March 2017 - 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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Re: [tdwg-content] tdwg-content Digest, Vol 89, Issue 6
by Deborah Paul 14 Mar '17

14 Mar '17

Hi Steve, Matt, et al On 2017-03-14 7:00 AM, tdwg-content-request(a)lists.tdwg.org wrote: > We are now midway through the 30 day public comment period on the SDS and so > far, that issue has not come up. I was recently listening to the recording > of John Wieczorek's nice Darwin Core Hour presentation on controlled > vocabularies and it was apparent to me that the creation of controlled > vocabularies is an issue of interest to many in the community. So I've > written a blog post > (http://baskauf.blogspot.com/2017/03/controlled-values-again.html) that > attempts to explain in non-technical terms how the SDS specifies that > controlled vocabularies should be expressed in machine-readable form. For > those who are interested in the gory details, I've also included at the end > a more detailed explanation of the rationale for specifying that controlled > vocabularies should, in most cases, be described as SKOS concept schemes > rather than ontologies. For those of you interested in the on-going controlled vocabularies discussion, please do come to the next iDigBio Darwin Core Hour, brought to you by the iDigBio Data Mgmt Interest Group. You'll discover a bit more about what's found in some of these 23 fields where dwc suggests use of a cv. Paula Zermoglio presents: Darwin Core Hour: Thousands of shades for “Controlled” Vocabularies <https://www.idigbio.org/content/darwin-core-hour-thousands-shades-%E2%80%9C…>. Having TDWG members present at dwc hours is invaluable - as the broader community in the webinar strives to understand what the related data quality issues are, and what they can do about them at from their vantage point. > If you care about the creation of controlled vocabularies, you should take a > look at this post and create an official comment if there are things you > don't like about the approach taken in the proposed specification. Our > review manager, Dag Endresen, has requested that issues be raised on the > issue tracker athttps://github.com/tdwg/vocab/issues . However, > historically back-and-forth discussion about proposed standards has also > taken place on this list, so I think that responding here for clarification > and discussion would be appropriate prior to submitting an official comment. I'd also like to suggest if you think of a topic for another dwc hour / and you've someone in mind to present (yourself maybe?), please send us your ideas - using the Darwin Core Hour Input Form: https://tinyurl.com/zja2muz Best, Deb, et al in the iDigBio Data Mgmt Interest Group -- -- 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

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Information about how controlled vocabularies would be handled under the draft Standards Documentation Specification
by Steve Baskauf 14 Mar '17

14 Mar '17

At the TDWG meeting in December, I led an informative session describing the main points of the draft Standards Documentation Specification (SDS) and its sister standard, the draft Vocabulary Management Specification. At that session, some participants seem to be taken aback at the prescription by the SDS that controlled vocabularies should be SKOS concept schemes rather than ontologies. There wasn't enough time at the meeting to fully explore that issue and I hoped that it would come up for further discussion during the public comment period. We are now midway through the 30 day public comment period on the SDS and so far, that issue has not come up. I was recently listening to the recording of John Wieczorek's nice Darwin Core Hour presentation on controlled vocabularies and it was apparent to me that the creation of controlled vocabularies is an issue of interest to many in the community. So I've written a blog post (http://baskauf.blogspot.com/2017/03/controlled-values-again.html) that attempts to explain in non-technical terms how the SDS specifies that controlled vocabularies should be expressed in machine-readable form. For those who are interested in the gory details, I've also included at the end a more detailed explanation of the rationale for specifying that controlled vocabularies should, in most cases, be described as SKOS concept schemes rather than ontologies. If you care about the creation of controlled vocabularies, you should take a look at this post and create an official comment if there are things you don't like about the approach taken in the proposed specification. Our review manager, Dag Endresen, has requested that issues be raised on the issue tracker at https://github.com/tdwg/vocab/issues . However, historically back-and-forth discussion about proposed standards has also taken place on this list, so I think that responding here for clarification and discussion would be appropriate prior to submitting an official comment. Steve -- Steven J. Baskauf, Ph.D., 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, fax: (615) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu http://vanderbilt.edu/trees

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2nd Darwin Core Hour Recording, Resources, and Upcoming Events of Interest
by Deborah Paul 08 Mar '17

