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plazi.org: new repository for taxonomic descriptions
by Donat Agosti 26 Feb '08

26 Feb '08

This is a live application based on TDWG standards and those under discussion (eg Taxonx for literature). It is making use of LSIDs. PLAZI.ORG - THE DIGITAL REPOSITORY FOR SPECIES DESCRIPTIONS. Knowledge of the actual number of species on planet Earth is one of the last frontiers in science. It is not known exactly how many species have been identified and described, much less the number of as yet undescribed species. However, the species we do know are documented in well over hundred million pages of printed scientific books and journals. This knowledge is hidden in libraries, and no single library holds all this knowledge. The species descriptions are very rich in data, essentially a quality controlled summary of what is known at any specific time about a particular species. In best cases, this information includes a detailed morphological description, drawings and images, a summary on behavior and ecology and a detailed list of all the specimens studied. In more recent publications, links to DNA sequences or video documentation among other forms of data may be provided. Recently e-publications have become available, but many of these are copyrighted and thus not generally available open to the public for perusal or use. Nor are they easily machine-searchable for discovery and re-use of contents. Recently, the Biodiversity Heritage Library as a large scale operation to digitize this biodiversity literature has been launched. Currently, it includes major US and UK natural history libraries, with the ultimate goal of including the entire global literature. All publications will be openly accessible to the public, unless they are copyrighted -- thus most of the recent publications are still out of reach. The BHL thus falls short of optimizing the potential uses of these publications. Tagging the boundaries of a species description and identifying the species dealt with, supports discovery and retrieval of data not possible through Google. Mark-up of species descriptions permits queries, such as which are the "red ant in London", a very common form of query. Under some national copyright legislation like the Swiss, descriptions can not be copyrighted because they are through historical constraints (there are tens of millions of descriptions) and peer review standardized and listing factual, in most cases morphological data describing species, and thus they can all be made readily accessible. Plazi.org is a new Web based service that offers access to descriptions of species and an archive to store the publications as marked up documents. GoldenGate, a dedicated editor has been developed to mark up the publications supporting the extraction of descriptions, based on a TaxonX, an XML schema modeling the logic content of these publications. The Plazi Search and Retrieval Server, building on this systematic mark-up of texts, allows powerful search functions to find species descriptions, or even simple mention of species, permitting users to answer questions like: Which species occur together? Plazi.org includes already more than 3,700 description of 3,000 taxa with a goal of archiving all the forthcoming new descriptions and, contingent upon additional funding, all the descriptions of the known 12,278 ant species listed in the Hymenoptera Name Server/ antbase.org, enhanced with globally unique species numbers (LSIDs: Life Science Identifiers). While ants provide the original test case, the service is not restricted to ants but is potentially open to all groups, from Bacteria to Plants, and will support most major languages. All descriptions are machine readable and thus can be picked up for mash-ups or individual Websites. Plazi.org is run and developed by Donat Agosti, Terry Catapano, Christiana Klingenberg and Guido Sautter, its development is supported by Grants from the US National Science Foundation (to the American Museum of Natural History), the German Deutsche Forschungsgemeinschaft (to University of Karlsruhe) and the Global Biodiveristy Facility (GBIF; to Plazi.org and Zootaxa), and is collaborating with the Hymenoptera Name Server at Ohio State University (Norm Johnson), Zoobank (Richard Pyle), University of Massachusetts (Robert Morris), antweb.org (Brian Fisher) and Zootaxa (Zhi-Qiang Zhang). Plazi.org has been released to the public at the EDIT "IPR and the web: challenges for taxonomy" meeting in London, Feb. 20, 2008 (http://www.editwebrevisions.info/content/ipr-and-web) Related Links: First descriptions of the first ant described (Linnaeus, 1758) http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=79860… recent publications with fine grained mark-up allowing extraction of specimen data and plotting automatically maps http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=4CED5… Description in Russian:(please set encoding=utf-8 in your browser. http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=AE3F8… Description in Chinese http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=5F64B… Fish http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=30E2A… Bacterium http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=A4EA4… Plant http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=59DE9… Fungi http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=C9BDF… Donat -- Dr. Donat Agosti Research Associate, American Museum of Natural History and Smithsonian Institution Email: agosti(a)amnh.org Web: http://antbase.org CV: http://research.amnh.org/entomology/social_insects/agosticv_2003.html Dalmaziquai 45 3005 Bern Switzerland +41-31-351 7152 -- Dr. Donat Agosti Research Associate, American Museum of Natural History and Smithsonian Institution Email: agosti(a)amnh.org Web: http://antbase.org CV: http://research.amnh.org/entomology/social_insects/agosticv_2003.html Dalmaziquai 45 3005 Bern Switzerland +41-31-351 7152

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LSID Authority Setup Guides
by Ricardo Scachetti Pereira 15 Feb '08

