November 2016 - 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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RDF list of terms as organized in the dwc-assistant?
by Matt Yoder 15 Dec '16

15 Dec '16

Hi All, I was wondering if there is an RDF document like https://github.com/tdwg/dwc/blob/master/rdf/dwcterms.rdf that had something like the dwcattributes:organizedInClass therein such that I could query it to return terms as organized in the dwca-assistant (http://tools.gbif.org/dwca-assistant/)? In other words I want to return all terms under Core::Occurence, Core::Taxon, Core::Extensions::Foo etc. Thanks for your time, Matt

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Polygon Madness! Upcoming iDigBio Webinar Dec 13th 3:00pm to 4:00pm EST 8:00 - 9:00 UTC
by Deborah Paul 12 Dec '16

12 Dec '16

Hi Everyone, Please mark your calendars for the iDigBio Webinar: Polygon Madness! Creating them, using them in research Details: https://www.idigbio.org/content/polygon-madness-creating-them-using-them-re… When: Tuesday, December 13, 2016 - 3:00pm to 4:00pm EST, that's 8:00 - 9:00 UTC AdobeConnect URL: http://idigbio.adobeconnect.com/geotrain At our recent iDigBio-CCBER Georeferencing for Research Use (GRU) short course <https://www.idigbio.org/content/georeferencing-and-visualizing-biodiversity…>, we discussed at some length, the creation of polygons around geospatial coordinates for expressing uncertainty. One of our course goals was to investigate if researchers are using these polygons and how they are using them. If they are not using them, we wanted to understand more about why not. This webinar is a step toward bringing in the broader community to include more researchers in the conversation along with the staff who are often creating these, especially for legacy data. *Webinar:* Polygon Madness! Georeferencing using polygons greatly reduces locality uncertainty. As a use-case, Michael Yost will walk through the protocols and best practices he's developed in drawing polygons around various localities. Join us as we work together on polygon protocols and increase the utility of polygon locality data. If you're someone using these in your research - we need you to attend to share your thoughts and questions. If you're actively involved in creating these as you digitize legacy collections data, please share your insights too! *Presenter: *Michael Yost, /Macrofungi Collection Consortium (MaCC) <https://www.idigbio.org/wiki/index.php/The_Macrofungi_Collection_Consortium> Project Assistant at the Denver Botanic Gardens <http://www.botanicgardens.org/> and active member of the iDigBio GWG <http://www.idigbio.org/wiki/index.php/IDigBio_Working_Groups#Georeferencing…>./ Start Date: Tuesday, December 13, 2016 - 3:00pm to 4:00pm EST, that's 8:00 - 9:00 UTC AdobeConnect URL: http://idigbio.adobeconnect.com/geotrain Polygonally yours, Deb Paul, et al from the GWG and the GRU team PS sorry for cross-posting -- -- 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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TDWG2016 Program PDF & moderators
by Kampmeier, Gail E 07 Nov '16

07 Nov '16

A full program PDF has now been posted (latest 6 Nov 2016) for TDWG2016 in Costa Rica https://mbgserv18.mobot.org/ocs/index.php/tdwg/tdwg2016/schedConf/program (latest printable program updates will always be available at this link). We are searching for non-student moderators for three of the contributed paper sessions, C02 (Thursday morning, Inventories), C04 (Friday morning; Catalogs, Checklists, Collections) and C05 (Friday morning; Data Gaps, Trust, Acquisition, Access). Moderators are responsible for keeping the sessions on time. Symposium and workshop organizers will be responsible for this in their own sessions. This year all talks in parallel sessions are allowed 15 minutes, which includes changing of speakers and questions. Speakers are asked to be mindful of these constraints. If you are attending TDWG 2016 and interested in being added to the next version of the program as a moderator, please email me as soon as possible, for which session you are interested in moderating. Hasta pronto en Costa Rica! Gail Gail Kampmeier Co-Program Chair, TDWG 2016

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sample Darwin Core Archives of various flavors
by Steve Baskauf 06 Nov '16

