October 2012 - tdwg-content

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

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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

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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

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Update on the TDWG RDF task group
by joel sachs 22 Oct '12

22 Oct '12

Hi Everyone, Since neither Steve nor I are at TDWG this year, we wanted to give an update on the efforts of the RDF Best Practices task group. Below is a run-down on activities, and also some opportunities for getting involved: 0. Background We were chartered last October under the Technical Architecture Group to document the advantages and disadvantages of various ways in which RDF and related technologies are being applied to TDWG standards. Details are at: http://code.google.com/p/tdwg-rdf/ Issues we are currently tracking are at: http://code.google.com/p/tdwg-rdf/issues/list (Not all issues are being worked on actively.) The core members of the team are listed at: http://code.google.com/p/tdwg-rdf/wiki/CharterOfTG If you are at TDWG this week, and have a question about RDF and TDWG, please relate it to one of the core members over beer. Core members: please answer as you see fit, and report back to the group. i. Beginner's Guide to RDF http://code.google.com/p/tdwg-rdf/wiki/Beginners Steve has written a comprehensive guide, based on extensive examples from the wild, and with many references. Time and effort spent reading this guide will be rewarded with an excellent understanding of RDF and its related technology. ii. Google group. https://groups.google.com/forum/?fromgroups#!forum/tdwg-rdf Steve and I both think that valuable distinctions and insights have surfaced in group discussions. Consensus has been rare, and alternative ways of doing things are documented in the archives. We plan on summarizing some of these discussions, and posting the summaries on the wiki. We may delegate some of this, and would be happy to see people volunteer to take on summarizing a thread. iii. Competency questions. We continue to collect competency questions at http://code.google.com/p/tdwg-rdf/wiki/CompetencyQuestions A competency question is used to help define both the structure and the content of a knowledge base capable of supporting specific use cases. Please share your competency questions for the knowledge base known as "the semantic web for biodiversity informatics". iv. Use case repository. In preparation for the Kansas workshop [1] that John Deck organized in May, use cases were contributed and collected here: http://bit.ly/Lb0A4C That page is being preserved as an artifact of the meeting, and is now closed to editing. We've copied the use cases to http://code.google.com/p/tdwg-rdf/wiki/UseCases Note that the term "use case" is used loosely here, as items on the list were meant as entry points to discussion at the workshop. Everyone is invited to add questions and comments to existing items, and to add new ones. Would someone like to tag or categorize these? Would someone like to map these to the the Issue Tracker? v. Class inventory http://code.google.com/p/tdwg-rdf/wiki/ClassInventory Is there a class you use or need that's not listed? Please add it. vi. Sandboxes See http://lists.tdwg.org/pipermail/tdwg-content/2011-December/002829.html vii. Data inventory This is a stub. See http://code.google.com/p/tdwg-rdf/wiki/DataInventory ----- Moving forward: i. Like all TDWG groups, we exist to serve the community. Feel free to share thoughts via email to me (jsachs(a)csee.umbc.edu) and Steve (steve.baskauf(a)vanderbilt.edu), or (preferably) to everyone. Let Steve know if you want to be added to the Task Group email discussion list. ii. Our goal remains the documentation of usage in the wild, coupled with discussion and, where consensus exists, recommendations. As noted above, summarizing recent discussions on the Google Group will be a part of that. iii. A number of more ambitious tasks have been proposed. For example, one of the follow-on activities from the Kansas workshop was creating a data testbed to be used for evaluating competing ontological approaches (http://bit.ly/JcAcKK). Who would like to be involved in taking this forward? iv. Other potential activities were identified in Kansas (http://bit.ly/Jzw0E9) and last year in New Orleans (http://code.google.com/p/tdwg-rdf/wiki/TDWG2012MtgNotes). More workshops may be useful. Do we have volunteers to host? v. Steve Baskauf, John Deck, and John Wieczorek (of the Darwin Core Task Group) have volunteered to draft an RDF Guide for Darwin Core similar to the existing XML and Text Guides. This guide would provide guidance to providers who would like to expose their existing metadata as RDF. It is NOT an attempt to turn Darwin Core into an ontology nor to resolve outstanding issues related to relationships among classes within and outside of Darwin Core. See https://groups.google.com/d/msg/tdwg-rdf/h2Sq5nu7Ja8/-dSAGXAOodoJ for more details. Questions and comments are welcome - Thanks, Joel. 1. http://biocodecommons.org/workshops/sob.html

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