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Re: [Taxacom] European Virtual Library of Taxonomic Literature - Requirements Survey
by Roderic Page 04 May '07

04 May '07

Some quick comments: This survey suggests the potential for a project that, in my opinion, is far too big and unwieldy. I suggest focussing on a core set of functions, and leave the rest to projects that do this sort of thing much better. I think the two most important things this project could do are: 1. provide an OpenURL service that will resolve a bibliographic citation (or a GUID) 2. provide GUIDs (e.g., SICIs and BICIs) that cost nothing for articles, books, and book chapters, and provide a resolver for these GUIDs. 3. provide a service to parse bibliographic citations (along the lines of Paratools). If you have 1, then you have a web service that people can use. For example, Connotea users can specify an OpenURL resolver to try and find an article online. By default it is CrossRef's service, which relies on DOIs. Imaging having a service that also supports literature that uses other GUIDs (such as Handles and SICIs). If you have 2, then everything in this project has a URI and therefore exists on the web (or, at least it's metadata does). This is one of the motivations behind the bioGUID project. If you have 3, then you have a service that would be useful in automatically integrating bibliographies from a range of sources (e.g., parsing lists of the literature on the web, or in bibliographies of papers). In terms of a portal, etc., in an age of Connotea this seems wasted effort -- they do this sort of thing well, why duplicate effort? Community tagging, etc., relies of communities, and Connotea already has one. The other lesson to learn from Connotea is that relies on existing web services, such as CrossRef's OpenURL resolver (to extract metadata associated with a DOI), and NCBI's PubMed service. By using these services, the developers could concentrate on other things. What I an arguing is that if you develop services, the "portal" (or whatever) becomes either (a) easy, or (b) largely irrelevant because you can use existing tools. Regards Rod On 3 May 2007, at 17:08, Charles Hussey wrote: > The European Distributed Institute of Taxonomy (EDIT) is a Network of > Excellence project, funded by the EU for 5 years > (http://www.e-taxonomy.eu/) One of the deliverables of the project > will > be a Bibliographic Resource to be known as the European Virtual Library > of Taxonomic Literature (E-ViTL). > > This part of the project is being managed by the Natural History > Museum, > London and we are in the process of defining detailed specifications > for > such a service. We are keen (naturally!) to ensure that the service > will > meet actual user needs and so, if this is an area dear to your heart, > you are warmly invited to participate in an online survey at: > http://www.surveymonkey.com/s.asp?A=193016818E830 (the survey will > close > at midnight on 11th May) > > This will ensure that your views are taken into account. > > NOTE: E-ViTL is likely to be a resource discovery tool rather than a > repository of full text articles. It could, however, point users to > repositories, such as the Biodiversity Heritage Library > (http://bhl.si.edu/) online journals and other sources. > > There is some debate over whether E-ViTL should attempt to provide > reference management functions, in addition to providing access to > literature. Also whether it should be a repository for reference lists, > rather than a portal to search distributed repositories. However, the > purpose of this survey is to gather user requirements and, although it > is unlikely that E-ViTL will be able to incorporate all possible > requirements, your views will provide a useful pointer for future > development. > > Yours sincerely, > > Charles Hussey, > > Science Data Co-ordinator, > Data and Digital Systems Team, > Library and Information Services, > Natural History Museum, > Cromwell Road, > London SW7 5BD > United Kingdom > > Tel. +44 (0)207 942 5213 > Fax. +44 (0)207 942 5559 > e-mail c.hussey(a)nhm.ac.uk > Species Dictionary project: www.nhm.ac.uk/nbn/ > Nature Navigator: www.nhm.ac.uk/naturenavigator/ > > _______________________________________________ > Taxacom mailing list > Taxacom(a)mailman.nhm.ku.edu > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom > > ------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html iChat: aim://rodpage1962 reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species: http://ispecies.org Rod's rants on phyloinformatics: http://iphylo.blogspot.com Rod's rants on ants: http://semant.blogspot.com

