October 2014 - 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 19 Nov '25

19 Nov '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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Wrapping up public comment on 204 - 226
by joel sachs 16 Oct '14

16 Oct '14

Hi Everyone, The following is a summary of the comments received since announcing the proposals encapsulated in Issues 204 - 226 [1]. Comment came in two forms - posts to tdwg-content, and comments in the Darwin Core Issue Tracker [2]. Only one issue attracted comment on tdwg-content, and five issues attracted (mostly clarifying) comments in the Tracker. (This is encouraging, since the proposals were the result of a years-long consensus building process.) The issue that was the subject of discussion on this list was Issue 205, the proposal to add a dwc:Organism class. The first comment came from Rob Guralnick, who did not see the need for this new class [3]. In reply, Steve Baskauf pointed out that we already have an Organism class, implied by the existing term dwc:individualID, and that the proposal simply describes what kinds of things could reasonably have their identifier be the value of dwc:individualID. There was concurrence with Steve from Rich Pyle and Bob Morris, with no further comment. The other comments on this issue were related to my suggestion [4] that the proposal be amended to i) remove the reference to OBI in our definition, and ii) to give the new class an opaque identifier. In regards (i), Rich, Bob, and Steve were in favour, and Hilmar opposed. In regards (ii), Bob was in favour, while Rich and Hilmar were initially opposed. After some conversation, however, it seemed acceptable to them that the term be given an opaque identifier, with organism as the label. Eamonn also seemed on board with an opaque identifier. Meanwhile, the Issue Tracker saw the following: Issue 204, the umbrella Issue for all the changes Bob wondered how we might notify those whose DwC Archives would be affected by the proposed changes. Steve and Markus argued that existing DwCAs would not be affected, for reasons they explain in their comments Issue 211, dwc:NomenclaturalChecklist JohnW pointed out that dwctype:NomenclaturalChecklist was to be replaced by dwctype:Nomen, which suggests that the correct label for the new term is dwc:Nomen. Issue 212, dwc:Occurrence I suggested expanding the definition of occurrence to include non-organismal things like genes, rocks, and metagenomic samples. For reasons I explain in my comment, I dont think we need to do this now. Issue 214, dwc:Event Some clarifying remarks from Bob and Steve. Issue 222, organismID Clarification from Steve (and an indication of support from Bob). Issue 226, AssociatedOrganisms Some questions from Bob, answered by Steve. --- If I have mischaracterized anything above, please let me know. Thanks! Joel.

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Audubon Core for STL media type?
by Stoner, Dan 08 Oct '14

08 Oct '14

The STL media type is used to store 3d geometry information (consumable by CAD software and 3D printing systems). iDigBio has one or more providers who are (or will be) generating STL files by scanning (stereolithography?) museum specimens to generate a 3D model. The 3D model is an example of digital media that is related to a physical specimen. I am attempting to determine the proper way to reference this "new" type of media in Audubon Core (dc:format). Wolfram Alpha suggests "application/sla": http://reference.wolfram.com/language/ref/format/STL.html However, other 3d model formats are listed in IANA as "model" types such as "model/x3d-vrml". The STL format is not listed as an IANA Media Type: http://www.iana.org/assignments/media-types/media-types.xhtml Is there a place to see pending types or those that are under future consideration? Any advice or pointers would be appreciated. Dan Stoner iDigBio / ACIS Laboratory University of Florida

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