- tdwg - lists.tdwg.org

Final Call: Tree-for-All: A hackathon to access OpenTree’s global phylogeny resources
by Julie Allen 02 Jul '14

02 Jul '14

A global “tree of life” will transform biological research in a broad range of disciplines from ecology to bioengineering. To help facilitate that transformation, the OpenTree <http://opentreeoflife.org/> project [1] now provides online access to >4000 published phylogenies, and a newly generated tree covering more than 2.5 million species. The next step is to build tools to enable the community to use these resources. To meet this aim, OpenTree <http://www.opentreeoflife.org/>, Arbor <http://www.arborworkflows.com/> [2] and NESCent’s HIP <http://www.evoio.org/wiki/HIP> working groups [3] are staging a week-long hackathon September 15 to 19 at U. Michigan, Ann Arbor. Participants in this “Tree-for-all” will work in small teams to develop tools that use OpenTree’s web services to extract, annotate, or add data in ways useful to the community. Teams also may focus on testing, expanding and documenting the web services. How could a global phylogeny be useful in your research or teaching? What other data from OpenTree would be valuable? How could OpenTree web services be integrated into familiar workflows and analysis tools? How could we add to the database of published trees, or enrich it with annotations? If you can imagine using these resources, and you have the skills to work collaboratively to turn those ideas into products (as a coder, or working side-by-side with coders), we invite you to apply for the hackathon. The full call for participation (http://bit.ly/1ioPPMc) provides instructions for how to apply, and how to share your ideas with potential teammates (strongly encouraged prior to applying). Applications are due July 8th. Travel support is provided. Women and underrepresented minorities are especially encouraged to apply. If you have questions, contact Karen Cranston (karen.cranston(a)nescent.org, @kcranstn, OpenTree), Arlin Stoltzfus (arlin(a)umd.edu, HIP), Julie Allen ( juliema(a)illinois.edu, HIP), or Luke Harmon (lukeh(a)uidaho.edu, Arbor). [1] http://www.opentreeoflife.org [2] http://www.arborworkflows.com/ [3] http://www.evoio.org/wiki/HIP (Hackathons, Interoperability, Phylogenies) -- Julie Allen Postdoctoral Researcher Illinois Natural History Survey University of Illinois www.juliamallen.com

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NMNH Paleo informatician job posting
by Cynthia Parr 27 Jun '14

27 Jun '14

Apologies to those of you not eligible, but Rusty Russell and I thought that the TDWG community might want to know about this job posting from Kathy Hollis (NMNH). Please don't ask me questions about it -- I'm just posting on their behalf. ----------- The Smithsonian National Museum of Natural History is seeking a paleobiology informatics specialist. The posting closes Friday July 11, 2014. This position is open to all U.S. Citizens or U.S. Nationals. Note: Federal employees with permanent status or individuals eligible for special appointing authorities may also apply to Job Announcement #14R-JW-299027-MPA-NMNH. *Duties* - Develops, designs, implements and maintains sustainable and extensible database-driven web applications. - Assists research staff in implementing digital collaboration with colleagues outside the Museum and will support a facility for two-way sharing of research data. - Establishes and oversees a georeferencing program to georeference Paleo and historical United States Geologic Survey collecting localities according to best practices and established standards. - Researches and reviews the applicability of new information technologies and processes that improve the efficiency and productivity of Department digitization and research programs. *For full details and to apply:* For all applicants with non-Federal status: https://www.usajobs.gov/GetJob/ViewDetails/373760000 For all Federal status applicants: https://www.usajobs.gov/GetJob/ViewDetails/373776500

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Standards for mobilising and integrating sample-based data
by Éamonn Ó Tuama [GBIF] 23 Jun '14