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TDWG 2007: 16-22 September, Bratislava, Slovakia
by Adrian Rissone 04 May '07

04 May '07

Preparations for the Annual Conference of Biodiversity Information Standards (formerly known as the Taxonomic Databases Working Group) are progressing well. The meeting will be held at a Conference Centre in the city of Bratislava, Slovakia, kindly hosted by the Department of Zoology of the Comenius University. The dates are confirmed as: Sunday 16 September: Arrival of delegates; Meeting of the Executive (no formal sessions) Monday 17 September - Wednesday 19 September: General sessions Thursday 20 September - Friday 21 September: Symposium Saturday 21 September: Informal Interest Group sessions if required; Departure of delegates These dates have been chosen partly because to secure space at the Conference Centre, partly to avoid conflict with other meetings that delegates may wish to attend (sorry - we can't avoid everything!). Over the next few weeks full details of the Conference (Themes, draft Programme, Registration, Accommodation) will become available on the web site at: http://www.tdwg.org/conference2007/ If you are not already registered on the TDWG website please do so. We will be using the registration membership list for the distribution of Conference information. http://www.tdwg.org/membership/ <http://www.tdwg.org/membership/> Please note that it is possible to register with TDWG *without* becoming a paying member. Obviously, we would welcome you as a full member and encourage you to join, but recognise that you may not wish to join at this time. We look forward to seeing you in Bratislava! Regards, Adrian Rissone Executive Secretary and Chair of the TDWG 2007 Conference Committee

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borders of Floras Europaea
by Marten Winter 02 May '07

02 May '07

Dear colleagues, has anybody of you a digitized map of the geographic regions of the Flora Europaea (my special interests are the eastern boundaries)? Thank you and kind regards, Marten -- *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 <mailto:Marten.Winter@ufz.de> http://www.ufz.de/index.php?en=7081 *DAISIE* - Delivering Alien Invasive Species Inventories for Europe http://www.europe-aliens.org <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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help with Taxon Srubber - Salvias
by Marten Winter 27 Apr '07

27 Apr '07

Dear colleagues, Is there anybody working with the program TaxonScrubber from the Salvias Project Page (http://www.salvias.net/pages/taxonscrubber.html)? If yes, please contact me, I need some help or better explanations :O) Thank you, Marten -- *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 <mailto:Marten.Winter@ufz.de> http://www.ufz.de/index.php?en=7081 *DAISIE* - Delivering Alien Invasive Species Inventories for Europe http://www.europe-aliens.org <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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Postdoc Position for WebService development for semantic data and tool integration
by Helmut Knuepffer 17 Apr '07

17 Apr '07

I would like to inform the TDWG mailing list members about a one-year postdoc position at IPK Gatersleben, Germany Regards, Helmut Knüpffer >Postdoc Position for WebService development for >semantic data and tool integration > >Job description: > >The Leibniz Institute of Plant Genetics and Crop >Plant Research (http://www.ipk-gatersleben.de) >is a leading institute in crop plant research. >This results in several international published >databases and developed software tools. This >data and software build an important >bioinformatics resource for the scientific community. > >The positive impact for the IPK bioinformatics >research can be increased by supporting >WebService repositories like BioMoby or BioCase. >The final goal is embedding the institute into >international bioinformatics resource networks. >Examples for such networks are the "Virtual >Plant Information Network" (VPIN), the >PlaNet-Network or the international initiative >"Global Biodiversity Information Facility" (GBIF). > >Thus, this scholarship focuses on the concrete >implementation of such a service and should >support the service work of the IPK >bioinformatics groups. This service has to be >implemented using standardized computer science >and bioinformatics methods, such as XML, Web >Services, ontologies, semantic Web and database integration. > >Specific Requirements to the candidate: > >The project goals require a Bioinformatics Postdoc with special experience in > >- database concepts and technologies, >- SQL, >- Web-service techniques, >- biological databases, >- XML processing, >- JAVA and Perl programming languages, >- UNIX operating systems. > >Contract: A contract of 1 year will be offered to the successful candidate. > >Closing date: 13 May 2007 Please, direct your questions or your application before the deadline stated above, to Dr. Uwe Scholz, head of IPK's Bioinformatics Research Group. Leibniz Institute of Plant Genetics and Crop Plant Research Dr. Uwe Scholz Corrensstr. 3 D-06466 Gatersleben Germany Phone: +49 (0)39482 5327 scholz(a)ipk-gatersleben.de Please include as job subject "DAAD postdoc research fellowship in the Bioinformatics group". The application should include a brief covering letter including your skills and scientific interest, as well as your cv and certificates. -- apologies for cross-postings --- Dr. Helmut Knüpffer Abt. Genbank, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Corrensstr. 3 D-06466 Gatersleben, Germany phone: +49-39482-5283 fax: +49-39482-5155 knupffer(a)ipk-gatersleben.de, HKnuepffer(a)web.de http://www.ipk-gatersleben.de/Internet/Forschung/Genbank/Genbankdokumentati… IPK Genebank Information System: http://gbis.ipk-gatersleben.de Mansfeld's World Database of Agricultural and Horticultural Crops: http://mansfeld.ipk-gatersleben.de

