December 2016 - 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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RDF list of terms as organized in the dwc-assistant?
by Matt Yoder 15 Dec '16

15 Dec '16

Hi All, I was wondering if there is an RDF document like https://github.com/tdwg/dwc/blob/master/rdf/dwcterms.rdf that had something like the dwcattributes:organizedInClass therein such that I could query it to return terms as organized in the dwca-assistant (http://tools.gbif.org/dwca-assistant/)? In other words I want to return all terms under Core::Occurence, Core::Taxon, Core::Extensions::Foo etc. Thanks for your time, Matt

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Polygon Madness! Upcoming iDigBio Webinar Dec 13th 3:00pm to 4:00pm EST 8:00 - 9:00 UTC
by Deborah Paul 13 Dec '16

13 Dec '16

Hi Everyone, Please mark your calendars for the iDigBio Webinar: Polygon Madness! Creating them, using them in research Details: https://www.idigbio.org/content/polygon-madness-creating-them-using-them-re… When: Tuesday, December 13, 2016 - 3:00pm to 4:00pm EST, that's 8:00 - 9:00 UTC AdobeConnect URL: http://idigbio.adobeconnect.com/geotrain At our recent iDigBio-CCBER Georeferencing for Research Use (GRU) short course <https://www.idigbio.org/content/georeferencing-and-visualizing-biodiversity…>, we discussed at some length, the creation of polygons around geospatial coordinates for expressing uncertainty. One of our course goals was to investigate if researchers are using these polygons and how they are using them. If they are not using them, we wanted to understand more about why not. This webinar is a step toward bringing in the broader community to include more researchers in the conversation along with the staff who are often creating these, especially for legacy data. *Webinar:* Polygon Madness! Georeferencing using polygons greatly reduces locality uncertainty. As a use-case, Michael Yost will walk through the protocols and best practices he's developed in drawing polygons around various localities. Join us as we work together on polygon protocols and increase the utility of polygon locality data. If you're someone using these in your research - we need you to attend to share your thoughts and questions. If you're actively involved in creating these as you digitize legacy collections data, please share your insights too! *Presenter: *Michael Yost, /Macrofungi Collection Consortium (MaCC) <https://www.idigbio.org/wiki/index.php/The_Macrofungi_Collection_Consortium> Project Assistant at the Denver Botanic Gardens <http://www.botanicgardens.org/> and active member of the iDigBio GWG <http://www.idigbio.org/wiki/index.php/IDigBio_Working_Groups#Georeferencing…>./ Start Date: Tuesday, December 13, 2016 - 3:00pm to 4:00pm EST, that's 8:00 - 9:00 UTC AdobeConnect URL: http://idigbio.adobeconnect.com/geotrain Polygonally yours, Deb Paul, et al from the GWG and the GRU team PS sorry for cross-posting -- -- Upcoming iDigBio Events https://www.idigbio.org/calendar -- Deborah Paul, iDigBio Digitization and Workforce Training Specialist iDigBio -- Steering Committee Member, SPNHC Liaison, SYNTHESYS3 Representative Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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Final PDF program for TDWG 2016 posted and more
by Kampmeier, Gail E 01 Dec '16

01 Dec '16

The final version (dated 1 Dec 2016) of the PDF program is ready for download, see http://www.tdwg.org/conference2016/#c1803. Updates (but not to the program PDF) will be online https://mbgserv18.mobot.org/ocs/index.php/tdwg/tdwg2016/index and posted at the conference. Note that this version has updated information about buses taking participants to and from campus and other events, as well as many small changes. Additional news: On Tuesday (2-5 PM) and all day Wednesday, Helenia Salazar will be accepting reservations in the CTEC lobby for three of the four “biocursos” sponsored by the Organization for Tropical Studies. Trips to Palo Verde, La Selva, and Osa Peninsula all still have room for participants, but Santa Rosa has been cancelled. The Soltis Center Bioblitz on Thursday afternoon is almost at capacity (110 people). Don’t wait if you were intending on registering for this trip in RegOnline ($20). Our ability to schedule transportation hinges on accurate information in your RegOnline record. Please make sure you have listed the hotel where you will be staying during the week (see link to RegOnline http://www.tdwg.org/conference2016/#c1807) and if you haven’t yet paid your registration, please do so before arrival if possible. Saludos! Gail Co-Program Chair, TDWG2016 #tdwg16

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