May 2017 - tdwg-content - lists.tdwg.org

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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Announcing Workshops and Symposia for TDWG 2017
by James Macklin 18 May '17

18 May '17

Dear Colleagues, We are excited to announce the list of accepted workshops and symposia at TDWG 2017, viewable here <https://tdwg.github.io/conferences/2017/program/>. Abstract submission, which will be via the Pensoft ARPHA tool, will be available soon. In the meantime, we invite you to begin considering your contributions to this year's meeting. Abstracts are required for all oral presentations (with the exception of “wild ideas”, see below), computer demonstrations, and posters. These categories are described below. Types of Contributions: Symposia or Workshop Presentations The backbone of a TDWG meeting are its symposia and workshops. At TDWG, a symposium is typically a collection of talks, sometimes with a panel or open discussion; a workshop may have talks, but typically encourages more active engagement through training activities, or through facilitated discussion around a key issue. Accepted symposia and workshops are listed here <https://tdwg.github.io/conferences/2017/program/>, along with an indication of whether or not the symposium/workshop is accepting submissions. If you would like to give a talk, you should see if any open workshops/symposia are suitable. Other Oral Presentations If no workshop or symposium is suitable, you can submit your abstract to the "Other Oral Presentation" track. Accepted abstracts will be arranged so that talks on similar subjects are in the same session. Computer demonstrations We will provide an opportunity for live computer demonstrations. Note that rooms for these presentations may have WiFi connections only (not wired), and you may want to have a backup plan should the internet connection not work to your satisfaction. Posters We will provide dedicated space for posters, and at least one dedicated poster session on the agenda. Instructions on poster size will be posted nearer the conference. 5-Minute Wild Ideas/Unconference Towards the end of the conference, we will have a “Wild Ideas” session, with talks selected via an unconference <https://en.wikipedia.org/wiki/Unconference>-style procedure. Abstracts will not be required for these. Best, James Macklin (Local Committee Chair) & Joel Sachs (Program Chair)

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BigDig 2017: High Throughput Digitization for Natural History Collections
by Stanley Blum 08 May '17

08 May '17

Hello TDWG and a special shout-out to TDWG'ers in New Zealand and greater Oceania, Please help the BigDig organizing committee reach a worldwide audience with this call for papers. Deadline: June 30th, 2017. RE: BigDig 2017: High Throughput Digitization for Natural History Collections DETAILS here: http://www.wikicfp.com/cfp/servlet/event.showcfp?eventid= 63603&copyownerid=49294 WHAT is it? A one-day workshop held in conjunction with the 13th IEEE International Conference on eScience (http://escience2017.org.nz/) WHEN: 24—27 October 2017 WHERE: Auckland, New Zealand The BigDig workshop will focus on high-throughput digitization, driven by the keen need to move the world’s physical collections into the digital realm where they are safer from the ravages of time, can be used by larger numbers of scientists and the public, and can contribute in new ways to the study of biodiversity. Topics of interest include but are not limited to: * Digitization technologies for high-throughput 2D and 3D capture of collection objects * Instrumentation strategies and algorithms * Specimen handling, label information capture, OCR, crowd-sourced label transcription, 3D reconstruction * Digitization requirements, metadata, image and 3D fidelity, time and resource constraints, speed * Workflows for high-throughput digitization of natural history collections * Data management for large and perhaps distributed digital collections of such data * Interface requirements, issues, and solutions both for scientific research and for public outreach to extremely large virtual collections * Applications of the resulting data resource to potentially new science and approaches as evidenced by theoretical models, case studies, parallels with existing similar data resources Thank you for your part in extending the reach of the organizing committee with this call for papers. Deadline: June 30th, 2017. With gratitude and in anticipation, Debbie Paul, et al on the Program Committee PS: Since TDWG-SPNHC 2018 is in NZ, this is an opportunity to cross-advertise both events?

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