November 2012 - 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/

3 2

iDigBio Train-the-Trainers Georeferencing Workshop Oct 8 - 12, 2012
by Deb Paul 09 Aug '13

09 Aug '13

** Hi Everyone, The Georeferencing Working Group at iDigBio is pleased to announce our first "Train-the-Trainers" Georeferencing Workshop for Thematic Collections Networks (TCNs) and others in engaged in the digitization of biological collections in the United States. See: https://www.idigbio.org/content/idigbios-first-train-trainers-georeferencin… for details. Three slots are still available in this workshop that is designed to focus on training participants to teach others to georeference. If you are interested, please send an application describing the reason(s) for your interest in the workshop, the current and future projects that will benefit from your attendance, and any previous experience you have with georeferencing to iDigBio's Program Assistant, Cathy Bester, cbester(a)flmnh.ufl.edu What: Train-the-Trainers -- Georeferencing Workshop Where: University of Florida, Gainesville, FL Who: Interested members of current TCNs and others in the biodiversity natural history collections community. When: October 8-12, 2012 Contact: Deborah Paul dpaul(a)fsu.edu for further information. Best, Deb and the iDigBio Georeferencing Working Group Deborah Paul User Services, iDigBio Institute for Digital Information, iDigInfo Florida State University Tallahassee, Florida 32308 850-644-6366

2 2

Announcing the VertNet Undergraduate Internship
by Russell, Laura 07 Jan '13

07 Jan '13

Call for Applications VertNet Undergraduate Internship VertNet is pleased to announce the VertNet Undergraduate Internship, scheduled for the Summer of 2013. This internship is an opportunity for two undergraduate students to gain valuable training and practical experience in biodiversity informatics, biodiversity research and systematics, and museum collection management. Two internship positions are available; one at the University of California, Berkeley, and one at the University of Colorado in Boulder. Internships will not exceed three months (12 weeks) and will include participation in VertNet’s Biodiversity Informatics Training Workshop in Boulder, Colorado, on June 24-28 (http://vertnet.org/about/BITW.php)<http://vertnet.org/about/BITW.php)>, as a part of the Interns’ training. Who should apply? We welcome applications from eligible student from within the United States and U.S. Territories interested in pursuing a biodiversity informatics project while exploring the practice of science as conducted at a natural history museum. Undergraduate students and students preparing to graduate in Spring 2013 are eligible to apply. We are interested in individuals who are self-motivated and can apply new tools and data resources creatively to questions of biodiversity, which may be in ecology, conservation, geography, evolutionary biology, environmental science, computer science, museums, or library and information science. Interns will work with the VertNet project team of experienced museum curators, researchers, and informaticists, as well as individuals from VertNet integration partners, such as AmphibiaWeb, Animal Diversity Web, and EOL, to design and conduct a research project that synthesizes and analyzes data from multiple biodiversity resources. These projects can be informatics-based, writing code and programming novel ways to analyze or display these kinds of data, or they can be biologically-focused, using data to answer questions about species diversity, ecology, evolution, or distributions. The internship will emphasize the creation, use, and analysis of aggregated biodiversity data from VertNet, and other sites, for research and data improvement and the contribution of data back to these sites. We expect research project to focus on assembling species dataset for use in spatial ecological modeling or global change biology. We are, however, open to other research topics and foci. Projects do not need to be fully realized at the time of application. Publication of the results from the internship is encouraged and will be supported by the VertNet team. Publication may take the form of web-based species accounts for VertNet integration partners, georeferencing species occurrence data, open-source software, or collaborations on other scientific publications. VertNet Project Team members (http://vertnet.org/about/team.php<http://vertnet.org/about/team.php)>) at CU Boulder include Robert Guralnick and Javier Otegui. Team members at UC Berkeley include Carla Cicero, Carol Spencer, Michelle Koo, David Bloom, John Wieczorek, and Aaron Steele. In addition to individual research project mentors, Interns will work with members of the VertNet Project Team and possibly other museum staff at both institutions to learn about daily operations of museum, and how those local activities tie into the larger perspective of global informatics. At the end of the internship, participants should have: 1. an understanding of the evolution of, and the workflows within, a research project; 2. basic skills and experience using data repositories, biodiversity informatics and analytic tools, and an understanding of which tools are appropriate for specific tasks; 3. an understanding of the operation and maintenance of a natural history collection; 4. knowledge of the abundant biodiversity resources and additional training available to them. Workshop Selection and Support Acceptance to the VertNet Undergraduate Internship is a competitive, nation-wide process and is limited to two (2) participants; one at UC Berkeley and one at CU Boulder. All applications materials and recommendations must be received by 11:59pm PT on January 11, 2013 for consideration. Accepted participants will be notified in March 2013. Individuals selected to participate will be considered full time employees of their respective institutions and paid at the monthly rate of $3150 (CUBoulder)/$3300 (UCBerkeley). Interns will receive additional support to cover costs during the workshop for travel between Berkeley and Boulder and accommodations and per diem (when in residence at the secondary institution). Interns will be responsible for their own travel to and from the internship and accommodations and daily needs while in residence at the primary institution. Support is available to help find accommodations in both locations. Application materials are available at <http://vertnet.org/about/BITW.php> http://www.vertnet.org/about/Internship.php. Submit all application materials online (http://www.vertnet.org/about/Internshipapplication.php) or send all completed materials and one letter of recommendation to dbloom(a)vertnet.org<mailto:dbloom@vertnet.org>. Laura Russell VertNet Programmer VertNet KU Biodiversity Institute 1345 Jayhawk Blvd. Dyche Hall, Room 606 Lawrence, KS 66045 Phone: +01 785 864-4681 Fax: +01 785 864-5335 email: larussell(a)vertnet.org email: larussell(a)ku.edu Skype: laura.anne.russell Gchat: larussell(a)vertnet.org url: www.vertnet.org

