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Multimedia Resources in Biodiversity - Survey launched
by Donald.Hobern＠csiro.au 05 May '08

05 May '08

GBIF has recently established a Multimedia Resources Survey Task Group ( http://www.gbif.org/News/NEWS1205258694) The Task Group has now commissioned a Survey of Multimedia Resources in Biodiversity. This survey is now open for responses at http://www.surveymonkey.com/s.aspx?sm=3IfGMGfEI3SMm_2f5h3yNuAw_3d_3d. More information on the survey can be found at http://www.gbif.org/News/NEWS1209648731. I would encourage TDWG participants to contribute to this survey. Many thanks, Donald 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

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TDWG mid-year message
by Donald.Hobern＠csiro.au 21 Apr '08

21 Apr '08

*** I apologise to those who receive this by multiple routes. *** Dear TDWG Members and Friends, We are just about at the mid-point between TDWG annual meetings and activity within subgroups is at a natural low. This is however a good time to review the status of all our projects and activities and to try to identify the key things we would like to see happen during the rest of the year. Biodiversity Informatics remains an active and developing area of research and we are getting closer to supporting a new generation of biodiversity data applications. The recent launch of the Encyclopedia of Life demo pages is a powerful reminder of several things. First, there is a great interest in marshalling information on the world's biodiversity. Secondly, there is an enormous need for us to find new and faster ways to bring large quantities of high-quality data online. Thirdly, we still have plenty of work ahead of us in finding better ways to make all of these data interoperate freely so that they can become part of a rich and developing store of knowledge. TDWG has a critical role to play in ensuring that all this happens in a well-structured way. TDWG is joining with a wide range of other biodiversity informatics organisations to plan the e-Biosphere conference to be held in London in 2009. This meeting is intended to showcase what is happening in our field and we must consider what we would most like to have demonstrated in such a forum. What are the big applications which our wider community could soon deliver to support science and sound policy? What tools would we like to be able to put in the hands of researchers, administrators or the general public? What do we need to start doing now to make these possible? I am of course facing these same questions in the Australian context. When I consider the key areas where the Atlas of Living Australia (ALA) needs to make rapid progress, TDWG has a significant role to play in all of them. Some particular focus areas include: * Improving the quality and management of metadata - the ALA needs a metadata repository to manage information on biodiversity data sets and will be seeking to develop a repository which is compatible both with other national repositories and also with international developments in biodiversity informatics * Lowering the technical threshold for sharing biodiversity data in structured forms - the ALA will be exploring ways to package provider software tools as bundles requiring minimal configuration (and will explore offering a centralised installation of these tools for those who do not wish to maintain a web server) * Developing tools to support online identification - we need to find efficient ways to exploit structured descriptive data where it is available. We also need to supplement these data with well-organised access to the original literature, images, distribution data, etc. in an environment which guides users to the best identifications possible. * Managing data on species interactions - I believe that the most significant class of data we do not handle today is information on the trophic and other relationships between taxa. Many new applications, and new ways to navigate biodiversity data, would become feasible if we could organise what is known in the literature of predator-prey, host-parasite, pollinator-plant and other relationships. I would really like to explore text mining or other approaches as routes to developing significant databases of such information. These are some of the areas where I would like us to make progress. What would you add to this list? Finally, I must make an apology. At the TDWG meeting in Bratislava, I made a call for those who would be interested in collaborating on developing a Java implementation of TAPIR. Unfortunately I failed to do anything about this in all the business of moving out to Australia. I do however still know of a couple of groups who would like to do this. If you have an interest in a Java TAPIR implementation, and could contribute to making it happen, please let me know (again) and I will try to get everyone concerned in contact with each other. Very best wishes, Donald 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

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Atlas of Living Australia jobs
by Donald.Hobern＠csiro.au 08 Apr '08

08 Apr '08

We are advertising IT-related positions for the Atlas of Living Australia. One of these, the Technical Architect position, is open to international applicants and has a closing date of 5 May 2008. Please see: https://recruitment.csiro.au/asp/job_details.asp?RefNo=2008%2F286 This is an exciting opportunity to take responsibility for development of the technical architecture for the Atlas of Living Australia. The Architect will be required to consider: * Data standards and protocols * Wrapper software for data providers * Metadata repositories * Use of domain ontologies * Central data indexes and caches * Integration with federated access frameworks * Web applications and web services * Support for tools for visualisation and analysis (e.g. GIS systems) * Linkages to other Australian data networks, in particular to other projects included within the NCRIS Strategic Roadmap * Linkages to international data sharing projects such as GBIF (Global Biodiversity Information Facility), Casimir (Coordination and Sustainability of International Mouse Informatics Resources), OBIS (Ocean Biogeographic Information System) and CBOL (Consortium for the Barcode of Life). The Atlas of Living Australia is also advertising three positions open to Australian residents and closing dates of 22 April 2008: * Metadata curator - see https://recruitment.csiro.au/asp/job_details.asp?RefNo=2008%2F292 * Java developer - see https://recruitment.csiro.au/asp/job_details.asp?RefNo=2008%2F290 * Web designer - see https://recruitment.csiro.au/asp/job_details.asp?RefNo=2008%2F291 The Atlas of Living Australia is a five-year project funded by the Australian Government to "develop an authoritative, freely accessible, distributed and federated biodiversity data management system that links Australia's biological knowledge with its scientific reference collections and other custodians of biological information". Thanks, Donald 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

