November 2017 - 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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Darwin Core Hour: Audubon Core and 3D Biodiversity Data - Tuesday 21 November 2017 3 PM EST
by Deborah Paul 03 Dec '17

03 Dec '17

Hello Everyone! Got 3D data and image files? How are you sharing, storing, and managing these media information resources and metadata? Wondering what others are doing to make media, and 3D in particular, more accessible? From the scientific collections perspective, please join us for our upcoming Darwin Core Hour Webinar: Audubon Core and 3D Biodiversity Data: Metadata, Practice, and Unification of Efforts We encourage people to bring or submit questions for discussion section of webinar. https://bit.ly/dwchour-input Date: Tuesday 21 November 2017 Time: 3pm EST, 12pm PST, 5pm ART, 9pm CET, 20:00 UTC Where: http://idigbio.adobeconnect.com/room Abstract: A growing mode of digitization of natural history collection objects is 3D digitization, which includes three main acquisition techniques: surface scanning (structured light or laser scanners), volumetric scanning (microCT or MRI), and photogrammetry (structure from motion). There is now burgeoning interest in and tremendous need for describing 3D data files with standard vocabularies in the interest of promoting broad accessibility and long-term digital preservation. Audubon Core is an existing vocabulary and extension to Darwin Core that is used to describe digital media files representing natural history objects. It is not an entirely new vocabulary with many terms borrowed from Dublin Core, Darwin Core and more. It also intended to describe different kinds of digital data representing different creation methods and file formats. We overview several different 3D data collection modalities specifying the details needed for understanding how 3D data was generated and processed. We investigate the utility of Audubon Core for describing these 3D modalities. Questions we ask are which existing terms can be used for describing new 3D modalities, whether new terms are needed, whether certain 3D modalities need specific terms not applicable to other modalities, what 3D data formats should be emphasized for preservation and access, and how to pursue formally acquiring new terms either through creation of new vocabularies or extending existing ones. Presenters Gary Motz - Chief Information Officer and Assistant Director for Information Services, Indiana Geological and Water Survery Doug Boyer - Assistant Professor, Department of Evolutionary Anthropology, Duke University; MorphoSource Moderator - Holly Little, Informatics Manager, Paleobiology Collections, Smithsonian Relevant links https://terms.tdwg.org/wiki/Audubon_Core_Term_List http://morphosource.org/ Darwin Core Hour Series Abstract: Darwin Core has become a broadly-used standard for biodiversity data sharing since its inception as a standard by the organization Biodiversity Information Standards (TDWG) in 2009. Despite, or because of, its popularity, people trying to use the standard continue to have questions about how to use Darwin Core and associated extensions. This webinar series looks at open questions related to Darwin Core. Though the topic is broad, individual chapters in the series will focus on specific topics to any adequate level of depth. We encourage people to bring or submit questions and to have open discussions in each webinar (https://bit.ly/dwchour-input) See https://github.com/tdwg/dwc-qa/wiki/Webinars for our webinar resources. See you soon! Deborah Paul from iDigBio, and the DwC Hour Team Link to how to get the most out of Adobe Connect https://www.idigbio.org/wiki/index.php/Web_Conferencing Please use headsets for best experience.t -- -- Upcoming iDigBio Events https://www.idigbio.org/calendar -- Deborah Paul, iDigBio Digitization and Workforce Training Specialist iDigBio -- Steering Committee Member, SPNHC Liaison and Member-At-Large, SYNTHESYS3 Representative Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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Audubon Core Maintenance Group
by Steve Baskauf 16 Nov '17

16 Nov '17

Section 2 of the new Vocabulary Maintenance Specification [1] specifies that a TDWG vocabulary standard should be maintained by an interest group charged specifically with the maintenance of that vocabulary. Of our two current vocabulary standards, Darwin Core now has a maintenance interest group. However, a maintenance interest group has not yet been chartered for Audubon Core. The upcoming Darwin Core hour [2] on Audubon Core and 3D Biodiversity Data has provided the impetus to start work on chartering an Audubon Core Maintenance Group. One of the key tasks of this group would be to shepherd requests for changes and additions to Audubon Core. If there are terms that should be added to Audubon Core to describe 3D biodiversity data, the maintenance group needs to be in place to make those additions happen. I have volunteered to work on getting a charter together for the Audubon Core Maintenance Group. If you are interested in serving as a core member of that group, please contact me and copy the group convener, Bob Morris (morris.bob(a)gmail.com) In your email, please give a brief indication of your interests and area(s) of expertise. Steve Baskauf [1] https://github.com/tdwg/vocab/blob/master/vms/maintenance-specification.md#… [2] Tuesday 21 November 2017 http://idigbio.adobeconnect.com/room -- Steven J. Baskauf, Ph.D., Principal Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582 https://my.vanderbilt.edu/baskauf/

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