23 Jun '14

We invite submissions for presentations on a symposium at TDWG 2014 on "Standards for mobilising and integrating sample-based data". Those interested should contact the conveners listed below. The closing date for submission is August 1st. Sample-based data is available from thousands of environmental, ecological, and natural resource monitoring programmes. Such data are usually quantitative, calibrated, and follow certain protocols so that changes and trends of populations can be detected. This is in contrast to opportunistic observation and collection data, which today form a significant portion of openly accessible biodiversity data. Sample-based data is often not shared because the underlying protocols have been hard to encode in a standardised way. This symposium will present recent work on a proposal for extending DwC with a minimal set of new properties (e.g., quantity, quantityType, samplingGeometry, samplingUnit, eventSeriesID) that allow encoding of the essential characteristics of sample-based data while drawing on the existing tool and support infrastructure offered by the GBIF Integrated Publishing Toolkit. Presentations on other publishing models for sample-based data are most welcome. We are particularly interested in submissions relating to extension of the Darwin Core Archive model, DataOne/LTER/KNB data integration, application of models such as OGC Observations and Measurements, and in new or emerging technologies such as Veg-X [1], JSON-LD [2] or CSV on the Web [3] [1] http://wiki.tdwg.org/twiki/bin/view/Vegetation/WebHome [2] http://json-ld.org/ [3] http://www.w3.org/2013/05/lcsv-charter.html Conveners Éamonn Ó Tuama (eotuama(a)gbif.org) Hannu Saarenmaa (hannu.saarenmaa(a)helsinki.fi) ____________________________________________________ Éamonn Ó Tuama, M.Sc., Ph.D. (eotuama(a)gbif.org) Senior Programme Officer for Interoperability, Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100, Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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TDWG 2014 in Jönköping, Sweden
by Cynthia Parr 17 Jun '14

17 Jun '14

Due to the unfortunate local situation and the recent attacks in Kenya, many governments have issued warnings to their citizens forbidding or strongly discouraging travel to Kenya. The local organizers made great efforts to ensure a proper and secure venue for a successful TDWG Conference. However, the executive received indications that quite a few participants would be unable to travel to the meeting. Low attendance and uncertainty raises concerns of high financial risks and lack of effective networking. We sent a survey to TDWG mailing lists and former conference participants for input. Of 140 respondents, only 30% were sure to come to Kenya. 67% were in favor of shifting location to the possible European alternative, and over 52% favored having TDWG 2015 in Africa, including the planned pre-meeting training workshops. The Executive of TDWG thus made the difficult decision to cancel the 2014 TDWG in Kenya and shift it to the alternative location in Europe. Considering all the efforts already made by the local organizing committee and the program chair, and the importance of having a venue in Sub-Saharan Africa, TDWG 2015 will be organized in Nairobi, Kenya. The Executive Committee will prepare a back-up plan and alternative location in Africa in case of further trouble or governmental travel warnings in 2015. Postponing the meeting by one year gives all concerned parties the time to organize an African meeting with the greatest chance of success. The venue for TDWG 2014 conference will thus be the town of Jönköping in Sweden co-organized by the Swedish GBIF node and Destination Jönköping. The dates are confirmed from 27th to 31st of October 2014. The Executive offers its deepest apologizes to the Kenyan local organizing committee for the major inconvenience and thanks them for their much appreciated efforts. Likewise, the Executive would like to thank the Swedish team for agreeing to host the 2014 edition on short notice. We hope to see you in large numbers both in Sweden this October and in Kenya next year. The TDWG Executive

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Final week to book for "Making metadata work", ISKO-UK/BCS/DCMI joint event
by DCMI Announce 10 Jun '14

