April 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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DwC Hour #4: Evolution of DwC Terms and Extensions - Tuesday 2 May 2017 5 PM CEST, 11 AM EDT, 10 AM CDT, 3 PM UTC
by Deborah Paul 28 Apr '17

28 Apr '17

Hi TDWG'ers, Darwin Core (DwC) Hour #4 is almost here: Evolution of DwC Terms and Extensions - two extant examples for community input. Go Here for Webinar Details and Meeting Link: https://www.idigbio.org/content/darwin-core-hour-evolution-darwin-core-term… ABSTRACT. Darwin Core Hour #4 shifts focus to understanding how the DwC standard terms and extensions evolve. Community input and implementation drive development of DwC. For this webinar, we selected dwc:preparations, dwc:occurrenceStatus, and dwc:establishmentMeans to show the broader community how the process works. In this way, we highlight the need for outside input - from those using TDWG standards to share biodiversity data. Two presenters, Andrew Bentley and Quentin Groom, invite you to join them and bring your TDWG expertise and insights to current issues surrounding these terms. Introduction by John Wieczorek. Please bring or submit questions for open discussions in each webinar: https://tinyurl.com/zja2muz When: Tuesday 2 May 2017 5 PM CEST, 11 AM EDT, 10 AM CDT, 3 PM UTC Where: https://idigbio.adobeconnect.com/room Please expect this DwC Hour to be 1.5 hours. EXTRAs. 1. Explore the Darwin Core Questions & Answers wiki! https://github.com/tdwg/dwc-qa/wiki - where all Darwin Core Hour (DwC) materials can be found. 2. See which of your questions have been asked and answered so far https://github.com/tdwg/dwc-qa/issues 3. Submit your question / volunteer (yourself or someone) to do a webinar on your darwin core topic: https://tinyurl.com/zja2muz 4. Here's a list of terms for which DwC recommends use of a controlled vocabulary - note many are in the Location class. https://github.com/tdwg/dwc-qa/wiki/Controlled-Vocabularies 5. See what's inside some of the DwC fields that suggest using a controlled vocabulary (data from GBIF, iDigBio, VertNet, and soon ALA): https://github.com/tdwg/dwc-qa/tree/master/data 6. Future DwC Hour webinars coming up feature discussions about the GBIF Integrated Publishing Toolkit (IPT) and Darwin Core, and the locality terms and sharing georeferenced locality data. See you soon! Happy Darwin Core and Data Quality, :-) Deb, et al from the iDigBio Data Mgmt Interest Group and the Darwin Core Hour Team (please kindly excuse cross-postings!) Webinar series brought to you by the iDigBio Data Management Interest Group (DMI). We welcome input for this series from everyone worldwide. We plan to make this happen 1x month. We use Adobe Connect for our webinars. See https://www.idigbio.org/wiki/index.php/Web_Conferencing for hints on best experience (hint: use headsets!) -- -- Upcoming iDigBio Events https://www.idigbio.org/calendar -- Deborah Paul, iDigBio Digitization and Workforce Training 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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3rd Darwin Core Hour: Thousands of Shades for Controlled Vocabularies - Tuesday 4th April, 11AM EDT, 12 noon ART, 3PM UTC
by Deborah Paul 01 Apr '17

01 Apr '17

Hello TDWG'ers, Please join us for the next installment of Darwin Core Hour: Thousands of Shades for “Controlled” Vocabularies, with presenter, Paula Zermoglio. DETAILS for webinar. https://www.idigbio.org/content/darwin-core-hour-thousands-shades-%E2%80%9C… That's this Tuesday 4th April, 11AM EDT, 12 noon ART, 3PM UTC ABSTRACT. In this third chapter in the Darwin Core Hour series we will visit some of the most colorful Darwin Core terms for which the use of *controlled vocabularies* is recommended. First, as a follow up to Chapter 2, we will expose the current content of particular terms as they are published right now via different aggregators. Second, we will try to disentangle the reasons, purposes and chances that lead us to observe this diversity of values in such fields. Then, we will explore the current availability of controlled vocabularies in different disciplines within our community and the initiatives that are addressing the problem from different perspectives. Finally, we will try to understand if there is actually a pot at the end of the rainbow: can we come up with solid, community-built controlled vocabularies? EXTRAs. 1. Explore the Darwin Core Questions & Answers wiki! https://github.com/tdwg/dwc-qa/wiki - where all Darwin Core Hour materials can be found. 2. See which of your questions have been asked and answered so far https://github.com/tdwg/dwc-qa/issues 3. Submit your question / volunteer (yourself or someone) to do a webinar on your darwin core topic: https://tinyurl.com/zja2muz 4. Here's a list of terms for which DwC recommends use of a controlled vocabulary - note many are in the Location class. https://github.com/tdwg/dwc-qa/wiki/Controlled-Vocabularies 5. See what's inside some of the dwc fields that suggest using a controlled vocabulary (data from GBIF, iDigBio, VertNet, and soon ALA): https://github.com/tdwg/dwc-qa/tree/master/data 6. Future DwC Hour webinars coming up in May and June feature discussions about how new dwc:terms and dwc:extensions come into being and another dwc hour on the GBIF Intergrated Publishing Toolkit (IPT) and Darwin Core. Happy Darwin Core and Data Quality, :-) Deb, et al from the iDigBio Data Mgmt Interest Group and the Darwin Core Hour Team (please kindly excuse cross-postings!) Webinar series brought to you by the iDigBio Data Management Interest Group (DMI). We welcome input for this series from everyone worldwide. We plan to make this happen 1x month. We use Adobe Connect for our webinars. See https://www.idigbio.org/wiki/index.php/Web_Conferencing for hints on best experience (hint: use headsets!) -- -- 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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