15 Feb '08

Dear list subscribers, The TDWG Secretariat and the TDWG Globally Unique Identifiers (GUID) Task Group announce the availability of the LSID Authority Setup Guides- http://www.tdwg.org/activities/guid/documents/lsid-setup-guides/ These guides were written by Richard Pyle, Kevin Richards and myself to help system administrators avoid common pitfalls in setting up their own LSID authorities. We hope that they will be useful to those interested in assigning LSIDs to their biodiversity information data records. Any feedback would be appreciated. Best regards, Ricardo Pereira Software Engineer TDWG Globally Unique Identifiers Task Group

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TDWG 2008 - Fremantle Australia AND membership reminders
by Lee Belbin 07 Feb '08

07 Feb '08

Dear TDWG'ians I have just added some basic information about the TDWG 2008 conference in Fremantle, Western Australia: http://www.tdwg.org/conference2008/. The information is preliminary and will be added to over the next few months. Information about accommodation, travel, presentations, sponsors, excursions and program will be loaded as soon as possible. I'd be keen to know if there are other things that would be useful to know. A REMINDER: Discounted institutional membership of TDWG (2008) is only available until the end of February. Individual membership is also open and we would appreciate all renewals as soon as possible. Please see http://www.tdwg.org/membership/. Best Wishes Lee Lee Belbin TDWG Secretariat

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Making LSID links into tags
by Andy Mabbett 15 Jan '08

15 Jan '08

[This is a summary of an idea discussed on the Taxacom mailing list; it has also been posted on the microformats wiki: <http://microformats.org/wiki/rel-tag-feedback#UIDs>] Many links on the TDWG's LSID resolver, for instance those on: <http://lsid.tdwg.org/summary/urn:lsid:ubio.org:namebank:11815> are marked up thus <a href="/summary/urn:lsid:ubio.org:classificationbank:1909656"> urn:lsid:ubio.org:classificationbank:1909656 </a> If TDWG would simply add rel="tag" to all such links, thus: <a rel="tag" href="... then all their pages would be "tagged" with the relevant LSIDs (i.e. everything to the right of the final slash), using the "rel-tag" microformat: <http://microformats.org/wiki/rel-tag> and then people could use those tags to find the equivalent tag on pages about (in blogs, for example) or pictures of (on, say Flickr) the organism concerned, thereby adding discoverability, without reducing or changing any of the current uses of LSIDs. -- Andy Mabbett * Are you using Microformats, yet: <http://microformats.org/> ?

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EDIT: IPR & Web Publishing Workshop
by Dave Roberts 08 Jan '08

08 Jan '08

Dear all, apologies for cross-posting. EDIT will hold a workshop on IPR and web publication to be held 20th Feb 2008 in the Royal Botanic Gardens, Kew. The topics will include both building content and the development of credit-metrics for contributors. Details can be found at http://www.editwebrevisions.info/content/ipr-and-web A booking form is accessible from the site. The morning symposium is open to all. The afternoon workshop sessions will be limited to 12 people per workshop. Participation in the workshops will basically be first-come-first-served, but we will seek to balance attendance between institutions. Travel funds for this meeting has already been distributed to partner Institutions as part of the first funding tranche. No further funding is available from EDIT. There is no registration fee. Cheers, Dave -- Dr D.McL. Roberts, Tel: +44 (0)20 7942 5086 European Distributed Institute of Taxonomy Project, Ccordinator WorkPackage 6 (Unifying Revisionary Taxonomy), Dept. Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD Great Britain Email: dmr(a)nomencurator.org Web page: http://www.editwebrevisions.info/ Web page: http://www.e-taxonomy.eu/ -- In general, it is easier to get forgiveness than to get permission. --

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NMNH Collections database survey
by Orrell, Thomas 19 Dec '07

19 Dec '07

The National Museum of Natural History, Smithsonian Institution (NMNH) is planning a new version of its biological collections database web interface. NMNH needs your help in understanding how you might use our collections databases (see at http://www.mnh.si.edu/rc/db/databases.html). The survey should take less than 15 minutes and will help ensure that your needs are incorporated in a future upgrade. We would like to close the survey by 30 January 2008. Note: NMNH has approximately 10-15% of its 126 million specimens represented in electronic form. Some of the records have minimal data, while a growing subset have literature, archival materials, photographs, illustrations, specimen images, attached. This survey will help us improve access to the data, images, etc., according to your needs. Thank you for taking a few minutes to help us improve our web database interface! Thomas Orrell & Anna Weitzman Smithsonian Institution PO Box 37012 National Museum of Natural History MRC-136 Washington, DC 20013-7012

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Neobiota 2008 - conference announcement
by Marten Winter 11 Dec '07

