July 2014 - 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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Proposed changes to Darwin Core
by joel sachs 25 Jul '14

25 Jul '14

Hi Everyone, I’d like to direct everyone’s attention to issues 204 - 226 in the Darwin Core issue tracker [1]. These issues describe proposed changes to the Darwin Core standard, and were entered back in January in follow up to the Documenting Darwin Core workshop held at TDWG 2013. These proposals reflect what the organizers of that workshop believe to be the consensus that was reached during the workshop’s four sessions in Florence. The background for this is that, for some time, a number of TDWGers have been working towards an applicability statement to provide guidance on expressing Darwin Core data using RDF. In the course of this work, it became apparent that the semantics of Darwin Core itself needed a slight re-think, in order to be usable on the semantic web. The goal was to be backward-compatible, i.e. to introduce and re-define terms in a way that does not affect the meaning of existing Darwin Core spreadsheet data, but which provides the semantic grounding necessary for meaningful RDF. I think this goal has, for the most part, been realized. If you have examples to the contrary, please share them. Steve Baskauf provides a good overview of the proposals in Issue 204. Of all of them, only Issue 205 (the introduction of a class to represent the taxonomically homogenous units that are described in Darwin Core occurrence data) was contentious, primarily because we disagreed on a good name for the class. (“We” refers to the ad-hoc group that worked on translating the notes from the workshop into concrete proposals - John Wieczorek, James Macklin, Markus Döring, Rich Pyle, Tim Robertson, Bob Morris, Hilmar Lapp, Steve Baskauf, Gregor Hagedorn, and myself.) I’ve mentioned my own concerns as a comment on that issue. There is one proposal that had the support of the group, but that is not yet entered into the Issue Tracker - the deprecation of dwc:basisOfRecord. The motivation for this proposal is that dwc:basisOfRecord is widely misunderstood and inconsistently used, coupled with the fact that GBIF currently uses basisOfRecord with the semantics of the (to be proposed) dwc:hasEvidence term. However, we have held back on proposing "hasEvidence", as there remain some unresolved issues regarding how it would be used. This will likely be left as future work, perhaps to be tackled at TDWG 2014. Many thanks to all who participated in the workshop, and to all who take the time to review its outcomes. Joel. 1. https://code.google.com/p/darwincore/issues/list ["ID" -> "Sort Down" to see in order]

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You're Invited - Data Management Interest Group - Kickoff Webinar 7 August
by Debbie Paul 20 Jul '14

20 Jul '14

Hello Everyone!, Got data in your database? Have you shared it? Is your data available via one or more other websites? Can you get enhanced, modified, standardized, georeferenced, annotated data from these sites back into your database? Re-integrating data can be challenging for many reasons. A new Data Management Interest Group at iDigBio plans to discuss issues surrounding shared data. We'd like to document the help, information, and infrastructure the community needs in order to re-integrate data. If you need help, please come to this meeting and share what issues you face. If you have ideas for how to help, please join us. *What:* Webinar to kickoff a new iDigBio Data Management Interest Group <https://www.idigbio.org/content/data-management-interest-group-kickoff-webi…> *What format*: A short presentation will be followed by open discussion for all participants. *When:* Thursday 7 August 2014, 1:00 - 2:00 PM EDT *Where: *http://idigbio.adobeconnect.com/datamgmt (nothing to install, use any browser) Headsets are recommended (they help remove echo). *Who: *All are welcome, please invite your colleagues, no registration needed. *Questions?* Please send to any member of the group: Data Management Interest Group <https://www.idigbio.org/wiki/index.php/IDigBio_Working_Groups#Data_Manageme…> See you soon! Deb Paul, et al *Wiki: *https://www.idigbio.org/wiki/index.php/Data_Management_Interest_Group (please excuse cross-postings) -- Upcoming iDigBio Events https://www.idigbio.org/calendar --Deborah Paul, on Twitter @idbdeb iDigBio Technology Specialist Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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