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Australian National Taxonomy Forum
by Lee Belbin 03 Apr '08

03 Apr '08

The report of a National Taxonomy Forum, held in October 2007 at the Australian Museum, has just been released- http://www.environment.gov.au/biodiversity/abrs/workshop-forum/pubs/ntf-proc eedings.pdf While the report is national in scope, the issues addressed and the associated recommendations should (noting recent taxacom postings) have wide applicability. Sober reading. Lee Lee Belbin TDWG Secretariat lee(a)tdwg.org

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Latin American Training Institute in BioEco Informatics
by Beach, James H 02 Apr '08

02 Apr '08

PanAmerican Advanced Studies Institute Cyberinfrastructure for International Collaborative Biodiversity and Ecological Informatics La Selva Biological Station, Costa Rica May 31 -- June 12, 2008 The University of Kansas and Florida International University, working with the University of Costa Rica and the Organization for Tropical Studies (OTS), are hosting a two-week course in biodiversity and ecological informatics at OTS's La Selva Biological Station in northeastern Costa Rica from May 31 through June 12. Thanks to a PanAmerican Advanced Studies Institute Award from the Office of International Science and Engineering at the US National Science Foundation, full scholarships plus airfare are available for US and Latin American graduates. All participation costs will be covered by the award. The program will be in English. Graduate students, postdocs and early-career faculty are strongly encouraged to apply. About 25 participants, half from the U.S. and half from Latin America will be accepted. Only students/researchers from Latin America and from the United States are eligible to apply. The online application and further information, including a draft curriculum is available at: www.ciara.fiu.edu/eco/index.htm Please note that the application date is rapidly approaching, potential participants need to act quickly. There is also some opportunity for additional resource faculty from the U.S. and from Latin America in the area of bioinformatics who could join the course for various periods during the two week schedule. Please contact Jim Beach, University of Kansas, beach(a)ku.edu, or Julio Ibarra, Florida International University, julio(a)fiu.edu, for more information but see the web site for details.

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TDWG's vision for 2008
by Lee Belbin 16 Mar '08

16 Mar '08

Dear TDWGians There are a number of issues that I'd like to raise- 1. As you may be aware, Ricardo has setup an Events Calendar at http://www.tdwg.org/events/ to advertise Biodiversity Informatics related meetings, grants and awards. I've seeded it with some events but I know there are more out there. This system complements the Biodiversity Informatics related Projects database (http://www.tdwg.org/biodiv-projects/) and the Biodiversity Informatics Networks database (http://www.tdwg.org/biodiv-networks/) If you are aware of other 'events' for 2008 or 2009, please either add them yourself (you must be logged in) or send me a URL and I'll add them. A related issue: I have produced a 'glossy' poster (see http://www.tdwg.org/fileadmin/executive/movies/TDWG_Poster_BioData_A1.pdf) and brochure (see http://www.tdwg.org/fileadmin/documentation/outreach/TDWG_Brochure.pdf) I have high-quality printed version of both resources available if any of you are planning to attend a conference/meeting and would like to help promote TDWG. Note: There are other related resources (PowerPoints, videos etc) available at http://www.tdwg.org/about-tdwg/resources-for-outreach/. BTW: A general TDWG video clip is currently being produced. 2. Attached is a v.preliminary draft program for TDWG 2008 in Fremantle. Few sessions are fixed at the moment and there are a number of free slots. If you have ideas for a session (or four) on one or more issues, please let me know ASAP. Input is always appreciated. We hope to get more information regards costs, recommended accommodation and excursion options and dates to the web site next week. 3. If you haven't already done so, please consider renewing your TDWG membership, taking out TDWG membership or making a donation to TDWG (see http://www.tdwg.org/membership/) . TDWG has a small (but enthusiastic!) membership and relies on your membership fees for basic operational costs. We would therefore appreciate any support you can provide. Best Wishes Lee Lee Belbin TDWG Secretariat

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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 06 Feb '08

06 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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