11 Dec '07

Dear colleagues, Institute of Botany, Průhonice & Faculty of Science, Charles University Prague are hosting the 5th European Conference on Biological Invasions NEOBIOTA. The organizing committee is pleased to invite all those who are interested in invasive plants and animals, to register and submit an abstract for either an oral or poster presentation at the conference homepage www.ibot.cas.cz/neobiota, where you will find more detailed information about the conference venue, topics accommodation, etc. The conference will take place on 23.-26 September 2008 in Prague, Czech Republic, starting with an invited evening keynote lecture presented by Marcel Rejmánek from the University of California, Davis, USA. The registration is now opened. Please note that the deadline for registration and submission of abstracts is 30 April 2008. Everyone interested in Biological Invasions is invited to participate and share thoughts, opinions and new results. All professions (ecologists, conservation agencies, and stake-holders), all organisms (plants, animals, pathogens, fungi) and ecosystems (marine, freshwater, and terrestrial) will be considered. For sharing the information with your colleagues interested in biological invasions, you may want to use the attached conference flyer. If you have any questions, please, please do not hesitate to contact us. Looking forward to see you next year in Prague Petr Pysek and Vojtech Jarosik (on behalf of the organizing committee)

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[Fwd: [Aliens-L] invitation to conference on biological invasions in Europe and DAISIE, 23 January 2008]
by Marten Winter 04 Dec '07

04 Dec '07

...may be of interest for some of you... -------- Original-Nachricht -------- Betreff: [Aliens-L] invitation to conference on biological invasions in Europe and DAISIE, 23 January 2008 Datum: Tue, 04 Dec 2007 11:06:08 +0100 Von: Melanie Josefsson <melanie.josefsson(a)snv.slu.se> Antwort an: aliens-l(a)indaba.iucn.org An: aliens-l(a)indaba.iucn.org Biological invasions in Europe and the DAISIE initiative - current threats and future perspectives *23 January 2008, Portoroz, Slovenia* Biological invasions by non-native or "alien" species are widely recognized as a significant component of human-caused global environment change. Alien species encompass many diverse taxa that threaten a wide range of European environments and have serious environmental, economic and health impacts. The DAISIE (Delivering Alien Invasive Species Inventories for Europe) portal has now brought together information on alien species and their impacts, and for the first time has developed an overview and assessment of biological invasions in the Pan-European region. Purpose of the conference: This conference will bring together decision-makers, environmental managers and researchers within the field of biological invasions and other interested parties to present and discuss the current situation with biological invasions by invasive alien species, their impacts and future perspectives for managing the risks. *Time* Wednesday, January 23, 2008, 9.00 a.m. - 17.30. *Place* Portoroz, Slovenia * *For more information please visit the DAISIE home page at www.europe-aliens.org <http://www.europe-aliens.org/>** * * *Register at the latest by January 16, 2008* Melanie Josefsson Swedish Environmental Protection Agency Melanie.Josefsson(a)snv.slu.se <mailto:Melanie.Josefsson@snv.slu.se> Telephone + 46 18 67 31 48 Telefax + 46 18 67 31 56 -- *Marten Winter* ___________________________________________________________________________________________________________________________________ Helmholtz Centre for Environmental Research - UFZ Department of Community Ecology Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Sektion Biozoenoseforschung Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany phone: ++49 (0) 345 558-5316 / fax:++49 (0) 345 558-5329 E-mail:_ Marten.Winter(a)ufz.de___ _http://www.ufz.de/index.php?en=708_1 *DAISIE* - Delivering Alien Invasive Species Inventories for Europe _http://www.europe-aliens.org_ +++++++++++++++++++++++++++++++++++++++++++++++++ Das UFZ hat einen neuen Namen: Helmholtz-Zentrum für Umweltforschung GmbH - UFZ The UFZ has a new name: Helmholtz Centre for Environmental Research - UFZ +++++++++++++++++++++++++++++++++++++++++++++++++ Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Registered Office: Leipzig Registration Office: Amtsgericht Leipzig Trade Register Nr. B 4703 Chairman of the Supervisory Board: MinDirig Hartmut F. Grübel Scientific Director: Prof. Dr. Georg Teutsch Administrative Director: Dr. Andreas Schmidt ___________________________________________________________________________________________________________________________________

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TDWG and OASIS
by Lee Belbin 03 Dec '07

03 Dec '07

Hi TDWG'ians TDWG is now a member of OASIS. Please see http://www.tdwg.org/homepage-news-item/article/tdwg-now-oasis-member/ for details and contact Paul Allen (pea1 (at) cornell (dot) edu) for further details. Cheers Lee Lee Belbin Manager, TDWG Infrastructure Project Email: lee(a)tdwg.org Phone: +61(0)419 374 133

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Metadata for biodiversity datasets
by Eamonn O Tuama 14 Nov '07

14 Nov '07

Dear TDWG Member, GBIF has identified metadata as a core component of the new distributed architecture model it will be developing as it seeks to scale up by orders of magnitude the numbers of records available through its network. We are planning to run a workshop early in 2008 to begin the process of defining a metadata profile for biodiversity datasets. As a precursor to the workshop, and to help identify and draw potential contributors together, we have created a metadata wiki on the GBIF portal. You will find some pages there to seed the discussions and you are invited to contribute to the wiki if this area is of interest to you. http://wiki.gbif.org/dadiwiki/wikka.php?wakka=CategoryMetadata Best regards, Éamonn ________________________________________________________________ Éamonn Ó Tuama, Ph.D. (eotuama(a)gbif.org), Senior Programme Officer for Data Access & Database Interoperability (DADI), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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