November 2020 - 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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Public Review of Chronometric Age Extension to Darwin Core open
by John Wieczorek 10 Feb '21

10 Feb '21

The Darwin Core Maintenance Interest Group ( https://www.tdwg.org/community/dwc/) is pleased to announce that the ChronometricAge Task Group (https://www.tdwg.org/community/esp/chrono/) of the Earth Sciences and Paleontology Interest Group ( https://www.tdwg.org/community/esp/) has prepared a vocabulary enhancement for Darwin Core consisting of a ChronometricAge class and its properties. A minimum 30-day period for public comment is now open (2020-11-21). To view the proposal and/or engage in the review, visit https://github.com/tdwg/chrono/issues/15, which will provide further guidance and the means to comment. If you are unable to create GitHub comments, you can reply to this message or send comments to the ChronometricAge Task Group convenor at gtuco.btuco(a)gmail.com. In the absence of objections or substantive amendment requests, the review will close on 2020-12-21. John Wieczorek Darwin Core Maintenance Interest Group convenor on behalf of the Task Group

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Re: [tdwg-content] Public Review of Chronometric Age Extension to
by Cox, Simon (L&W, Clayton) 24 Nov '20

24 Nov '20

FYI there is an ontology for the geological timescale here https://github.com/CGI-IUGS/timescale-ont and a dataset representing the international chronostratigraphic chart nearby https://github.com/CGI-IUGS/timescale-data The International Commission on Stratigraphy are planning to adopt this as the point-of-truth for the standard geological timescale. This is possibly of overlapping scope with the DWC requirements. ---------------------------------------------------------------------- Message: 1 Date: Sat, 21 Nov 2020 14:51:26 -0300 From: John Wieczorek <tuco(a)berkeley.edu> To: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Subject: [tdwg-content] Public Review of Chronometric Age Extension to Darwin Core open Message-ID: <CAHwKGGeaOoovkWPYd8+Ug=knHVJqcKOeZkBNhUd42VomZ85Bpg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" The Darwin Core Maintenance Interest Group ( https://www.tdwg.org/community/dwc/) is pleased to announce that the ChronometricAge Task Group (https://www.tdwg.org/community/esp/chrono/) of the Earth Sciences and Paleontology Interest Group ( https://www.tdwg.org/community/esp/) has prepared a vocabulary enhancement for Darwin Core consisting of a ChronometricAge class and its properties. A minimum 30-day period for public comment is now open (2020-11-21). To view the proposal and/or engage in the review, visit https://github.com/tdwg/chrono/issues/15, which will provide further guidance and the means to comment. If you are unable to create GitHub comments, you can reply to this message or send comments to the ChronometricAge Task Group convenor at gtuco.btuco(a)gmail.com. In the absence of objections or substantive amendment requests, the review will close on 2020-12-21. John Wieczorek Darwin Core Maintenance Interest Group convenor on behalf of the Task Group

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Inviting You to #TaxonWorks Together 2020 - Nov 30 - Dec 4th
by Deborah Paul 22 Nov '20

22 Nov '20

Greetings TDWG folk, RE: #TaxonWorks Together 2020 If you would like to find out more about TaxonWorks, and get together to contribute your ideas, and maybe even some code, please join us for a variety of events next week (Nov 30 - Dec 4). It's an opportunity to be part of fostering collaboration across software development efforts of our biodiversity informatics communities. Please peruse our plans: Details and to register (it's free), see https://github.com/SpeciesFileGroup/taxonworks_together_2020 <https://github.com/SpeciesFileGroup/taxonworks_together_2020> Do join us for all or at least some of the planned activities. Also feel free to forward to potentially interested parties.In addition, we're hosting the second "TaxonWorks at Nite" session during the week, a very chill session to just hang out with folks thinking in the veins of what we are trying to do. NOTE: if you're keen to install TaxonWorks on your local machine, there's a special session this Tuesday (Nov 24th) devoted to getting that done before next week. See you there! Debbie Paul and Matt Yoder (cc'd) -- - Deborah Paul, Biodiversity Informatics (BI) Community Liaison -/The Species File Group/ https://speciesfilegroup.org/ - University of Illinois -- BI Standards (TDWG) Deputy Chair and (BISS) Managing Editor -- Florida State University Courtesy Appointment -- Upcoming iDigBio Events https://www.idigbio.org/calendar new email: dlpaul(a)illinois.edu

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