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TED-prize for EO Wilson: some thoughts regarding the future of science communication
by Donat Agosti 23 Feb '07

23 Feb '07

Sorry for crossposting: but I think the essence of the posting below ought to be discussed.. Donat EO Wilson recipient of the TED award http://www.ted.com/conference/flashpage.cfm?conferenceKey=2007 On March 8, EO Wilson will receive the TED Prize. It is a very prestigious award by the 1000 thought-leaders, movers and shakers in Technology, Entertainment and Design. The winners receive USD100,000 and can formulate a wish which the members of the TED community pledged to help to fulfill. Congratulations to Ed Wilson to yet another great award, another confirmation of his outstanding achievements! Let's speculate that Ed Wilson is going to fulfill his boyhood dream of an encyclopedia of life for ants. So, what would be needed to make this dream reality? Ants are already on of the best documented group of animals in the world. There is an online catalogue of all the ants of the world updated as soon as another species is added to the currently known 11,981 species. This includes a digital library linked to from the species citations to pdfs of all the non-copyrighted descriptions. Currently, all these over 4,000 publications are being transformed to text by the Internet Archive, and the special mark-up schema, taxonx. is added for species and treatments or the descriptions of the species. There are an estimated 6,500 species documented with high resolution, magnificent standard images, even well worth printing in large scale and hanging them on your wall. Through Brian Fisher's and Jack Longino's superb collecting efforts in such biologically important areas as Madagascar and Costa Rica, ants have most likely one of the best documented surveys for any group of animals world wide, easily accessible online. The evolution of ants is well documented through large scale DNA-based analysis. On top of this, data aggregator such as ispecies are using mash-up technologies to collect all these information automatically - information which is added by a large, sprawling community worldwide. This infrastructure and its content already has a broad impact beyond the ant world, especially into education and other life sciences sectors What is missing? There are three issues, that is building up and maintaining the global infrastructure, the transfer of legacy data, that is publications and specimen data into the digital realm, and the generation of new research as input into such a system, which . TED could help make advances in each of these three areas. Most likely, the biggest impact, and one with an impact well beyond ants alone, would be to get the TED crowd to agree to build up a Digital Object Identifier (DOI) repository and resolver for all the systematics legacy publications, the descriptions of the species, the species names, and the specimens. These are the basic building blocks of systematics through which the entire information on animals and plants could be pulled together now, but especially in a semantic Web or Web2.0 environment. It would also be the best complement to the Biodiversity Heritage Library by the large US and UK natural history museums and institutions which will free knowledge hidden in millions of published literature. Linking a statement with its evidence Such a DOI based system would allow linking any comment made on the distribution or behavior of a species to its original observation or reference specimen with an attached Global Positioning System record. This will allow to pinpoint not only the proper name of and the specimen itself, but also its precise geographic origin which is living up to and can made the best out of high resolution satellite or map data, such as now publicly available at Google-Earth. Mash-up technologies would allow getting all additional information needed automatically, such as DNA-BarCode sequence, conservation status, studies on the biology or medical use or the increasing number of images and movies on Youtube or Yahoo as examples. Open access to biodiversity knowlege An agreement by the publishers to allow open access to all the articles in their journal covering the description of species, or even better biodiversity and conservation will have a similar impact as the applications of DOI's. Alternatively, the use of specific mark-up in their journal articles, delimiting the description allowing automatic data mining and extraction and thus building up the global Encyclopedia of Life. Imaging Finally, taking images of all those groups of ants which are increasingly used in surveys and to measure the loss of biodiversity ought to be another priority, since images are by far the most important element to identify species. This would ideally complement ongoing world wide efforts by a rapidly increasing crowd of specialists and amateurs. Getting this infrastructure up would enable anybody in the world, from E.O. Wilson in his little home town in Alabama to any place in the developing world to participate in this feast of knowledge and motivate more people like Awatif Omer in Khartoum to pursue the discovery of new species in such places like Sudan. The usage of all this information by the crowd, rather then expert's opinion, would then decide what the most authoritative contributions are ------------ Catalogue of the ants of the World: http://antbase.org <http://antbase.org/> (in collaboration with the Hymenoptera Name Server): literature digitized with partial support from the Atherton Seidall Foundation at the Smithsonian Institution. Online scientific images of ants: http://antweb.org <http://antweb.org/> ; http://www.evergreen.edu/ants/AntsofCostaRica.html, http://mcz-28168.oeb.harvard.edu/mcz/FMPro Mashups: ispecies ( http://darwin.zoology.gla.ac.uk/~rpage/ispecies/?q=Proceratium+google <http://darwin.zoology.gla.ac.uk/~rpage/ispecies/?q=Proceratium+google&#x002 6;#x0026;submit=Go> &#x0026;submit=Go) and http://ispecies.blogspot.com/ Biodiversity Heritage Library: http://bhl.si.edu/ Taxonx: an example of a systematics specific mark-up schema: http://sourceforge.net/projects/taxonx An overview of the global ant community: http://antbase.org/ants/publications/21146/21146.pdf Dr. Donat Agosti Science Consultant Research Associate, American Museum of Natural History and Naturmuseum der Burgergemeinde Bern Email: agosti(a)amnh.org Web: <http://antbase.org/> http://antbase.org Blog: <http://biodivcontext.blogspot.com/> http://biodivcontext.blogspot.com/ Skype: agostileu CV <http://antbase.org/agosticv_2003.html> Current Location <http://antbase.org/agosti_loc_bern.kmz> Dalmaziquai 45 3005 Bern Switzerland +41-31-351 7152

