May 2012 - 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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Citizen Science Interest Group home
by andrea thomer 31 May '12

31 May '12

Hello all, Over the last few months Arthur Chapman and I have been (unfortunately rather slowly) pulling together a charter for a Citizen Science Interest Group (CSIG); this charter (available at http://bit.ly/JPQpal) was ratified on March 9. We've had a bit of trouble pulling a wiki together, so until we get that figured out, we're using a Google Group for messages and other information. If you'd like to join, please request an invitation through the Google Group: https://groups.google.com/group/tdwg-CSIG If you have any questions, comments, or concerns, please don't hesitiate to post to the group's forums, or email me or Arthur directly. Thanks, Andrea Thomer RA, Center for Informatics Research in Science and Scholarship Graduate School of Library and Information Science University of Illinois at Urbana-Champaign

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Semantics of Biodiversity Webcast/Voice access
by John Deck 16 May '12

16 May '12

Yes, we were able to get web/voice access running for semantics of biodiversity workshop which is happening right now! 9am-5pm Central time, US -- Agenda: https://docs.google.com/document/d/1Z-RytvBlinIcSD3ctK1kiWUs2rr4TOxijT2TQb9… You can follow along and provide feedback via the chat window (which i'll monitor) using the following instructions *********** Anyone can join the meeting during scheduled meeting times and listen/view slides using the access code below. The audio portion is via phone conference and visuals via web-conference. Step 1: Dial-In U.S. & Canada: 866.740.1260 Germany: 08006645316 (Toll Free) United Kingdom: 08004960576 (Toll Free) List of global toll-free numbers: http://www.readytalk.com/legacy/an.php?tfnum=8667401260 Access Code: 8585349 Step 2: Web Login https://cc.readytalk.com/r/osfex4x22ka6 -- John Deck (541) 321-0689

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BioJS
by Bob Morris 13 May '12

13 May '12

http://www.ebi.ac.uk/~jgomez/biojs/registry/index.html describes an object-oriented library (and mechanisms for extending it) of JavaScript components that can probably be easily extended to other biodiversity informatics concerns than the ones in the library. This could make it quite easy to have common look-and-feel web apps within and between projects. Further details and participation at http://code.google.com/p/biojs/ --Bob -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Harvard University Herbaria Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram === The content of this communication is made entirely on my own behalf and in no way should be deemed to express official positions of The University of Massachusetts at Boston or Harvard University.

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W3C best practices for publishing RDF vocabularies
by Bob Morris 12 May '12

12 May '12

http://www.w3.org/TR/swbp-vocab-pub/ Although it is 4 years old, I don't recall having seen this before. Sorry for duplication if it is already on the radar of the tdwg rdf best practices task group. -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Harvard University Herbaria Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram === The content of this communication is made entirely on my own behalf and in no way should be deemed to express official positions of The University of Massachusetts at Boston or Harvard University.

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Call for Challenge entries for iEvoBio conference
by Cellinese,Nico 10 May '12

10 May '12

Many trees enter. Fresh analysis ensues. New insights emerge. As a reminder, the iEvoBio conference is again holding a Challenge competition in 2012, this time on the theme, "Synthesizing Phylogenies." Further information on the nature of challenge entries and how to submit them can be found on the iEvoBio website at http://ievobio.org/challenge.html. Submissions are due by June 25, 2012. Cash prizes will be awarded for first place (USD 1,500) and runner-up entries. The winning entries will be selected by a vote of the iEvoBio meeting participants. Also, alongside the iEvoBio Challenge, 2012 iEvoBio sponsor Biomatters Ltd is running the Geneious Challenge. The goal of this challenge is to develop a new plugin to Geneious Pro, using the public API, that enables a new and exciting visualization or analysis. The winning entry will receive a $1000 cash prize, and all entrants who submit by the deadline will receive a 12-month subscription license. The deadline for the Geneious Challenge is the same as for the iEvoBio Challenge. Seehttp://ievobio.org/geneious_challenge.html for more information. More details about the iEvoBio conference and program are available at http://ievobio.org<http://ievobio.org/>. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign

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Fwd: First Draft of Core Open Annotation Specification (Community Draft 1) published by Open Annotation Community Group [via Open Annotation Community Group]
by Bob Morris 05 May '12

05 May '12

Also see the Community Draft of the associated Extension Specification ---------- Forwarded message ---------- From: Search Team <webmaster(a)w3.org> Date: Fri, May 4, 2012 at 2:18 PM Subject: First Draft of Core Open Annotation Specification (Community Draft 1) published by Open Annotation Community Group [via Open Annotation Community Group] To: public-openannotation(a)w3.org On 2012-05-04 the Open Annotation Community Group published the first draft of the following specification: Core Open Annotation Specification (Community Draft 1). Participants contribute material to this specification under the W3C Community Contributor License Agreement (CLA). If you have any questions, please contact the group on their public list: public-openannotation(a)w3.org. Learn more about the Open Annotation Community [...] ---------- This post sent on Open Annotation Community Group 'First Draft of Core Open Annotation Specification (Community Draft 1) published by Open Annotation Community Group' https://www.w3.org/community/openannotation/2012/05/04/first-draft-of-core-… Learn more about the Open Annotation Community Group: http://www.w3.org/community/openannotation -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Harvard University Herbaria Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram === The content of this communication is made entirely on my own behalf and in no way should be deemed to express official positions of The University of Massachusetts at Boston or Harvard University.

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