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Re: [TDWG] TDWG Digest, Vol 8, Issue 1
by Alina Freire-Fierro 11 Apr '07

11 Apr '07

Hi: I will be in visiting the Missouri Botanical Garden until December 2, but I will be regularly checking my personal email (alina_ff(a)yahoo.com) If it is urgent, please contact Carrie Kiel (kiel(a)ansp.org) Many thanks! Alina

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GBIF e-conferences to be held 10 through 24 April
by David Remsen 02 Apr '07

02 Apr '07

Dear TDWG members, GBIF will make seed money awards in 2007-2008. Advice and input is sought concerning priorities for these awards. Please see http:// www.gbif.org/News/NEWS1175263670 for details. We look forward to widespread participation in these e-conferences. -- David Remsen (dremsen(a)gbif.org) Senior Programme Officer Electronic Catalog of Names of Known Organisms Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321472 Fax: +45-35321480 ------------------------------------------------------------------------ ----

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need help with threatened species or red lists
by Marten Winter 15 Mar '07

15 Mar '07

Dear colleagues, I?m looking for data of extinct plants and animals from North America and Europe. But I don`t want to use the IUCN Red Lists, cause these are very raw (big differences in numbers between the country lists and those data from the IUCN list). I need data from each country or at least from most of them. Is there any source available with an overview of red lists from Europe and/or from the single states in the USA and Canada? I appreciate every hint and help... Thank you very much and greetings from sunny Halle (Germany), Marten Winter -- *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 <mailto:Marten.Winter@ufz.de> http://www.ufz.de/index.php?en=7081 *DAISIE* - Delivering Alien Invasive Species Inventories for Europe http://www.europe-aliens.org <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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FW: TED Prize
by Lee Belbin 12 Mar '07

12 Mar '07

Dear TDWG'ians See below: A project of significance to Biodiversity Information Standards (TDWG <http://www.tdwg.org> ). Cheers Lee Lee Belbin Manager, TDWG Infrastructure Project Email: lee(a)tdwg.org Phone: +61(0)419 374 133 -----Original Message----- From: Richard Pyle [mailto:deepreef@bishopmuseum.org] Sent: Sunday, 11 March 2007 10:12 AM To: 'Richard Pyle'; leebel(a)netspace.net.au; 'David Patterson'; 'Blum, Stan'; 'ICZN-AP' Cc: 'Roger Hyam'; 'Ricardo Pereira'; dremsen(a)gbif.org Subject: RE: TED Prize Another link of interest.... http://www.ted.com/tedprize/2007/wilson.cfm Someone should really get this out to the various lists. I would, of course, be happy to do it, but it doesn't feel like my place. Rich > -----Original Message----- > From: Richard Pyle [mailto:deepreef@bishopmuseum.org] > Sent: Thursday, March 08, 2007 11:01 PM > To: 'leebel(a)netspace.net.au'; 'David Patterson'; 'Blum, Stan'; > 'ICZN-AP' > Cc: 'Roger Hyam'; 'Ricardo Pereira'; 'dremsen(a)gbif.org' > Subject: TED Prize > > > FYI... > > http://www.nytimes.com/2007/03/09/technology/09ted.html > > Rich > > P.S. Someone should forward to the various lists... > > >