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ZooBank Guiding Principles Document
by Richard Pyle 23 Feb '07

23 Feb '07

Greetings TDWGers: First, my apologies for the cross-posting (a sentence many of you will read three or four times in the next few minutes...) Attached to this email message is a PDF document representing a draft version of the "Guiding Principles and Policies" for the future development of ZooBank, the proposed electronic registry of Zoological names and nomenclatural acts, as governed by the ICZN Code. A copy of this document has also been temporarily placed at this URL: http://www2.bishopmuseum.org/iczn/docs/ZooBank-GPP.pdf A more permanent home for the evolving document will be posted as soon as it is established. Please take the time to review this document and provide comments, criticisms and questions. This message has been distributed to the ZooBank email list, ICZN email list, TAXACOM, and TDWG email lists. Please feel free to forward this message and the document to any individuals or discussion forums with an interest in the future development of ZooBank. As stated in the document itself, from this point forward the goal is to develop ZooBank in a completely transparent way, with as much community input as possible. All feedback via whatever mechanism is, of course, most welcomed! However, to help consolidate the discussions, as much of the feedback as possible should be posted through the ZooBank email list. Information for how to subscribe to that list and access its archives is available here: http://list.afriherp.org/mailman/listinfo/zoobank-list Obviously, feedback on any aspect of this document, or relating to ZooBank in general, will be gratefully received. In particular, however, it would be most helpful to receive comments on what minimal data attributes (and in what format) should be required in order for a record to be considered "verified", and what standards of quality control should be applied to such records. There will be a gathering of a number of ICZN Commissioners at the IUBS Meeting in Washington, D.C., in May (http://www7.nationalacademies.org/IUBS/), so it would be especially useful to have feedback before then. Aloha, Richard L. Pyle, PhD Commissioner, International Commission for Zoological Nomenclature Database Coordinator for Natural Sciences and Associate Zoologist in Ichthyology Department of Natural Sciences, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef(a)bishopmuseum.org http://hbs.bishopmuseum.org/staff/pylerichard.html

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The TDWG mailing list has moved
by Ricardo Pereira 22 Feb '07

22 Feb '07

Dear TDWG list subscribers, Along with other TDWG on-line resources, the TDWG mailing list has now been moved to the new TDWG servers. This message has been sent using the new list to tdwg(a)lists.tdwg.org. The new web address for the list is: http://lists.tdwg.org/mailman/listinfo/tdwg No action needs to be taken, except new messages to the TDWG list should be sent to tdwg(a)lists.tdwg.org. TDWG thanks the University of Kansas Natural History Museum and Biodiversity Research Center, Jim Beach and Rob Dewhirst in particular for kindly and efficiently running this list for us. Please email me for any further information on the TDWG lists. Best Wishes Ricardo Pereira TDWG Systems Administrator TDWG Infrastructure Project (TIP) ricardo(a)tdwg.org

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EMu Contract Application Support Specialist at NMNH, Smithsonian Institution
by Orrell, Thomas 12 Dec '06