10 Jun '14

Dear Colleagues, *Making metadata work* Monday 23rd June 2014 - BCS Office, 5 Southampton Street, London WC2E 7HA. Please don't forget to book for this popular event before the deadline of 16 June. There are still places for the afternoon session, with an array of first class speakers. See more at < http://www.iskouk.org/events/metadata_June_2014.htm#introduction>. The morning workshop and tutorial are already full booked. We're sorry to disappoint anyone who's missing them, but we hope to repeat the Sharepoint tutorial on another date - possibly 15 Sept and/or 26 November. Do please let us know if you are interested. *Afternoon meeting on 23 June* (Plenary, 14.00 – 18.00) Martin White: The importance of metadata for high quality Search Sean Bechhofer: Wf4Ever: metadata for “Research Objects” Mark Sandler: Semantic Media: a new paradigm for navigable content for the 21st century Richard Ranft: Enhancing discovery of the British Library's audio collections Antoine Isaac: A portrait of Europeana as a Linked Open Data case (in progress) Andrew MacFarlane: Analysing creative image search queries to determine important facets The speakers and presentations are described in more detail on our website at <http://www.iskouk.org/events/metadata_June_2014_pm.htm>. As usual there will be more networking, wine and nibbles from 18.00. *Morning options* *a) Tutorial: Metadata management in Sharepoint* (10.00 -12.00) While Sharepoint 2013 offers more metadata capabilities than ever before, the range of options can make it hard to implement the most effective way. Management of controlled vocabularies is a particular challenge. This tutorial will enable you to pick the brains of an experienced consultant, Marc Stephenson of Metataxis. *b) Workshop: Vocabularies and the potential for linkage* (9.30 – 12.30; now fully booked) Various approaches to the linkage of value vocabularies (KOSs) and/or element set vocabularies (metadata schemas) will be described by Pierre-Yves Vandenbussche (Fujitsu, Ireland), Dan Brickley (Google), Gordon Dunsire and Stella Dextre Clarke, with emphasis on the opportunities as well as the barriers to widespread adoption. After that is a case study from Johan De Smedt and Agis Papantoniou, both of TenForce, that draws on more than one technique. The subsequent discussion will address the prospects for take-up, aiming to help participants with application or development of similar techniques and projects. *Registration fee and booking* Full day, including lunch and a choice of tutorial or workshop: £120 (or £70 for members of ISKO, IRSG or DCMI and for full-time students); Afternoon only: £60 (or £25 for members of ISKO, IRSG or DCMI and for full-time students). *Booking is open at* < http://www.iskouk.org/events/metadata_June_2014.htm#introduction> *About ISKO UK* ISKO (International Society for Knowledge Organization) is a not-for-profit scientific/professional association with the objective of promoting research and communication in the domain of knowledge organization, within the broad field of information science and related disciplines. Founded in 2007, our UK Chapter has been attracting lively and steadily growing audiences to its afternoon meeting series (see slides and recordings at http://www.iskouk.org/events.htm) Its third conference was held in July 2013 on the general theme of “Knowledge organization – pushing the boundaries” http://www.iskouk.org/conf2013/. *About BCS IRSG* Established in 1978, the main aim of the BCS IRSG is supporting the communication between information retrieval (IR) researchers and practitioners, promoting the use of IR methods in industry and raising public awareness of IR-related topics. Recognizing IR as an interdisciplinary field, a further aim of the BCS IRSG is to act as a link between computer science, library and information science and also cognate communities (like natural language processing). *About DCMI* The Dublin Core Metadata Initiative (DCMI) is an open, international forum for the development of interoperable online metadata standards with diverse applications. DCMI’s activities include consensus-driven working groups, global conferences and workshops, standards liaison, and educational efforts to promote widespread acceptance of metadata standards and practices. DCMI is a project of ASIS&T (the Association for Information Science and Technology).

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Tree-for-All: A hackathon to access OpenTree’s global phylogeny resources
by Julie Allen 09 Jun '14

