August 2025 - 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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TIME SENSITIVE: 2 Days till TaxonWorks Together 2025!
by Deborah Paul 03 Nov '25

03 Nov '25

Greetings Biodiversity Information Standards TDWG'ers, RE: Just TWO Days till TaxonWorks Together 2025 <https://together.taxonworks.org/> - Registration open and free! May 6 - 8 online. Please remember to share this with colleagues and students not on the TDWG listserv so they don't miss out. Thanks! ‪This year's #TWT2025 offers a wide variety of topics. Perhaps of special interest to the TDWG community: * Building biodiversity informatics tools with the AI-lephant in the room * geoBoundaries: Challenges to curating (and using) global gazetteers - a conversation with Dan Runfola * Stories of (Data) Transition in the Realm of Biodiversity Informatics * Exploring emerging practical informatics needs surrounding the rapidly expanding use of eDNA * Adapting our biodiversity informatics infrastructure to keep pace with the evolution of what we think a taxon is - a conversation with Wayne Maddison * Natural History Collections in TaxonWorks: Entering a Community Consensus Phase Why TaxonWorks as digitization software? Status and vision. Opportunity for questions focusing on digitization functionality. Announcement of *a year-long working group on SpecimenPages*, facilitated by the SFG. * Informatics opportunities integrating field stations and collections, with special reference to the practical needs and opportunities at the Illinois Natural History Survey - a panel with Field Station and Collection Managers: Auriel Fournier, James Lamer, Arianna Kuhn, Enrique Santoyo Brito, and Jamie Minneart-Grote * Why are the Earth's scientific collections important? Perspectives from a catalyzed series of events emerging during COVID 19 - with guests Pam Soltis and Cody Thompson Most sessions are moderated discussions with opportunities for your input. Hear from people that inspire us, and add your voice to the conversation. Check the agenda for more session time and date details <https://together.taxonworks.org/>. We welcome everyone and look forward to your participation and insights. In anticipation, Debbie, for the SFG and TWT2025 /PS -- *please (please) share with your colleagues and students far and wide, thanks!* PPS -- yes there is cross-posting :-)/ -- - Deborah Paul, Biodiversity Informatics Community Liaison - Species File Group (INHS), University of Illinois -- Natural History Collections and Museomics NHCM Editor-in-Chiefhttps://nhcm.pensoft.net -- Biodiversity Information Standards (TDWG) Past Chair 2021-2022 -- Florida State University Courtesy Appointment -- Species File Group and Eventshttps://speciesfilegroup.org

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you are invited to participate in the Open Data Community Survey 2025
by Daryl Hepting 03 Nov '25

03 Nov '25

Dear All, We are writing to you as researchers from the University of Regina in Regina, Canada who are studying open data. We invite you to participate in the Open Data Community Survey 2025 if you use or provide open data or FAIR data or if you are interested in using semantic metadata to improve the usability of your data. The survey is estimated to take 15-20 minutes to complete, and it is available at the following link:https://uregina.eu.qualtrics.com/jfe/form/SV_2ryvDaooieWaAjY Your responses will provide invaluable insights into the state of the open data community in 2025. You may choose to answer as open data user or provider if one of those roles dominates your time or both if they make equal demands of your attention. Please help to improve the power of the survey by sharing this invitation to participate widely within your networks. However, there is no obligation for you to pass along this invitation, and there will be no penalty to you if you do not share it. You can read more about the survey at: https://www2.cs.uregina.ca/~hepting/projects/open-data/community-survey-202… Data from the study will be posted as open data at these locations: * https://<https://www2.cs.uregina.ca/~hepting/projects/open-data/community-survey-202…>www2.cs.uregina.ca/~hepting/projects/open-data/community-survey-2025<https://www2.cs.uregina.ca/~hepting/projects/open-data/community-survey-202…> * https://borealisdata.ca/dataverse/heptingd<https://www2.cs.uregina.ca/~hepting/projects/open-data/community-survey-202…>/ The survey has been approved by the Research Ethics Board at the University of Regina in Regina, Canada. Funding for this survey has been provided by the DDI (Data Documentation Initiative) Alliance, an international collaboration dedicated to developing metadata standards and semantic products for describing social science data, data covering human activity, and other data based on observational methods. Please let us know if you have any questions or concerns. Please note that there are inherent security issues when using email as a communication tool. By default, emails are not encrypted and are vulnerable to interception by outside sources or someone may see that you are involved in this research if you leave your browser open. We will use the phrase “Meeting Reminder” in the subject-line of all email correspondence so you will know the email is from us and recommend you submit any email queries using the same term. Daryl Hepting, Ph.D. daryl.hepting(a)uregina.ca<mailto:daryl.hepting@uregina.ca> Alain Maubert Crotte alain.maubertcrotte(a)uregina.ca<mailto:alain.maubertcrotte@uregina.ca>

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