- tdwg - lists.tdwg.org

FW: [Taxacom] Biodiversity Informatics Survey for VertNet, Participation Requested
by Lee Belbin 11 May '09

11 May '09

And another survey... Lee Belbin TDWG Secretariat -----Original Message----- From: taxacom-bounces(a)mailman.nhm.ku.edu [mailto:taxacom-bounces@mailman.nhm.ku.edu] On Behalf Of Heather Constable Sent: Saturday, 9 May 2009 10:29 AM To: taxacom(a)mailman.nhm.ku.edu Subject: [Taxacom] Biodiversity Informatics Survey for VertNet, Participation Requested Hello, Your feedback can help guide biodiversity informatics development. We are conducting a survey on potential tools and data sets to incorporate into the search portals of the MaNIS <http://manisnet.org/>, HerpNET<http://www.herpnet.org/>, ORNIS <http://olla.berkeley.edu/ornisnet/> and FishNet II<http://www.fishnet2.net/index.html>distributed database networks for natural history collections. Specifically, we would like to build tools that benefit users and publishers of biodiversity data. Your feedback is greatly appreciated. Please take a few minutes to complete this survey: http://www.questionpro.com/akira/TakeSurvey?id=1229513 Here <http://68.111.46.217/pres/PresentationServlet?action=home> is a demo portal serving MaNIS, HerpNET, ORNIS and FishNet II data through into a single VertNet search portal, in its current form. The survey does not specifically critique the functions of the this portals, but it may help to imagine the exciting potential for mapping, visualization and validation tools. Results will be posted on the VertNet website: http://vertnet.org<http://vertnet.org/index.php>/ VertNet is a collaboration between the National Biological Infrastructure ( NBII <http://www.nbii.gov/portal/server.pt>), the Museum of Vertebrate Zoology at the University of California, Berkeley (MVZ<http://mvz.berkeley.edu/>), University of Kansas Natural History Museum and Biodiversity Research Center (KUNHM <http://www.nhm.ku.edu/>), Tulane University Museum of Natural History (TU <http://www.museum.tulane.edu/>), Harvard University Museum of Comparative Zoology (MCZ <http://www.mcz.harvard.edu/>), University of Colorado Museum (UCM) <http://cumuseum.colorado.edu/>, Field Museum (FMNH<http://www.fieldmuseum.org/>) and the American Museum of Natural History (AMNH <http://www.amnh.org/>) with over 100 other participating institutions. Apologies for cross postings. -- Heather Constable VertNet Coordinator Museum of Vertebrate Zoology University of California, Berkeley 3101 Valley Life Sciences Building 3160 Berkeley, California 94720 (510) 643-1620 http://vertnet.org/ _______________________________________________ Taxacom Mailing List Taxacom(a)mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/taxacom The Taxacom archive going back to 1992 may be searched with either of these methods: (1) http://taxacom.markmail.org Or (2) a Google search specified as: site:mailman.nhm.ku.edu/pipermail/taxacom your search terms here

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FW: [Taxacom] GBIF Content Needs Assessment Survey launched
by Lee Belbin 11 May '09

11 May '09

Apologies for the cross-posts but.... Lee Belbin TDWG Secretariat -----Original Message----- From: taxacom-bounces(a)mailman.nhm.ku.edu [mailto:taxacom-bounces@mailman.nhm.ku.edu] On Behalf Of Vishwas Chavan (GBIF) Sent: Friday, 8 May 2009 8:15 AM To: taxacom(a)mailman.nhm.ku.edu Subject: [Taxacom] GBIF Content Needs Assessment Survey launched GBIF CONTENT NEEDS ASSESSMENT SURVEY LAUNCHED The GBIF Secretariat is pleased to announce the launch of the 'Content Needs Assessment Survey' prepared by the GBIF Content Needs Assessment Task Group. The Survey in English, Spanish and French will be open for respondents until 12th June 2009. Please click on the link below to see details of the survey announcement in English, Spanish and French. http://www.gbif.org/News/NEWS1241701184 Link to Survey: English version: http://www.surveymonkey.com/s.aspx?sm=XWXP0hKQSbFwb4fgn5uZ_2bQ_3d_3d Spanish version: http://www.surveymonkey.com/s.aspx?sm=0if6UAmPkGpjVb_2felOHV0w_3d_3d French version: http://www.surveymonkey.com/s.aspx?sm=qCDkmXzlQJYB5Ph5m2vk4w_3d_3d Through this announcement we request stakeholders and users of primary biodiversity data to participate in the Survey. We further request scientific institutions, multi-lateral organisations, national, regional and global funding agencies, academicians, and citizen scientists to participate in the Survey. Please forward this announcement to all potential respondents. -- Vishwas Chavan, Ph.D. Senior Program Officer for DIGIT Global Biodiversity Information Facility 15 Universitetsparken, DK 2100, Copenhagen, Denamrk Tel. +45 35 32 14 75, Fax. +45 35 32 14 80 Email - vchavan(a)gbif.org Web - www.gbif.org _______________________________________________ Taxacom Mailing List Taxacom(a)mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/taxacom The Taxacom archive going back to 1992 may be searched with either of these methods: (1) http://taxacom.markmail.org Or (2) a Google search specified as: site:mailman.nhm.ku.edu/pipermail/taxacom your search terms here