2 1

VertNet Biodiversity Informatics Training Workshop Announcement
by Russell, Laura 07 Jan '13

07 Jan '13

CALL FOR APPLICATIONS VertNet Biodiversity Informatics Workshop 2 VertNet is pleased to announce the second Biodiversity Informatics Training Workshop (BITW), scheduled for June 24-28, 2013. The workshop will provide training and experience in the use of primary biodiversity data sources and the tools necessary to become proficient in biodiversity informatics and conduct high-level research. Led by experienced informaticists and researchers, the BITW will emphasize the use and analysis of aggregated biodiversity data from VertNet, and other sources, for a wide variety of research. During the five-day course, participants will work closely with trainers to address compelling biodiversity research questions and focus on the entire scope of a research project, including data acquisition, tools for data evaluation, analysis, and project dissemination and outreach. Participants are expected to bring high levels of motivation and desire to learn the fundamentals of biodiversity informatics and become users of cutting edge tools in GIS and modeling although not necessarily expected to have experience in them. The workshop will include large and small group exercises on a common curriculum, as well as the opportunity for participants to discuss and explore their own research goals/questions. Virtual talks by research professionals from across the U.S. will provide opportunities to discuss how others use informatics tools and workflows. Participants will explore and utilize: ● Data sources for discovery, acquisition, data standards, database creation and organization (VertNet, GBIF, Darwin Core) ● Organization, analysis, workflow, and data improvement tools ● Biodiversity measurement and analysis techniques ● Species distribution modeling approaches ● Dissemination, education, and outreach mechanisms (e.g., citizen science) The goal of the workshop is to provide conceptual frameworks and hands-on experience with a suite of data sources such as VertNet (including MaNIS, FishNet, HerpNET, and ORNIS), EOL, Map of Life, and other software tools (e.g., BioGeomancer, GEOLocate, Quantum GIS, R Statistics, ArcGIS, Maxent). At the end of the week, participants should leave the workshop with: 1. an understanding of the evolution of, and the workflows within, a research project; 2. a set of basic skills to use data repositories, informatics and analytic tools, and an understanding of which tools are appropriate for specific tasks; 3. knowledge of the abundant resources and additional training available to them. Who should attend? Advanced undergraduates, recent post baccalaureates, and early-career graduate students currently working, or interested in a career in a biodiversity related field, including, but not limited to, ecology, conservation, geography, biology, environmental science, computer science, and library science. Workshop Selection and Support Acceptance to the BITW is a competitive process and the workshop is limited to 20 participants. All applications materials and recommendations must be received by 11:59pm PT on January 11, 2013 for consideration. Accepted participants will be notified in March 2013. Individuals selected to participate will receive support for six nights accommodation, support for transportation to and from the workshop, and per diem to help cover daily expenses. Accommodations will be provided on the campus of the University of Colorado Boulder. Application materials are available at http<http://vertnet.org/about/BITW.php>://<http://vertnet.org/about/BITW.php>vertnet<http://vertnet.org/about/BITW.php>.<http://vertnet.org/about/BITW.php>org<http://vertnet.org/about/BITW.php>/<http://vertnet.org/about/BITW.php>about<http://vertnet.org/about/BITW.php>/<http://vertnet.org/about/BITW.php>BITW<http://vertnet.org/about/BITW.php>.<http://vertnet.org/about/BITW.php>php<http://vertnet.org/about/BITW.php>. Submit application materials online (http<http://vertnet.org/about/BITW.php>://<http://vertnet.org/about/BITW.php>vertnet<http://vertnet.org/about/BITW.php>.<http://vertnet.org/about/BITW.php>org<http://vertnet.org/about/BITW.php>/<http://vertnet.org/about/BITW.php>about<http://vertnet.org/about/BITW.php>/<http://vertnet.org/about/BITW.php>BITW<http://vertnet.org/about/BITW.php>.<http://vertnet.org/about/BITW.php>php<http://vertnet.org/about/BITW.php>) or send all completed materials and one letter of recommendation todbloom<mailto:dbloom@vertnet.org>@<mailto:dbloom@vertnet.org>vertnet<mailto:dbloom@vertnet.org>.<mailto:dbloom@vertnet.org>org<mailto:dbloom@vertnet.org>. Laura Russell VertNet Programmer VertNet KU Biodiversity Institute 1345 Jayhawk Blvd. Dyche Hall, Room 606 Lawrence, KS 66045 Phone: +01 785 864-4681 Fax: +01 785 864-5335 email: larussell(a)vertnet.org email: larussell(a)ku.edu Skype: laura.anne.russell Gchat: larussell(a)vertnet.org url: www.vertnet.org