06 Nov '16

I have been playing around with turning Darwin Core Archives into RDF [1] and would like to extend my experiments to attempting to integrate data from archives that have very different core files. I have played with the dwcaMolluscsAndorra.zip Occurrence archive mentioned in Annex 3 of the DwC-A How-To Guide [2], but the Whales-DWC-A.zip file isn't available any more (I guess because of the demise of Google Code). A little bit of Google searching failed to turn up additional obvious example files. If anyone would be interested in making DwC-A archives available to me, I'd appreciate it. I'm particularly interested in archives that have cores other than Occurrence (although an Occurrence archive that has more complex data, including extensions, than the mollusc example would be welcome). If there are any MaterialSample or Event core arcives, that would be particularly interesting. Preferably, I'd like to have access to archives that contain publicly available data, since I'm likely to blog about the outcome and potentially use the data in examples. If there are publicly available archives downloadable via a URL, you can reply to the list - otherwise let me know how I could access your example. Thanks in advance for your help! Steve Baskauf [1] http://baskauf.blogspot.com/2016/10/guid-o-matic-meets-darwin-core-archives… [2] http://www.gbif.org/resource/80636 -- 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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TDWG 2016 Bioblitz - making it happen
by joel sachs 04 Nov '16

04 Nov '16

Hi Everyone, We are organizing a bioblitz-like activity at TDWG this year. Rob Stevenson has volunteered to coordinate. Over the course of the week, meeting participants will be encouraged both to post ad hoc observations, and to lead or attend organized observing sessions (e.g. birding outings, moth lighting evenings, etc.). This will culminate in a visit to the Soltis Centre [1], which the organizing committee has arranged for Thursday afternoon. One goal is to finish the meeting with a nice "biodiversity snapshot of TDWG 2016". Another is to shepherd the data into GBIF. Here are some details, and some requests: i. We will create an iNaturalist project for the bioblitz, and encourage the use of iNaturalist to make observations. You can browse through some iNaturalist-based bioblitzes at http://www.inaturalist.org/pages/bioblitz+guide. It's straightforward to browse by taxon or by observer, and by observations for which help with identification has been requested. ii. eBird and Pl@ntNet are also great apps, and we will also support (in the sense described below) their use for recording observations. Steve Kelling (eBird) , and Pierre Bonnet (Pl@ntNet), are participating in the meeting and even though iNaturalist co-director Scott Loarie can not be with us, he has agreed to help us on line. Pl@ntNet's Central American project is not yet public, but Pierre has offered to give us access. iii. It would be great to have a data team, similar to the one we put together in Woods Hole in 2010, that interacts with the APIs of the observation apps to harvest, integrate, and present/visualize the data. One of the purposes of this exercise will be to gain some insight regarding citizen science app interoperability. REQUEST 1: Would anyone like to volunteer for the data team? iv. Rob has compiled a list of taxa and associated experts who will either be at the meeting, or who are resident in Costa Rica, and who may be able to join for bioblitz activities. He's in the process of contacting people on this list. But Rob doesn't know everyone. This brings us to REQUEST 2: Can anyone volunteer to lead an observing session, or to liaise with a local colleague or guide who can do so? With the exception of the trip to the Soltis Centre, which is on the program, opportunities to observe will need to be carved out of free time in and around La Fortuna (where most of us are staying) and San Carlos (site of the conference). REQUEST 3: This is for people both attending and not attending the meeting. If you can assist in identifying observations in specific taxonomic groups, please volunteer to do so. You can use iNaturalist to monitor observations of your group, and to weigh in on unidentified or mis-identified images. v. This is very important. Unless you have a permit, don't collect anything, and don't kill anything. This email's main purpose is to motivate everyone to start thinking, and some people to start planning. More, better details will follow in the coming days and weeks. In the meantime, please chime in with questions and ideas. On behalf of Rob Stevenson and the TDWG 2016 program committee - All the best, Joel. --- 1. http://soltiscentercostarica.tamu.edu/

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