08 Mar '17

Hi TDWG'ers, Thank you so much to all the TDWG community who added their voices to the Darwin Core Hour yesterday, very rich conversations and community / cross-discipline expertise and experience sharing :-) In case you weren't one of the 90-or-so folks who joined us and you want to hear Darwin Core Hour #2 presentation and discussion about controlled vocabularies, or if you want to share the conversation with your colleagues, here are places where you can go to do that. 1. iDigBio Calendar Announcement for DwC Hour #2 https://www.idigbio.org/content/darwin-core-hour-even-simple-hard has link to the recording. An mp4 version is in-the-works. 2. Explore the Darwin Core Questions & Answers wiki! https://github.com/tdwg/dwc-qa/wiki - where all Darwin Core Hour materials can be found. 3. See what questions have been asked and answered so far https://github.com/tdwg/dwc-qa/issues 4. Submit your question / volunteer (yourself or someone) to do a webinar on your darwin core topic: https://tinyurl.com/zja2muz 5. See what's inside some of the dwc fields that suggest using a controlled vocabulary (from GBIF, iDigBio, VertNet, and soon ALA too): https://github.com/tdwg/dwc-qa/tree/master/data Upcoming Events of Interest. A. The iDigBio Paleo Digitization Interest Group brings a talk by Erica Clites (University of California Museum of Paleontology, Berkeley, CA):**Serving your georeferencing data via data aggregators. Thursday, March 16, 2017 - 3:00pm to 4:00pm EDT. This webinar will define and discuss common Darwin Core terms related to georeferencing and discuss factors to consider when serving your georeferencing data online. If you are currently serving your georeferencing data, come prepared with the list of terms you serve or just bring your questions! https://www.idigbio.org/content/paleo-working-group-webinar-0 B. Our next formal Darwin Core Hour is Tuesday April 4th, 2017 by Paula Zermoglio: Thousands of shades for “Controlled” Vocabularies https://www.idigbio.org/content/darwin-core-hour-thousands-shades-%E2%80%9C… Happy Darwin Core and Data Quality, :-) Deb, et al from the iDigBio Data Mgmt Interest Group and the Darwin Core Hour Team (please excuse cross-postings) -- -- 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

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Fwd: 'Data Quality' Task Group 2 - Tests and Assertions
by Lee Belbin 03 Mar '17

03 Mar '17

Dear TDWG-Content(ed) *Task Group 2 (Tests and Assertions) of the 'Data Quality' Interest Group seek your comments.* A select group of TDWGians (highlighted on the Members worksheet on the link below) have invested time to produce what I am calling a *core suite of standard tests and associated assertions that can be applied to occurrence records*. These tests are to help identify potential occurrence record issues. Why are we doing this? Largely to try to better align Data Publishers/Data Aggregators/Biodiversity Research Infrastructures/Data Custodians, and hopefully anyone who generates occurrence data. Users would appreciate consistency. A practical example: Merging records from say GBIF and the ALA etc would be greatly facilitated if they both applied the same set of tests. As a start and to keep it simple, these tests are based on one or more Darwin Core terms. We realize that tests could be applied to all Darwin Core terms, but we wanted a core set that would cover the significant terms that could be implemented relatively easily by all. The spreadsheet can be found at *https://tinyurl.com/h49zwof*. Note that this spreadsheet contains a series of worksheets. Please start by reviewing the Principles as they provide a context for what has been learnt during the process. The main worksheet is "Tests-current". We have to start somewhere, and this is the start. *PLEASE: Only add comments on the tests/principles to the Comments worksheet, but any additions to KEY references and tools worksheets would also be appreciated.* Comments would also be appreciated by 31/3/2017. Lee Lee Belbin The Atlas of Living Australia Tasmania http://spatial.ala.org.au

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Job opening at the GBIF Secretariat
by Federico Mendez 02 Mar '17

02 Mar '17

Hi everyone, A quick announcement, the GBIF Secretariat is currently seeking applications for a Web Developer, see complete details here: http://www.gbif.org/newsroom/news/web-developer-job-2017 Deadline for applications is Monday, 20 March 2017. Please be aware that the successful candidate will be locally recruited (no-relocation involved), according to the GBIF Staff Rules Please feel free to share this position with your own networks and contacts. Thanks, Federico Mendez fmendez(a)gbif.org<mailto:fmendez@gbif.org> skype: fede.mendez Lead Software Developer

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