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Wikipedia entries
by Lee Belbin 11 May '09

11 May '09

Dear TDWG Members and Friends There are two current issues that you may be able to help us with. One of our members noted that the Wikipedia entry for Darwin Core was out of date and possibly about to be deleted. Markus Döring subsequently added an excellent update for DwC. Thanks Markus! I then thought that it would be really helpful for our community to have similar useful entries for ABCD, NCD, SDD (BD), TAPIR, TCS...? Donald has also raised the need for a better introduction to Biodiversity Informatics, and there are other topics that would be good to see an entry for. I've just done a minor update on my original TDWG entry but more input would be good to see. This relates to the second issue. We have had a request from a biology historian about a history of TDWG. A few of us are unaware of anything written specifically about TDWG's history, but do have links to various past meetings at http://www.tdwg.org/about-tdwg/past-meetings/, but we are missing 1987-1997. I've put the request through to Frank Bisby, Jim Croft, Adrian Rissone and Stan Blum. Frank and Jim have some paper material that may be able to be scanned, but if anyone is aware of anything that may be useful for this, please let me know. From what I can tell, an uncensored of TDWG would make a nice read. J Thanks Lee Lee Belbin TDWG Secretariat

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Ideas on having Harvesters like GBIF clean, flag inconsistencies, and add additional value to the data
by Peter DeVries 09 May '09

09 May '09

Arthur Chapman sent me some good comments regarding Datums etc. The discussion made me realize that there may be a need for two types of formats. One for the providers and a second one that is output by the harvesting service. This is because the needs and abilities of the data providers are different than the needs and abilities of those who would like to consume the data. Consumers, who analyze and map the data, would like something that is easy to process, standardized and as as error free as as possible. It could work in the following way. Data harvesters, like GBIF, collect the records. Run them through cleaning algorithms that check attributes including that the lat and long actually match the location described. These harvesters would then expose this cleaned data via XML and RDF with tags that flag possible inconsistencies. The harvesters would also add a field for the lat and long in WGS84 if the original record contains a valid Datum. Those records without a Datum would still be exposed but the added geo:latitude and geo:longitude fields would be empty. I can imagine that that data uploaded to GBIF and other harvester services will be replete with typo's and inconsistencies that will frustrate people trying to analyze or simply map the data, the harvester services could add value by minimizing these frustrations. Originally, it seemed that a global service should standardize on a global Datum like WGS84. After all, we have standardized on meters? However, after discussing this with Arthur, I realize that this is not possible for a number of reasons. That said, I think the data would be much more valuable and less likely to be misinterpreted if if a version of it was available in WGS84. This solution would eventually encourage data providers to understand what a Datum is and include it in their data. It would also help solve a number of other data integration problems. Respectfully, Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

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Test Example of Occurrence RDF with DarwinCore/TDWG (might not be correct :-\)
by Peter DeVries 08 May '09

08 May '09

I thought I would try to start using the DarwinCore vocabulary in my observation RDF. I thought it might be easiest to start with the SimpleDarwinCore. The following URL takes you to an RDF file that combines my older vocabulary with my attempt at the SimpleDarwinCore. There is some redundancy in this version but it looks like I can probably replace a number of my terms with DarwinCore terms. The DarwinCore representation appears at the bottom of the RDF. http://species.geospecies.org/observations/a3c39dad-6756-4129-9a61-fbd32883… I would appreciate comments or suggestions. Thanks! Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

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Test Example of Occurrence RDF with DarwinCore/TDWG (might not be correct :-\)
by Peter DeVries 08 May '09

08 May '09

I thought I would try to start using the DarwinCore vocabulary in my observation RDF. I thought it might be easiest to start with the SimpleDarwinCore. The following URL takes you to an RDF file that combines my older vocabulary with my attempt at the SimpleDarwinCore. There is some redundancy in this version but it looks like I can probably replace a number of my terms with DarwinCore terms. The DarwinCore representation appears at the bottom of the RDF. http://species.geospecies.org/observations/a3c39dad-6756-4129-9a61-fbd32883… I would appreciate comments or suggestions. Thanks! Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

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Call for Nominations for a GBIF LSID-GUID Task Group
by Eamonn O Tuama (GBIF) 24 Apr '09

24 Apr '09

Dear TDWG Members and Friends, The Call for Nominations to a GBIF LSID-GUID Task Group is attached. Please observe the deadline of 10 May 2009 for nominating candidates. Kindly send your nominations directly to Éamonn Ó Tuama (eotuama(a)gbif.org) Best regards, Éamonn _______________________________________________ Éamonn Ó Tuama, M.Sc., Ph.D. ( <mailto:eotuama@gbif.org> eotuama(a)gbif.org), Senior Programme Officer, Inventory, Discovery, Access (IDA), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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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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TDWG motto
by Lee Belbin 06 Apr '09

06 Apr '09

Dear TDWG Members and Friends We need a 'pithy' (brief, punchy, memorable) motto for TDWG for use on a banner, web site, stationary etc. All suggestions and comments would be appreciated at http://wiki.tdwg.org/twiki/bin/view/Executive/TdwgMotto before April 18. Thanks Lee Lee Belbin TDWG Secretariat

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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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