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Contract web developer needed for INOTAXA project
by Weitzman, Anna 06 Mar '07

06 Mar '07

A contract position is open at the National Museum of Natural History, Smithsonian Institution (USA) for someone to work on the INOTAXA project. The contractor must have web development and informatics skills and at least some knowledge of biological taxonomy. The INOTAXA (INtegrated Open TAXonomic Access) project is developing a web-based workspace where taxonomy-related information and data from different sources can be accessed together in a context required by the user. The core of the system is taxonomic literature transformed into XML using a schema designed for the purpose (taXMLit - see http://www.sil.si.edu/digitalcollections/bca/status.cfm <https://webaccess.si.edu/exchweb/bin/redir.asp?URL=http://www.sil.si.edu/di…> ). The schema has been written to allow interoperability with information held in other relevant schemas, particularly ABCD, Darwin Core and TCS, so that taxon names and specimen data can be accessed with the literature. The project is discussed in greater detail at http://www.sil.si.edu/digitalcollections/bca/status.cfm <https://webaccess.si.edu/exchweb/bin/redir.asp?URL=http://www.sil.si.edu/di…> . The testbed taxonomic literature includes the Biologia Centrali-Americana (BCA), which the project has already made this available on the web in JPEG format, at http://www.sil.si.edu/digitalcollections/bca/ <https://webaccess.si.edu/exchweb/bin/redir.asp?URL=http://www.sil.si.edu/di…> . Scripts are being produced to automate transformation of text to taXMLit format in a separate part of the project. As with any project, a pilot implementation before production implementation has the benefit of increased likelihood of success, leveraging input from the domain experts and other prospective users, and optimizing the choice of technology solutions. Because this is a starting point of a multi-phase initiative, its successful implementation is critical. The pilot implementation will not only provide a reference for production implementation, but also facilitate the formulation of data exchange protocol for taxonomic information to allow interoperability with other systems (e.g., GBIF). The prototype will include search, browse and display functionality, extending across all data types served. It will enable users to compare the position of taxa in different classifications derived from different resources within the system and displaying the result so users can move between these resources. The products required from the successful applicant will be: 1. Detailed system and functional requirements documentation; 2. Complete system design documentation and system design review; 3. Mock up system(s) for technology and functionality verification; with specific elements: a. Functioning SQL database; b. Simple search of indexed fields; c. Display of search result screens; d. Navigation between screens on search results; e. Image search; f. Boolean search; g. Tree browse; h. Display and comparison of taxonomic classifications; i. Access and display of multiple classifications of the same taxon; j. Search and display of specimen data. 4. Complete pilot system hosting data from BCA and selected other sources. Complete application package due 30 March 2007. Anticipated start date: 1 May 2007, running for one year. Payment and schedule subject to tender and negotiation. The selected contractor must be enrolled in the CCR system located at http://www.ccr.gov <http://www.ccr.gov/> . For further information on the project, a full statement of work, application procedures, and applicable Smithsonian Institution Independent Contractor and Rights-in-Data Clauses please contact the INOTAXA Project Managers: Anna Weitzman, National Museum of Natural History, Smithsonian Institution; e-mail: weitzman(a)si.edu; phone 1-202.633.0846 or Chris Lyal, The Natural History Museum, London; e-mail: c.lyal(a)nhm.ac.uk; phone 44-(0)207.942.5113 Anna L. Weitzman, PhD Informatics Branch Chief, ITO Informatics, Botany and Biodiversity Research National Museum of Natural History Smithsonian Institution 202.633.0846 weitzman(a)si.edu

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