March 2009 - tdwg - lists.tdwg.org

Consolidating TDWG work
by Donald.Hobern＠csiro.au 06 Apr '09

06 Apr '09

Dear TDWG Members and Friends, Those of you who attended the conference in Perth last year will remember Annie Simpson's explanation of how hard it still is for a group like the Global Invasive Species Information Network (GISIN) to take TDWG's work and apply it directly to solve data integration issues in their community. As I have previously suggested, I believe we should look closely at GISIN's requirements and make sure that those in a similar situation have all the tools and documentation required to start connecting data easily in ways that are compatible with TDWG standards. We have most of the pieces in place. We just need to organise and document them better. Invasive species are of great significance to many countries. This means that addressing GISIN's requirements is directly relevant to a large number of TDWG participants. However their scenario is also a template for data sharing in many other biodiversity-related projects. They need to aggregate information from many sources to populate several inter-related data models (BioStatus, Occurrences, ProfileURLs, ImpactStatus, ManagementStatus and DispersalStatus). Several of these are very close to existing data models based on TDWG standards (for example, the Occurrence model can be considered to be extended Darwin Core). Others are examples of the kind of community-specific data which all biodiversity projects need to share. TDWG's goal should be to ensure that GISIN and similar groups can follow a simple set of instructions (a "cook book") and use standard tools to build a network of this kind, and that they can do so in a way which ensures that related communities can also benefit from the data they share. For example, if GISIN members use the GISIN toolkit to share data, we ought to make sure that no further steps are required for GBIF, OBIS and others to integrate GISIN Occurrence data into their own indexes of species occurrences, or for EOL, ALA and others to integrate GISIN ImpactStatus, ManagementStatus and DispersalStatus data into their species profiles. I am therefore writing this email as an appeal for TDWG members to step forward and help to complete the work we have started. I am setting a challenge for us to do whatever still needs to be done to our standards, tools and data sharing recommendations so that we can produce such a cook book by the end of 2009. I don't believe this is an unrealistic goal. We can start work now on identifying and resolving issues. We can plan activities at the 2009 TDWG conference in November to resolve any issues still outstanding at that point and to hold hackathon activities to fill any gaps in our tool set. This work also aligns well with the e-Biosphere conference's plan to develop a roadmap for biodiversity informatics for the next 10 years. We have added a page to the TDWG Invasive Species wiki to seed discussion of what we need to do - http://wiki.tdwg.org/twiki/bin/view/InvasiveSpecies/GisinRequirements. Please take the time to look at this page (and at the information on GISIN's requirements at http://wiki.tdwg.org/twiki/bin/view/InvasiveSpecies/WebHome and http://www.niiss.org/cwis438/websites/GISINDirectory/Tech/ProtocolSpecifica…). Append comments and suggestions on what else we may need to do to the wiki, or simply reply to this message. In particular, if you are interested in being involved with the relevant TDWG Interest Groups in addressing some of the listed requirements, please contact me or the relevant Interest Group leaders. I believe this is the most significant thing that TDWG can do right now to support the work of biodiversity informatics worldwide. Please consider making your own contribution to make it happen. Best wishes, Donald [cid:736345722@24032009-2DA9] Donald Hobern, Director, Atlas of Living Australia CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern(a)csiro.au<mailto:Donald.Hobern@csiro.au> Web: http://www.ala.org.au/

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FW: Cyberinfrastructure Summer Traineeships for repository interoperability
by Donald.Hobern＠csiro.au 31 Mar '09

31 Mar '09

We have received the following notice, which may be of interest to some TDWG participants. Best wishes, Donald *** Please disseminate widely to students at your institution *** CYBERINFRASTRUCTURE SUMMER TRAINEESHIPS 2009 VIRTUAL DATA CENTER FOR BIODIVERSITY, EARTH, ECOLOGICAL, AND EVOLUTIONARY SCIENCE DATA http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_200 9 Summer traineeships are available for up to four students and postdocs interested in informatics as applied to scientific data ranging from the fields of biodiversity, ecology, and evolutionary biology. The program provides a unique opportunity for undergraduate, masters, and PhD students as well as postdocs to obtain hands-on experience writing and extending open-source software as part of a distributed collaborative software development team building a Virtual Data Center (VDC) that includes major data and metadata repositories in those fields. Trainees accepted into the program will receive a stipend ($4,500), and with the exception of attending one meeting near the beginning and one near the end of the 3-month program period may work from their home, or home institution. Travel costs incurred in connection with the meetings will be reimbursed. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. Initial project ideas are listed on the website. These range from validation of metadata and identifier resolution, to supporting LSID and semantic-web compliant PURLs for digital data objects, to implementing modern web-service APIs, to cataloging the diversity of metadata schemas. The project ideas are flexible and can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. The traineeships are supported by a National Science Foundation (NSF) grant to a consortium of major repositories for biodiversity, earth and environmental, ecological, and evolutionary science. The consortium includes the LTER Network Office, the U.S. Geological Survey, NASA and Oak Ridge National Laboratory, the Global Biodiversity Information Facility (GBIF), the National Evolutionary Synthesis Center(NESCent), and the National Center for Ecological Analysis and Synthesis (NCEAS). It aims to develop the cyberinfrastructure and technologies necessary to build a Virtual Data Center (VDC) based on a network of existing and new physical repositories ("nodes") that interoperate using open standards and protocols. The network will enable discovery of as well as open, stable, and secure access to data in any of its member nodes. TO APPLY: Students apply online. Instructions for applying are at the website (see "When you apply"), along with program rules and eligibility requirements. The 15-day application period for students opens on Monday March 30th and runs through Monday, April 13th, 2009. INQUIRIES: vdc-twg {at} ecoinformatics {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early as possible. Cyberinfrastructure Traineeships Website: http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_200 9 2009 NESCent Phyloinformatics Summer of Code (NESCent's participation in the Google Summer of Code; managed separately; postdocs not eligible; ***student application period ends April 3rd***) http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009 To sign up for quarterly NESCent newsletters: http://www.nescent.org/about/contact.php --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org

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e-Biosphere 09 Forum on standards
by Donald.Hobern＠csiro.au 26 Mar '09

26 Mar '09

Dear TDWG Members and Friends, The e-Biosphere conference to be held this June in London (http://www.e-biosphere09.org/) aims to develop a roadmap for biodiversity informatics for the next 5-10 years. As part of this, the conference organisers have established an "Online Conference Community" (OCC - see http://www.e-biosphere09.org/page/22/online-conference-community) to host a range of discussion groups, each of which is intended to produce a position paper to feed into the roadmap discussions. One of these communities is for "Standards development and management" - see http://forum.e-biosphere09.org/viewforum.php?f=60. I have just posted two messages to this group to try to foster some discussion on the future of standards development within our community. Clearly this is all core business to TDWG and I would encourage you to participate in this forum and make your views known. Many thanks, Donald [cid:127130500@26032009-2E97] Donald Hobern, Director, Atlas of Living Australia CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern(a)csiro.au<mailto:Donald.Hobern@csiro.au> Web: http://www.ala.org.au/

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