April 2020 - 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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Darwin Core Hour + 2BBQs: Imagining a global gazetteer of georeferences
by Paula Zermoglio 30 Apr '20

30 Apr '20

A new *Darwin Core (DwC) Hour + 2BBQs!* are almost here: *Imagining a global gazetteer of georeferences* [image: Promotion_v2.jpg] This Darwin Core Hour will consist of a 1hs Webinar and two 2hs BBQ sessions. Please see Webinar and BBQs Details and Meeting Links at https://www.idigbio.org/content/darwin-core-hour-2-bbqs-imagining-global-ga… *Abstract:* We want our georeferencing to be just right: complete, as accurate as possible, and usable for research. However, it takes a great effort and resources to do so, right? Although the majority of the records shared online are not georeferenced, we have invested a huge, collective effort already; there ARE a lot of georeferenced locations already published. In GBIF, for example, there are >54M unique location strings that are georeferenced, affecting >530M occurrence records. We know that many collection/observation sites tend to be repeated across institutions and even taxa. Could we take advantage of all the effort already invested by the community? Could we use those georeferences to complete records that do not have them? The answer is: (probably) yes, and it would be awesome! In this Darwin Core Hour and BBQ we will present and discuss the idea of building a global gazetteer of georeferenced localities for everyone to use. When: 1. *Darwin Core Hour Time (~1 Hour **13:00 to 14:00 UTC)*: 9:00 AM EDT, 10:00 AM ART, 14:00 BST, 15:00 CEST, 13:00 GMT Click for your local time <https://www.timeanddate.com/worldclock/fixedtime.html?iso=20200504T1300> . 2. *Darwin Core Hour BBQ 1* (Monday 4 May 2020, 14:00 to 16:00 UTC) 3. *Darwin Core Hour BBQ 2* (Thursday 7 May 2020, 20:00-22:00 UTC <http://www.timeanddate.com/worldclock/fixedtime.html?iso=20200507T2000>) 4:00 PM EDT, 5:00 PM ART, 9:00 PM BST, 10:00 PM CEST, 20:00 GMT EXTRAS: - Explore the Darwin Core Questions & Answers wiki: https://github.com/tdwg/dwc-qa/wiki - See which of your questions have been asked and answered so far: https://github.com/tdwg/dwc-qa/issues - Submit your question / volunteer (yourself or someone) to do a webinar on a darwin core topic: https://tinyurl.com/zja2muz Happy Darwin Core and Data Quality, and hope to see you soon! Paula Zermoglio, et al. from the Darwin Core Hour Team (please kindly excuse cross-postings!)

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Your Part In a Pursuit of a Worldwide Collection Catalogue
by Deborah Paul 19 Apr '20

19 Apr '20

Hi TDWG folks, RE: Your Part In a Pursuit of a Worldwide Collection Catalogue Some of you work with / in collections, or know people that do, or support gathering, using and discovery of bio/geo-collections data. Please participate in this event (see next) and encourage your colleagues (FB, Twitter, email, etc). Thanks! Please note that at least some of the content is available in Spanish, Chinese (simplified), and French in an effort to make it easier for more folks to participate. Español: Adelantando el Catálogo de Colecciones de Historia Natural del Mundo 13 <https://urldefense.com/v3/__https://discourse.gbif.org/t/adelantando-el-cat…> Français: Faire avancer le Catalogue des Collections d’Histoire Naturelle du Monde <https://urldefense.com/v3/__https://discourse.gbif.org/t/progressant-le-cat…> 简体中文: 建立《全球自然历史馆藏名录》 <https://urldefense.com/v3/__https://discourse.gbif.org/t/topic/2039__;!!PhO…> Right now (through April 27th) you have a unique opportunity to add your voice to an online consultation about Advancing the Catalogue of the World’s Natural History Collections. Please help to capture the value of collections and your insights about potential for them as well that will help shape a new online resource. Please start here: https://discourse.gbif.org/t/advancing-the-catalogue-of-the-worlds-natural-… A few example Technical and Information questions that need your experience and insights: * Would the collections community benefit from a comprehensive directory of all natural history collections? * Who would make use of such a directory? * How should ownership and access control for collection records be managed? * What interfaces and APIs are required to maximise access to the collection catalogue? * What is the best way to include these communities as part of an interconnected solution? * Is there a role for content to be created and improved by a wider audience (e.g. through Wikidata)? * What is required to ensure that this meets the needs of collections and is fully adopted and owned by the collections community? * What challenges need to be addressed to minimise duplication of content and effort within an integrated catalogue? * How can the catalogue best support diverse user communities, including speakers of different languages? * How should appropriate editors be recognised and validated? * What do these communities require to be able to carry out their work efficiently and support their collections? * What present or future requirements are there for interfaces directly between CMS platforms and the collection catalogue? * Are there special opportunities that should be considered? * Could CMS platforms become a source of metadata for institutional collections within a global catalogue? * Which existing tools, databases and websites can help to mobilise and maintain collection records? * Is it possible to identify additional tools or pathways that need to be developed or supported Please share this call with your colleagues too so that input can truly be worldwide and cross-discipline. We're very much looking forward to talking with you in the forum (at GBIF) where the questions are posted. We are waiting for you. In anticipation, from Deb, on behalf of the consultation team: Donald Hobern, Alex Asase, Quentin Groom, Maofang Luo, Deborah Paul, Tim Robertson, Patrick Semal, Barbara Thiers, Matt Woodburn, Eliza Zschuschen -- -- Upcoming iDigBio Events https://www.idigbio.org/calendar -- Deborah Paul, iDigBio Digitization and Workforce Development Manager iDigBio -- Steering Committee Member SPNHC Liaison, Member-At-Large and Member International Relations Committee ICEDIG External Advisory Board Member https://icedig.eu/ Vice Chair, Biodiversity Information Standards Organisation (TDWG)(2019-2021) Managing Editor, Biodiversity Information Science and Standards (BISS) https://biss.pensoft.net/board/ Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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Darwin Core Hour: BioCASe Provider Software - the Hands-on/Demo Session
by Deborah Paul 14 Apr '20