09 Jun '14

A global “tree of life” will transform biological research in a broad range of disciplines from ecology to bioengineering. To help facilitate that transformation, the OpenTree <http://opentreeoflife.org> project [1] now provides online access to >4000 published phylogenies, and a newly generated tree covering more than 2.5 million species. The next step is to build tools to enable the community to use these resources. To meet this aim, OpenTree <http://www.opentreeoflife.org/>, Arbor <http://www.arborworkflows.com/> [2] and NESCent’s HIP <http://www.evoio.org/wiki/HIP> working groups [3] are staging a week-long hackathon September 15 to 19 at U. Michigan, Ann Arbor. Participants in this “Tree-for-all” will work in small teams to develop tools that use OpenTree’s web services to extract, annotate, or add data in ways useful to the community. Teams also may focus on testing, expanding and documenting the web services. How could a global phylogeny be useful in your research or teaching? What other data from OpenTree would be valuable? How could OpenTree web services be integrated into familiar workflows and analysis tools? How could we add to the database of published trees, or enrich it with annotations? If you can imagine using these resources, and you have the skills to work collaboratively to turn those ideas into products (as a coder, or working side-by-side with coders), we invite you to apply for the hackathon. The full call for participation (http://bit.ly/1ioPPMc) provides instructions for how to apply, and how to share your ideas with potential teammates (strongly encouraged prior to applying). Applications are due July 8th. Travel support is provided. Women and underrepresented minorities are especially encouraged to apply. If you have questions, contact Karen Cranston (karen.cranston(a)nescent.org, @kcranstn, OpenTree), Arlin Stoltzfus (arlin(a)umd.edu, HIP), Julie Allen ( juliema(a)illinois.edu, HIP), or Luke Harmon (lukeh(a)uidaho.edu, Arbor). [1] http://www.opentreeoflife.org [2] http://www.arborworkflows.com/ [3] http://www.evoio.org/wiki/HIP (Hackathons, Interoperability, Phylogenies)

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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 (apologies for cross-posting) -- 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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URGENT Update on TDWG 2014 meeting
by Cynthia Parr 04 Jun '14

04 Jun '14

Dear TDWG friends, As you may know, due to acts of violence against foreigners in Kenya a number of governments have issued travel advisories to their citizens. The TDWG Executive Committee has been very aware of general concerns about security. This has made planning for a 2014 TDWG conference in Nairobi especially challenging. Hank Bart (program chair) recently visited Nairobi and he and Lucy Waruingi (chair of local organizing committee) report that life is going on much as usual. They have arranged for a venue with exceptional security and Lucy has obtained a letter of re-assurance from the Kenyan government. There are reasonable cost estimates should we have 200 attendees (there were ~300 in Florence). Many TDWG members may feel comfortable attending the conference; this isn't the first time many of us have travelled under similar conditions. However, some governments are restricting travel and funding may be pulled for travel supplements or workshops. We are uncertain how many people this affects and how many would choose not to attend even if their travel were not officially restricted. A meeting that is too small and missing key people will not achieve our goals for African outreach or advancing standards. Finally, there is a real risk that a last minute incident might require complete cancellation. At the request of the Executive Committee, Paul Flemons has confirmed a solid alternate host in Europe this year should we decide to delay the Kenya meeting until next year. This Europe meeting would need to be one week earlier, however. Funding for pre-workshop training in Kenya will still be available for next year. I am confident that Lucy's team can host an excellent meeting either this year or next year. Please let us know your thoughts by completing a very brief survey at https://www.surveymonkey.com/s/L9YRKXQ by *Friday midnight*. We expect to announce a decision early next week. Thanks very much for your patience. Cyndy Parr TDWG Chair on behalf of the Executive Committee Cynthia Sims Parr, Chief Scientist Encyclopedia of Life http://eol.org Office: 202.633.9513, Fax: 202.633.8742 Room W118 http://orcid.org/0000-0002-8870-7099 Skype: cyndy.parr http://google.com/+CynthiaParrPhd/ @cydparr Mailing address: National Museum of Natural History Smithsonian Institution P.O. Box 37012, MRC 106 Washington, DC 20013-7012

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Position Announcement: Collections/Digital Data Manager in Copenhagen
by Kampmeier, Gail E 20 May '14

