June 2014 - 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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[Job Announcement Bonn, Germany] 2 Information Scientists - DFG Project "eScience-Compliant Standards for Morphology"
by Lars Vogt 19 Jun '14

19 Jun '14

Job Announcement -------------------------------------------------------------------------------------------------------------------------------------------------------- The *Institute of Evolutionary Biology and Ecology* of the *Friedrich-Wilhelms University of Bonn, Germany*, invites applications for the positions of *2 Information Scientists (f/m; TV-L 13 = app. 42.000€ year's salary, pre-tax; 100%)* for three years for the *DFG projekt „eScience-Compliant Standards for Morphology“*, anticipated *starting date August 1^st 2014*. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- *Project Aims and Scope:*Following a user-centered-design approach and in close coordination with four use-cases, new modules for ontology-based morphological descriptions, taxonomic descriptions, and image annotation will be developed for the morphological data repository /Morph·D·Base/ (www.morphdbase.de) It should be possible to create the descriptions either through natural language processing and semantic annotation (text markup) or by entering RDF triplets using ontologies. The development of these modules is done in close collaboration with the US-American project „TaxonWorks“ (taxonworks.org) For additional information about the project please refer to http://emorphology.morphdbase.de. *Work Environment:*We provide the opportunity to work for a large national project, in a team of three programmers and other scientists from scientific research collections and biodiversity informatics. You will work in the interdisciplinary, still very young and exciting field of research of ontology applications. You will develop new approaches for solving very complex questions of comparative morphology and taxonomy. *Responsibilities:*Setting up an ontology-server and reasoner, adaptation of different modules for display and input of ontologies and the development of missing functionality for the Web interface of Morph·D·Base. Furthermore, participating in regular meetings of all persons involved in the project is necessary. For the most part, these meetings will be held in Germany. *Requirements: *If you have knowledge in dealing with ontologies and programming of ontology applications, you are welcome in our team! Further, we would like applicants to have experience in setting up an ontology-server and reasoner, in the implementation of Web interfaces, as well as in the design of databases. In case the applicant is correspondingly qualified, payment will be according to German TV-L 13 pay scale (app. 42.000€ year's salary, pre-tax). Part-time work is possible. Disabled applicants will be given preference when equal qualifications are present.To increase the number of women in the scientific staff, female candidates are especially asked to apply. Please forward your applications including CV, list of successfully completed projects, references and copies of certificates *online until 10th of July 2014* to: *Mrs. K. Hennes (**secretary(a)evolution.uni-bonn.de* <mailto:secretary@evolution.uni-bonn.de>*)*. For further questions please contact Dr. Lars Vogt (lars.m.vogt(a)googlemail.com) or Dr. Peter Grobe (p.grobe(a)zfmk.de) --- Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv. http://www.avast.com

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DataONE Users Group Meeting, Registration Closing Soon
by David Bloom 05 Jun '14

05 Jun '14

*DMPTool v2 workshop at the DataONE Users Group Meeting* The DMPTool partners are pleased to announce a half-day workshop at the upcoming DataONE Users Group (DUG) meeting in Frisco, CO July 6th and 7th. The DUG meeting is co-located with the ESIP summer meeting. The half day workshop on the afternoon of Monday July 7th will introduce the recently released version 2 of the widely used DMPTool. It will introduce new and existing users to data management plan requirements, features of the new tool for the completion of comprehensive Data Management Plans that meet funder requirements, highlight key features for specific user groups, and will culminate with hands-on practice using the tool. All stakeholders are invited, with particular emphasis on researchers, research administrators, funders, and librarians/IT managers. Registration for the workshop, and the broader DataONE User Group (DUG) meeting, is free. Further information on the DUG, meeting and workshop agendas (see also below) and registration information is available at: http://www.dataone.org/dataone-users-group . Attendees can register directly at: http://www.dataone.org/dataone-users-group-meeting-registration-2014 . Reduced rate hotel reservations can be made at: http://inntopia.travel/aspnet/09/packageselect.aspx?salesid=912471&packagec… until *Today, Thursday June 5th*. The workshop will be led by Andrew Sallans (Center for Open Science), Patricia Cruse (California Digital Library) and Amber Budden (DataONE). The DataONE Users Group Meeting will include sessions led by Bill Michener, Dave Vieglais, Amber Budden, Chris Jones, Laura Moyers, Bruce Wilson among others. We look forward to seeing you there. *DMPTool Workshop Agenda* 1. Overview of data management planning requirements 2. Creating a plan with the DMPTool; funder templates, collaborative workspace, supporting materials 3. Specialized tracks (hands-on section): Researchers: writing and collaborating on data management plans Research administrators/funders/librarians/IT managers: customization of the DMPTool for institutions, funders, etc. 4. Next Steps and feedback; round table discussion exploring usability of the current tool and desired functionality for v3. David Bloom VertNet Coordinator Museum of Vertebrate Zoology University of California, Berkeley 3101 Valley Life Sciences Building Berkeley, CA 94720-3160 Phone: 510.643.1620 Fax: 510.643.8238 Email: dbloom(a)vertnet.org Email: dbloom(a)berkeley.edu URL: http://www.vertnet.org VertNet Portals: MaNIS: http://www.manisnet.org HerpNET: http://www.herpnet.org ORNIS: http://www.ornisnet.org FishNet2: http://www.fishnet2.net

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Biodiversity Informatics Course open to Nordic graduate students, postdocs, and researchers
by Deb Paul 05 Jun '14

05 Jun '14

Hi Everyone, Thought you'd all like to know about this upcoming Biodiversity Informatics course, offered to Nordic graduate students, postdocs, and researchers. Kilpisjärvi calling: Order and Sense to Your Data at the Polar Frontier ForBio: proudly presents the first-time-ever course on biodiversity informatics and data management *More info:* http://www.forbio.uio.no/events/courses/2014/biodiv_informatics.html *When:* 29 July -1 August 2014 *Where:* Kilpisjärvi Biological Station, University of Helsinki, Finland http://www.helsinki.fi/kilpis/english/ *What:* A course for Nordic graduate students, postdocs, and researchers which explores data tools beyond MS Excel and R! What are the modern, efficient, mistake-proof ways to collect and manage field and lab data, identifiers, traits, and environmental variables? How can you store your data to easily integrate with external databases? This course covers basics of data collecting and data management but leaves out data analysis to other courses. *How much:* No course fee. Danish, Swedish, Norwegian, or Finnish PhD students and postdocs are encouraged to join ForBio - the Research School in Biosystematics, since members are reimbursed for course-related travel costs and accommodation in shared rooms and food at Kilpisjärvi Station. ForBio may also support masters students registered at Danish, Swedish, Norwegian, or Finnish universities who provide compelling evidence that they need the course for their thesis work. ForBio will not cover any expenses (e.g., food, travel, or accommodation costs) for other participants who have to be registered as ForBio associates to attend the course. Please pass along to any who might be interested in taking the course -- or developing a similar one. Best, Deb -- Upcoming iDigBio Events https://www.idigbio.org/calendar --Deborah Paul iDigBio Technology Specialist Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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