14 Apr '20

Hello TDWG Family, RE: Darwin Core Hour Topic: BioCASe Provider Software - the Hands-on/Demo Session <https://www.idigbio.org/content/darwin-core-hour-biocase-provider-software-…> BioCASe Provider Software and ABCD: A Universal Approach for Biodiversity Collection Data Date: Thursday, 16 April 2020 Where: https://fsu.zoom.us/j/962488863 Time (1 Hour): 11 AM (EDT), 16:00 CET, 17:00 CEST, 15:00 GMT Find your time here: Thursday, April 16, 2020 at 15:00:00 <https://www.timeanddate.com/worldclock/fixedtime.html?iso=20200416T1500> *Presenter: *Jörg Holetschek <https://www.bgbm.org/en/staff/jorg-holetschek>, Biodiversity Data Networks Coordinator, Botanic Garden & Botanical Museum Berlin-Dahlem (BGBM), joined by colleagues Gabi Dröge <https://www.bgbm.org/en/staff/gabriele-droge>, and David Fichtmüller <https://www.bgbm.org/en/staff/david-fichtmueller>. *Moderator*: Erica Krimmel, from the Darwin Core Hour Team The most recent webinar of the DarwinCore Hour series <https://github.com/tdwg/dwc-qa/wiki/Webinars#chapter15> provided an introduction to the BioCASe Provider Software <https://www.biocase.org/> and the Access to Biological Collections Data standard <https://abcd.tdwg.org/> (ABCD). */This follow-up seminar/* will show this tool in action: After installing BioCASe as a Docker container we will connect it to a small sample database, create the mapping for ABCD and show how a BioCASe installation can be tested, debugged, and/used to query datasets./ The webinar is intended for a non-technical audience, only for the first part (installing the software from a Docker image) some knowledge about the Docker <https://www.docker.com/> virtualization platform is advantageous. *Related Links* BioCASe Provider Software <https://www.biocase.org/products/provider_software> BioCASe Provider Software Wiki <https://wiki.bgbm.org/bps> ABCD XML Primer <https://abcd.tdwg.org/xml/documentation/primer/2.06/> TDWG ABCD Standard <https://www.tdwg.org/standards/abcd/> and note a new group working on merging ABCD and Darwin Core And ... Past Darwin Core Hour Webinars <https://github.com/tdwg/dwc-qa/wiki/Webinars> Submit your question <http://bit.ly/dwchour-input> Contribute an answer <https://github.com/tdwg/dwc-qa/issues> - please share your expertise and experience! See questions-answered-so-far <https://github.com/tdwg/dwc-qa/wiki> on the Darwin Core Q & A site See you Thursday! The Darwin Core Hour Team PS. Past Darwin Core Hour Webinars <https://github.com/tdwg/dwc-qa/wiki/Webinars> Submit your question <http://bit.ly/dwchour-input> Contribute an answer <https://github.com/tdwg/dwc-qa/issues> - please share your expertise and experience! See questions-answered-so-far <https://github.com/tdwg/dwc-qa/wiki> on the Darwin Core Q & A site -- -- Upcoming iDigBio Events https://www.idigbio.org/calendar -- Deborah Paul, iDigBio Digitization and Workforce Development Manager iDigBio -- Steering Committee Member SPNHC Liaison, Member-At-Large and Member International Relations Committee ICEDIG External Advisory Board Member https://icedig.eu/ Vice Chair, Biodiversity Information Standards Organisation (TDWG)(2019-2021) Managing Editor, Biodiversity Information Science and Standards (BISS) https://biss.pensoft.net/board/ Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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