September 2019 - 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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Proposal to revise Audubon Core Usage guidelines for dc:type and dcterms:type
by Baskauf, Steven James 24 Sep '19

24 Sep '19

In its 2019-08-29 meeting, the Audubon Core Maintenance Group approved moving forward on a proposal to revise the Usage notes for the terms dc:type and dcterms:type in Audubon Core. This email is to announce the beginning of a 30 day public comment period on that proposal. To read and comment on the proposal, see https://github.com/tdwg/ac/issues/144 The public comment period is scheduled to end on 2019-10-24. Steve Baskauf Audubon Core Maintenance Group convener on behalf of the group -- Steven J. Baskauf, Ph.D. Data Science and Data Curation Specialist Jean & Alexander Heard Libraries, Vanderbilt University Nashville, TN 37235, USA Office: Eskind Biomedical Library, EMB 111 Phone: (615) 343-4582 https://my.vanderbilt.edu/baskauf/

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Request for use cases for views controlled vocabularies
by Baskauf, Steven James 23 Sep '19

23 Sep '19

The Views Controlled Vocabularies Task Group has been tasked by the Audubon Core Maintenance Group to develop controlled vocabularies for the terms ac:subjectPart and ac:subjectOrientation. In order to determine the requirements for the controlled vocabularies, the Task Group is collecting use cases from the community. If you have used or would like to use either of these two properties of a media item that describe what is being viewed and how, we would love to have your input. To submit one or more use cases, use the form at https://forms.gle/R8b329g5y12ybT347 . For additional information and to see use case examples, visit this page at the Task Group Github site: https://github.com/tdwg/ac/blob/master/views/use-case-examples.md . If you have questions, please email me at steve.baskauf(a)vanderbilt.edu or any of the other core members listed on the Task Group home page: https://github.com/tdwg/ac/tree/master/views Use cases will be accepted through 2019-11-01. Steve Baskauf on behalf of the Views Controlled Vocabularies Task Group -- Steven J. Baskauf, Ph.D. Data Science and Data Curation Specialist Jean & Alexander Heard Libraries, Vanderbilt University Nashville, TN 37235, USA Office: Eskind Biomedical Library, EMB 111 Phone: (615) 343-4582 https://my.vanderbilt.edu/baskauf/

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Proposal to add the ac:ServiceAccessPoint class to Audubon Core
by Baskauf, Steven James 20 Sep '19

20 Sep '19

In its 2019-08-29 meeting, the Audubon Core Maintenance Group approved moving the proposal to add the class ac:ServiceAccessPoint to public comment. To read about the proposed term and the justification for adding it, and to comment on the proposal, see this issue: https://github.com/tdwg/ac/issues/137 Steve Baskauf Audubon Core Maintenance Group convener on behalf of the group -- Steven J. Baskauf, Ph.D. Data Science and Data Curation Specialist Jean & Alexander Heard Libraries, Vanderbilt University Nashville, TN 37235, USA Office: Eskind Biomedical Library, EMB 111 Phone: (615) 343-4582 https://my.vanderbilt.edu/baskauf/

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Proposal to remove layers property from Audubon Core
by Baskauf, Steven James 18 Sep '19

18 Sep '19

In its 2019-08-29 meeting, the Audubon Core Maintenance Group approved moving forward on a proposal to remove the "layers" property from all terms in Audubon Core. This email is to announce the beginning of a 30 day public comment period on that proposal. To read the proposal, see https://github.com/tdwg/ac/blob/master/historical/remove-layers-proposal-20… To comment on the proposal, make comments on this issue: https://github.com/tdwg/ac/issues/143 Steve Baskauf Audubon Core Maintenance Group convener on behalf of the group -- Steven J. Baskauf, Ph.D. Data Science and Data Curation Specialist Jean & Alexander Heard Libraries, Vanderbilt University Nashville, TN 37235, USA Office: Eskind Biomedical Library, EMB 111 Phone: (615) 343-4582 https://my.vanderbilt.edu/baskauf/

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