August 2020 - 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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Request for public comment on Darwin Core proposals
by John Wieczorek 01 Oct '20

01 Oct '20

The Darwin Core Maintenance Group is pleased to announce the opening of a 30 day review period (ending 30 September) and seek your feedback for the following changes to Darwin Core that are of particular interest to those documenting evidence of invasive and introduced species: - Change the definition of establishmentMeans ( https://github.com/tdwg/dwc/issues/235 <https://tdwg.us9.list-manage.com/track/click?u=50f3cc44307841383062ca0d6&id…> ) - Add two new terms: pathway https://github.com/tdwg/dwc/issues/236 <https://tdwg.us9.list-manage.com/track/click?u=50f3cc44307841383062ca0d6&id…>) and degreeOfEstablishment (https://github.com/tdwg/dwc/issues/237 <https://tdwg.us9.list-manage.com/track/click?u=50f3cc44307841383062ca0d6&id…> ) - Add controlled vocabularies to use with these three terms ( https://github.com/tdwg/dwc/issues/257 <https://tdwg.us9.list-manage.com/track/click?u=50f3cc44307841383062ca0d6&id…> , https://github.com/tdwg/dwc/issues/258 <https://tdwg.us9.list-manage.com/track/click?u=50f3cc44307841383062ca0d6&id…> , https://github.com/tdwg/dwc/issues/259 <https://tdwg.us9.list-manage.com/track/click?u=50f3cc44307841383062ca0d6&id…> ) Please leave comments on the issues linked above. If you are unable or prefer not to create GitHub comments, send them to the Maintenance Group convenor at gtuco.btuco(a)gmail.com. They will be added to the issues on your behalf, crediting you as the source. About the Process: Because the Vocabulary Maintenance process is being put into effect publicly for only the second time, and the first time for Darwin Core, it is worthwhile to call out from the TDWG Vocabulary Maintenance Specification (http://rs.tdwg.org/vms/doc/specification/#33-changes-to-vocabulary-terms <https://tdwg.us9.list-manage.com/track/click?u=50f3cc44307841383062ca0d6&id…>) how this works and where we are in the process. "*Because the primary purpose of TDWG vocabularies is to facilitate data sharing, it is necessary to show that multiple parties will benefit from the change. As such, it is a minimum requirement that two independent entities indicate that they desire the change (the demand requirement). Additionally, it is required that there is a consensus within the community that the proposed change will accomplish the desired outcome (the efficacy requirement), and that making the change will not adversely affect the interoperability of existing implementations that depend on the stability of the vocabulary (the stability requirement).*" The *demand requirement* has already been met and documented in the issues. We are now interested in finding consensus in confirming the *efficacy* and *stability requirements*. This brings us to the public review, commencing with this announcement. The steps, from the Specification, are as follows: " *If the maintaining Interest Group determines that the proposed term change is likely to meet the demand, efficacy, and stability requirements, it will conduct a minimum 30 day comment period. The start of the comment period will be announced on the TDWG email list [TDWG-CONTENT]. In an effort to reach consensus, the proposal may be modified based on discussion during the comment period. Consensus is indicated by no dissenting opinion expressed publicly on the mailing list for 30 days from the most recent modification of the proposal. The term change proposal may be modified by its submitter or the Interest Group in an attempt to shape a proposal that can achieve community consensus. A change in the official proposal will trigger the start of a new 30 day period.If the Interest Group believes that a consensus has been reached, the proposal will be presented by the Interest Group to the Executive Committee for a decision.*" We look forward to your participation in this community process.

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Request for public comment on Audubon Core proposals
by Baskauf, Steven James 31 Aug '20

31 Aug '20

The Audubon Core Maintenance Group is advancing six proposals to update terms in the Audubon Core. A 30 day period for public comment is now open. It closes at the end of September. Three of the proposals create controlled vocabularies that were envisioned during the initial formulation of the Audubon Core, but were incomplete when the vocabulary was ratified. Three proposals are for adding new terms to Audubon Core that are important for biodiversity sound descriptions (i.e., metadata for biodiversity sound files). To view the proposals, visit https://github.com/tdwg/ac/milestone/2<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftdwg.us9.…> and view the individual proposal issues and their associated documents. To comment on the proposals, leave comments on the relevant proposal issue. If you are unable to create GitHub comments, send them to the Maintenance Group convener at steve.baskauf(a)vanderbilt.edu <mailto:steve.baskauf@vanderbilt.edu?subject=Audubon%20Core%20Comment> . 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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