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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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2 NEW At-Large VerNet Steering Committee Positions Open
by Russell, Laura 20 Nov '12

20 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.

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Invitation to Apply: First iDigBio Augmenting OCR Hackathon, February 2013 and iConference 2013 Workshop
by Deb Paul 18 Nov '12

18 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

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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

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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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DwC Image Archive Issues
by Christopher Gwilliams 26 Sep '12

26 Sep '12

Hello All, I have been playing with Darwin Core as a means to standardise sending images from my wildlife cameras and I expect to set up a data store on my computer. However, the Reader java archive struggles with printing some of the values, despite it validating successfully. Although the successful validation seems to imply that the columns do not match in all records (which is not the case). I have attached the archive that I am working with and I was wondering if someone would be willing to take a look and see if I am missing anything glaring? Much of this is based on the template archives on the core website. Thank you! Chris

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Change of DwC terms stateProvince, county, and municipality?
by Markus Englund 06 Sep '12

06 Sep '12

Hi everyone, I have noticed that use of the Darwin Core terms stateProvince, county, and municipality sometimes can be quite confusing. This confusion may arise when a term name does not reflect the content, like when the term stateProvince does not refer to a state or province, or when the term county does not refer to a county. Take my own country Sweden for example, where the Darwin Core term stateProvince refers to the name of a county, the term county refers to the name of a municipality, and the term municipality refers to the name of a parish... As long as everyone stick to the definitions, literal meaning of term names doesn't really matters. Unfortunately, however, people sometimes tend to focus more on the literal meaning of term names than on the actual meaning of defined concepts. To make the Darwin Core terminology less confusing, I think words associated with geographic ranks should be removed from the term names. I suggest the following changes (you may come up with better ones yourself!): “stateProvince” --> “countryFirstOrderSubdivision” “county” --> “countrySecondOrderSubdivision” “municipality” --> “countryThirdOrderSubdivision” After having delved into the Darwin Core geography specifications, I also feel that these three terms would benefit from more consistent and clear-cut definitions. I have included proposed new definitions at the end of this mail. My intention is not to alter the meaning of any of the existing terms, just to make the definitions more precise. Each proposed new definition is also accompanied by a revised comment with examples. To conclude, here are some questions to think about: 1) Would it be desirable to have other names for the terms stateProvince, county, and municipality? If so, what names should be used instead? 2) Are the current definitions of the terms stateProvince, county, and municipality sufficiently good? If not, how should they be defined? Does the definitions proposed here make things clearer? 3) Would more elaborate examples in the comments like the ones presented here improve the Darwin Core standard? Looking forward to hear of any response! Markus Englund Department of Biodiversity Informatics Swedish Museum of Natural History P.O. Box 50007 SE-104 05 Stockholm, Sweden -------------------- SOME RELATED LINKS Wikipedia: Table of administrative divisions by country http://en.wikipedia.org/wiki/Table_of_administrative_country_subdivisions_b… UN Second Administrative Level Boundaries http://www.unsalb.org UN Gazetetteer - a global place name database and search engine http://dma.jrc.it/services/gazetteer GADM database of Global Administrative Areas http://www.gadm.org -------------------- PROPOSED NEW DEFINITIONS AND COMMENTS Term Name: countryFirstOrderSubdivision Definition: The full, unabbreviated name of the primary administrative division below country level in which the Location occurs. The named region should be a subdivision of the region referred to in the country term. Comment: Examples: "Montana" (a federal state in the USA), "Minas Gerais" (a federative unit in Brazil), "Neuquén" (a province in Argentina), "Hesse" (a federal state in Germany), "Stockholms län" (a county in Sweden). Term Name: countrySecondOrderSubdivision Definition: The full, unabbreviated name of the second-order administrative division below country level in which the Location occurs. The named region should be a subdivision of the region referred to in the countryFirstOrderSubdivision term. Comment: Examples: "Missoula" (a county located in the federal state Montana, USA), "Los Lagos" (a department located in the province Neuquén, Argentina), "Darmstadt" (a government district located in the federal state Hesse, Germany), "Sigtuna" (a municipality located in the county Stockholms län, Sweden). Term Name: countryThirdOrderSubdivision Definition: The name of the third-order administrative division below country level in which the Location occurs. The named region should be a subdivision of the region referred to in the countrySecondOrderSubdivision term. Comment: Examples: "Hainburg" (a municipality located in the government district Darmstadt in Hesse, Germany), "Norrsunda" (a parish located in the municipality Sigtuna in Stockholms län, Sweden)

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DwC - Java Reader failing to read archives
by Christopher Gwilliams 29 Aug '12

29 Aug '12

Hello All, I have recently created a small dwc archive that validates fine (with some minor column errors) on the validator online. However, the jar fails to read any values from each record, printing null, although the validator shows the values fine. I have attached the archive if it is of any use but I am assuming it is due to the lack of updates for the jar? Thanks, Chris Gwilliams

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iDigBio Augmenting OCR October Workshop, February Hackathon Invitation
by Deb Paul 22 Aug '12

22 Aug '12

Invitation to Augmented OCR Best Practices Workshop and Hack-a-thon Planning iDigBio (https://www.idigbio.org/) is running a workshop (October 1-2, 2012) and hack-a-thon (February 2013) to identify best practices and develop tools to get information from museum labels into computers. We are seeking individuals to participate in the "iDigBio Augmenting OCR" workshop on October 1-2. The objective of the workshop is to improve OCR output and subsequent manipulation by algorithms to extract the content of biological collection specimen labels and notes and have them efficiently and accurately inserted into a database for future use. Participants in the October workshop plan to narrow the hack-a-thon focus down to specific programmatic goals for software developers working at a hackathon to be held in February of 2013. Most broadly there can be four main steps to digitization: create an image, process the image to text using Optical Character Recognition (OCR) and/or human typists, break the content of the text into semantically useful fields such as family, scientific name, collector, date collected, location, habitat, growth habit and other fields and finally format this information for injection into a database. The participants will help to identify and collect images that are representative of those that will be needed by the biology community. This collection of images will serve as the working set for developers in the February Hack-a-thon. The October workshop participants plan to identify OCR output products that will be useful for the community as well as metrics that help evaluate how well different automation approaches produce these products. This may include measures of accuracy of the OCR but also accuracy of automated error correction, effectiveness of breaking text into meaningful semantic units such as precision, recall and F-Score. We seek biologists, programmers and others involved in the digitization process to participate in this October workshop to plan the February hack-a-thon and participate in the hackathon itself. Anyone can view our wish list at http://tinyurl.com/OCRHackathonWishList of some possible goals we have for optimizing machine and natural language processing algorithms used on OCR output from specimen labels. If interested in participating and you would like to know more please email asap to: Debbie Paul, dpaul(a)fsu.edu Deadline Thursday, August 30th to participate in the Oct 1 - 2 workshop. Looking forward to your participation, From all of us in the iDigBio Augmenting OCR Working Group Please forward to other interested listserves - thanks! -- Deborah Paul User Services, iDigBio Institute for Digital Information, iDigInfo Florida State University Tallahassee, Florida 32308 850-644-6366

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BCI et al. merger
by Bob Morris 10 Aug '12

10 Aug '12

Can anyone tell me authoritatively what is the status of the merger of BCI, Biorepositories.org and Index Herbariorum? In particular, what will the new portal be called and at what URL? I need to update some Audubon Core citations as we near the AC public comment effort. Thanks 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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