20 May '14

Posted on behalf of Nikolaj Scharff--please pass this to potential candidates. --Gail --------------------------- Collections Manager/Digital Data Manager to the Natural History Museum of Denmark. The Natural History Museum of Denmark (NHMD) is searching for a Collections Manager/Digital Data Manager to help coordinate and oversee its digital data and head a small Digital Assets Office (digital data from the zoological, botanical, palaeontological, and geological collections). Application deadline: June 15, 2014. About the Natural History Museum of Denmark. The Natural History Museum of Denmark is the Danish national museum for zoology, botany and geology, and it contains large global scientific collections of preserved animals, plants, fossils, and minerals. In its current form the museum was established on January 1, 2004 by the merging of four long-standing institutions: the Botanic Garden, the Botanical Museum & Central Library, the Geological Museum, and the Zoological Museum. Even though the Natural History Museum of Denmark is young, the history of the individual departments and collections can be traced back to the 17th century. A new museum of natural history in the Botanical Garden is being planned (www.nyt.snm.ku.dk/english/) and will present the museum with a number of big challenges in relation to the coming move of the collections, the establishment of new storage facilities and new exhibits. The collection support staff collaborates with the Head of Collections, the scientific curators of the museum and the members of the exhibitions department in the curation of specimens, including preparation, preservation, registration, etc. The collection support staff is organized in a cross-cutting unit under the Head of Collections. The Natural History Museum of Denmark (NHMD) is part of the Faculty of Science at the University of Copenhagen, and therefore host and supervise undergraduate, graduate and PhD students as well as postdocs that use the museum collections for their research. The museum is an international institution with many foreign students and researchers and English is widely used as working language. An increasing part of the collections has been digitized these years, and the museum needs expertise in the field. The museum has therefore established a Digital Assets Office, responsible for the digital archives/collections at NHMD, and for the initiation and coordination of digitization of the collections of NHMD together with other sections at NHMD. Qualification. • MSc in biology, geology, or other relevant background. • good knowledge about IT and experience with databases and digital registration of natural history collections. • Well versed in biodiversity informatics standards and definitions, such as GUID, Darwin Core, ABCD, Linked Open Data etc. (http://www.tdwg.org/) • knowledge about, and preferably hands-on experience with international initiatives within collection based biodiversity informatics. • experience with people management. • good organizing skills and experience with project management and administration. • an interest for museum work. • good language skills, particularly written and spoken English. Additional information. More information about the position can be obtained by contacting the Head of Collections, Nikolaj Scharff (phone: +45 35 32 11 07; e-mail: nscharff(a)snm.ku.dk) or Christian Lange (phone +45 35 32 11 13). More general information about the Natural History Museum of Denmark is available from our website http://snm.ku.dk/english/ Applications. For more details on the position and application procedure see http://snm.ku.dk/english/omsnm/vacancies/collections-manager-digital-data-m… The University of Copenhagen actively influences current and future generations through excellent research, education and co-operation. UCPH is one of the highest ranked universities in Europe and is Denmark’s oldest university, founded in 1479. Today, the University has 37,000 students and 9,000 employees affiliated across six faculties: humanities, law, natural sciences, social sciences, health sciences and theology. www.ku.dk/english/. Best wishes Nikolaj ------------------------------------------------------ Nikolaj Scharff, PhD Director of Collections Professor, Curator of Arachnida Biodiversity Section Natural History Museum of Denmark University of Copenhagen Universitetsparken 15 DK-2100 Copenhagen Denmark Tel. +45 42408088 Email. nscharff(a)snm.ku.dk Webpage: http://snm.ku.dk/people/nscharff ---------------------------------------------------------

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DataOne Users Group Meeting - Copper Mt CO July 6-7, 2014
by Dean Walton 19 May '14

19 May '14

Hi, I think that there are some TDWG members that would have interest in this. The DataOne Users Group (DUG) is meeting this July 6-7, 2014 in Copper Mountain, CO. Here is a chance to learn more about DataOne, show off your current research in data management, and learn about the Data Management Toolkit (DMT). http://www.dataone.org/dataone-users-group Sincerely, Dean __________________________________ Dean Walton, PhD Science Librarian/Associate Professor University of Oregon Eugene, OR 97403 (541) 346-2871

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