2 1

2 NEW At-Large VerNet Steering Committee Positions Open
by Russell, Laura 19 Nov '12

19 Nov '12

VertNet<http://vertnet.org/about/project.php> is a community data sharing project built around solving solutions regarding scale and sustainability of biodiversity data publishing networks. VertNet is built by the community for the community. Given its strong focus on community involvement, we seek two (2) new at-large members to join the VertNet Steering Committee. The purpose of the Steering Committee is “to provide scientific, technical, and managerial guidance and support to the VertNet project team and to serve as the primary engine for outreach to the collections community.” The current steering committee composition and more about the project can be found at http://vertnet.org/<http://vertnet.org/help/contact.php> and http://vertnet.org/help/contact.php. Steering Committee members will work with the VertNet project team to: (1) develop and expand the network of data contributors participating in VertNet through outreach, including, but not limited to, those activities defined in the project narrative<http://goo.gl/dPPyP> approved and funded by the National Science Foundation (NSF); (2) identify opportunities and help secure funding for VertNet staff and the development and maintenance of VertNet beyond the NSF funding period; and (3) work with the VertNet team to develop a sustainability plan for VertNet. Responsibilities of all Steering Committee members include: * Participate in monthly conference call discussions, email correspondence, and additional meetings as necessary. * Review project documents, reports, and outreach plans * Provide guidance and direction to VN Project PIs and team members on matters including, but not limited to, science and research, project management, funding raising, and the creation and development of outreach activities. * Represent and promote VertNet tools and services to professional societies and interest groups, the collections community (domestically and abroad), government agencies, biodiversity scientists and researchers, informaticians, educators, and the general public. * Other responsibilities as necessary. The term for each At-Large member will be one (1) year with the opportunity for renewal at the completion of the term. At-Large members should have significant experience in at least one of the following: * collection management * informatics development and big data * community and academic outreach * biodiversity-oriented research * business management and sustainability * grant writing and fundraising VertNet welcomes applications from members of the private, non-profit, academic, governmental, and broad biodiversity communities. “Service on the committee is recognized throughout the community, provides a chance to understand a key set of social and technical processes governing data sharing projects, and is simply rewarding on many levels, from professional contacts to engagement on key issues.” - VertNet Steering Committee Chair, Dr. Robert Guralnick. Applicants may be resident in any location, but must be able to attend regular “virtual” meetings during the hours of 10am-4pm Pacific Time in the United States. To apply, please complete the application<http://vertnet.org/help/scannouncement.php> on the VertNet web site. Applications must be submitted by 11:59pm on January 11th, 2013.

