracker > at https://code.google.com/p/darwincore/issues/detail?id=197. > The justification given for inclusion of the term is: > > "Clear separation of the type status and the typified scientific name that is > typified by a type specimen, the subject. Looking at how dwc:typeStatus has > been used in all of GBIFs specimen data one can see there is the need to > express this, but it should better be handled with a term on its own and > leave typeStatus for the status of the type only. The term name itself is also > used by ABCD: > http://wiki.tdwg.org/twiki/bin/view/ABCD/AbcdConcept0603." > > The proposal is as follows: > > Definition: > The scientific name that is based on the type specimen. > > Comment: > It is recommended to also indicate the typeStatus of the specimen. > > Refines: > > Has Domain: > > Has Range: > > Replaces: > > ABCD 2.06: > DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignation > s/NomenclaturalTypeDesignation/TypifiedName > _______________________________________________ > 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 -- -- --------------------------------- Dr. Gregor Hagedorn Head of Digital World Museum für Naturkunde Leibniz-Institut für Evolutions- und Biodiversitätsforschung Invalidenstrasse 43, 10115 Berlin +49 (0)30 2093 8576 <tel:%2B49%20%280%2930%202093%208576> (work) +49-(0)30-831 5785 <tel:%2B49-%280%2930-831%205785> (private) gregor.hagedorn(a)mfn-berlin.de http://www.naturkundemuseum-berlin.de http://linkedin.com/in/gregorhagedorn This communication, together with any attachments, is intended only for the person(s) to whom it is addressed. Redistributing or publishing it without permission may be a violation of copyright or privacy rights.

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