February 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/

3 2

1st Darwin Core Hour - 7 February 2017 @ 1 PM EST, 6 PM UTC
by Deborah Paul 28 Feb '17

28 Feb '17

Hello Everyone, You're invited! To: Darwin Core Hour 7 February 2017 @ 1 PM EST, 6 PM UTC Details: https://www.idigbio.org/content/darwin-core-hour-webinar-series Got questions? Get answers! Provide answers! For the best Darwin Core Hour experience, add your input here Darwin Core Hour Form https://goo.gl/forms/YCaJ8zjTaW3n6BKr1 Chapter Abstract In this first webinar in the Darwin Core Hour series, the basics of how Darwin Core functions in the biodiversity community as a dynamic standard will be covered. Topics will include what the standard consists of, how to use it, how it can be changed, sources of information, and where to go for help. Presenter: John Wieczorek Your input: 1) improves Darwin Core documentation (examples, definitions) 2) helps those in the Standards community address gaps and implementation of the standard terms 3) provides a forum for everyone to learn about each others data mapping, data sharing, software needs, standards issues and insights. 4) facilitates higher data quality! Go here for details: https://www.idigbio.org/content/darwin-core-hour-webinar-series In anticipation of our 1st Darwin Core (Happy) Hour, Debbie Paul, et al 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

1 3

Public review for TDWG Vocabulary documentation and maintenance standards
by Dag Endresen 27 Feb '17

27 Feb '17

Hi everyone, A brief reminder to participate in the public review <https://github.com/tdwg/vocab/blob/master/README.md> for the Vocabulary documentation and maintenance standards - as announced with the TDWG Announcements newsletter last week. The Documentation Specification will proscribe the format of human- and machine-readable documents that form TDWG (vocabulary) standards. The Vocabulary Maintenance Specification proscribes the process by which TDWG vocabularies will be modified and amended. https://github.com/tdwg/vocab/blob/master/README.md Please submit any comments, questions, or criticisms as "issues" in the issue tracker. If you would like to register an issue anonymously, please send it via email to the review manager, Dag Endresen <dag.endresen(a)gmail.com?subject=Issue%20with%20Vocabulary%20standards>. Public review will be open at least through March 27th, and may be extended if a valuable discussion is on-going. https://github.com/tdwg/vocab/issues (sorry for cross-posting)

1 0