1 0

Invitation to Apply: First iDigBio Augmenting OCR Hackathon, February 2013 and iConference 2013 Workshop
by Deb Paul 17 Nov '12

17 Nov '12

Subject: You are invited to apply to participate in the First iDigBio Augmenting OCR Hackathon, February 2013 Apply at:http://tinyurl.com/iDigBioAOCRHackathon <http://tinyurl.com/PhyloTastic2> Natural Language Parsing, Optical Character Recognition, User Interfaces Fort Worth, Texas in February! Integrated Digitized Biocollections, iDigBio <https://www.idigbio.org/home>, along with theBotanical Research Institute of Texas (BRIT) <http://www2.brit.org/> are hosting their 1st hackathon.The iDigBio Augmenting Optical Character Recognition Working Group (AOCR) <https://www.idigbio.org/wiki/index.php/Augmenting_OCR> invites you to help us improve OCR output and natural language parsing of natural history museum's specimen label data. Be a part of helping to get "dark data" out of millions of museum cabinets and into online databases. Who can participate? We're looking for scientists, citizen scientists, information scientists, software engineers, students, faculty, post-docs, and staff of both genders and from different backgrounds. While we need hackers who write great code, we are also seek individuals who have experience with writing, applying and optimizing natural language processing algorithms, image processing and analysis, as well as: designing user interfaces, testing software, developing tutorials, and documenting user experiences. Applications are now being accepted for the iDigBio AOCR Hackathon, which will take place February 13-14, 2013 at theBotanical Research Institute of Texas (BRIT) <http://www2.brit.org/>. Information on how to apply is provided below. Partial support (and, if funds allow, full support) for travel, food and lodging will be available to each successful applicant who indicates need. We particularly welcome applications from women and members of underrepresented groups. FYI, this hackathon is being held concurrent withiConference 2013 <http://www.ischools.org/iConference13/2013index/> in Fort Worth, where the iDigBio AOCR Working Group is presenting a half-day workshop on February 12th: Help iDigBio Reveal Hidden Data: iDigBio Augmenting OCR Working Group Needs You! To understand how you might be able to contribute, please review the Google doc at http://tinyurl.com/aocrHack or contact one of the members of the iDigBio AOCR working group (see below). In Anticipation!, Deborah Paul - on behalf of the iDigBio AOCR working group, BRIT andiConference 2013 <http://www.ischools.org/iConference13/2013index/> HOW TO APPLY Before 30 November, 2012 at midnight, EST if possible. Space is limited to 20 people. Please fill out the online form: http://tinyurl.com/iDigBioAOCRHackthon <http://tinyurl.com/PhyloTastic2> * The application form asks you to describe how you can contribute to the iDigBio AOCR Hackathon. We are not just looking for coders. * Support for travel, housing and meals will be available to each successful applicant who indicates need. * Please understand that your application is not a guarantee of participation in the event. Funds and space are limited: we may not be able to sponsor every individual who is qualified to participate. * iDigBio AOCR Working Group Contacts Bryan Heidorn,heidorn(a)email.arizona.edu Edward Gilbert,egbiodiversity(a)gmail.com Jason Best,jbest(a)brit.org Deborah Paul,dpaul(a)fsu.edu -- Deborah Paul User Services, iDigBio Institute for Digital Information, iDigInfo Florida State University Tallahassee, Florida 32308 850-644-6366

1 1

launch of pro-iBiosphere
by Donat Agosti 06 Nov '12

06 Nov '12

Pro-iBiosphere is a European Union FP7 funded project to develop an outline of a future European open biodiversity knowledge management system. The Pro-iBiosphere project has been launched on September 1, 2012 for the period of 2 years addressing technical and semantic interoperability issues and challenges that will ultimately lead to a more efficient system of the management of biodiversity information. For practical reasons and to demonstrate the functionality of the proposed ideas, the test beds are primarily the production of floras and faunas produced at the partner's institutions, how they can be linked to external datasets, and how the new information can be made more widely accessible. A series of open workshops are scheduled in the coming two years to help to discuss, challenge and improve the specific tasks in the envisioned system. A great emphasis is given on pilot studies that demonstrate the proposed avenue. Since a great emphasis is put on data, data standards, exchange and export a big hope is put into getting the input from TDWG members. Consortium partners are the Naturalis Leiden, the Royal Botanical Garden Kew, the National Botanic Garden Belgium, the Botanic Garden and Botanical Museum Berlin-Dahlem, Sigma Orionis, Pensoft and Plazi. More information is available at http://www.pro-ibiosphere.eu/ Donat Agosti Plazi / Pro-IBiosphere

1 0