12 Dec '06

NMNH Informatics is soliciting prospective contractors for an Application Support Specialist for EMu. Please forward this to anyone that you might know that would be interested in bidding on the contract. The Request for Quotation (RFQ) can be found at: http://acsmith.si.edu/rfq/RFQ_EMu_Application_Support.doc (MS Word) http://acsmith.si.edu/rfq/RFQ_EMu_Application_Support.pdf (PDF) OVERVIEW: The Smithsonian Institution (SI), National Museum of Natural History (NMNH), Information Technology Department, located at 10th Street at Constitution Avenue, NW, Washington, DC 20560 seeks an Application Support Specialist -EMu (Electronic Museum system) to provide professional services. The Contractor shall provide support for users of the Museum's primary Research and Collections Information System (RCIS) during public operation hours (Monday through Friday, 9:00 a.m. to 5:00 p.m. ET, excluding Federal holidays). The RCIS is based on KE EMu software ("EMu") from KE Software. NMNH has undertaken a program to develop a modern, integrated RCIS and foster similar efforts within the international collections community. RCIS is a distributed, multimedia system supporting the documentation, management, analysis, and delivery of the collections and research resources held and produced by the Museum. The foundation of the system is a series of databases describing: specimens and their current and past uses, observations taken in the field, collecting sites and habitats, geographic areas, species and higher taxa, cultural groups, and relevant literature. The system is based on a multi-server architecture, integrating text databases, digital objects including image and sound recordings, files containing results of scientific analyses, geographic information, and data thesauri. The Contractor may be in the business of performing work of this type; independent, or college intern. QUESTIONS Due no later than December 18, 2006, 4:00 p.m. ET * Questions shall be submitted not later than the date and time established for the RFQ. Should any question cause a material concern that may have some effect on the basis of award and/or other material elements of the RFQ, an electronic Amendment shall be furnished to all prospective contractors. Furnish questions to the COTR. RFQ DEADLINE Due no later than December 22, 2006, 4:00 p.m. ET * Prospective contractors shall submit electronic responses to the attention of the COTR, on or before, but not later than date and time established for the RFQ. Late submission may be subject to not meeting the requirements of the RFQ, unless, it is the only submission received. Thank you, Thomas M. Orrell, Ph.D. Research Biologist ITIS Program Manager/Acting Informatics Branch Chief Smithsonian Institution PO Box 37012 National Museum of Natural History, W623, MRC-153 Washington, DC 20013-7012 Phone: 202 633-2151 Cell: 202-294-0514 Fax: 202 786-2934 Email: orrellt(a)si.edu URL: http://www.itis.gov For UPS and FedEx shipments please use: National Museum of Natural History, MRC-153 10th and Constitution Avenues, NW Washington, DC 20560-0153

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FW: Wikipedia and Geonames. was: AW: ANN: RDF Book Mashup - IntegratingWeb 2.0 data sources like Amazon and Google into the Semantic Web
by Donat Agosti 02 Dec '06

02 Dec '06

Here a new thread in simile, a semantic web list serve, which might interest those involved in extracting geographic names. Donat -----Original Message----- From: general-bounces(a)simile.mit.edu [mailto:general-bounces@simile.mit.edu] On Behalf Of Chris Bizer Sent: Saturday, December 02, 2006 10:36 AM To: Richard Cyganiak; Richard Newman Cc: semantic-web(a)w3.org; 'Damian Steer'; general(a)simile.mit.edu; 'Karl Dubost' Subject: Wikipedia and Geonames. was: AW: ANN: RDF Book Mashup - IntegratingWeb 2.0 data sources like Amazon and Google into the Semantic Web >>> I wish that wikipedia had a fully exportable database >>> http://en.wikipedia.org/wiki/Lists_of_films >>> >>> For example, being able to export all data of this movie as RDF, >>> maybe a templating issue at least for the box on the right. >>> http://en.wikipedia.org/wiki/2046_%28film%29 >> >> Should be an easy job for a SIMILE like screen scraper. >> >> If you start scraping down from the Wikipedia film list, you should get >> a fair amount of data. Some further ideas along these lines. What about scraping information about geograpic places like countries and cities from Wikipedia and linking the data to geonames (http://www.geonames.org/ontology/)? Something like http://XXX/wikipedia/Embrun owl:sameAs http://sws.geonames.org/3020251/ The Wikipedia articles about countries and cities all follow relatively similar structures (for instance http://en.wikipedia.org/wiki/Berlin) so it should be easy to scrape them. They already contain links to other places, like the Boroughs and localities in Berlin, which could easily be transformed to RDF links. Many places have geo-coordinates which together with the place name allow scrapers to automatically create links to localities from geonames. Wikipedia is GNU, thus there aren't any problems with licensing as with the Google and Amazon data. As most articles follow the same structure, an approach to implement such a information service could be to: - Use a crawling/screenscraping framework that fills a relational database with the information from Wikipedia. - Use D2R Server (http://sites.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/) to publish the database on the Web and to provide a SPARQL end-point for querying. I once read about some pretty sophisticated screen-scraping frameworks that fill relational databases with data from websites but forgot the exact links. Does anybody know? Cheers, Chris ----- Original Message ----- From: "Richard Cyganiak" <richard(a)cyganiak.de> To: "Richard Newman" <r.newman(a)reading.ac.uk> Cc: "Chris Bizer" <chris(a)bizer.de>; "'Karl Dubost'" <karl(a)w3.org>; "'Damian Steer'" <damian.steer(a)hp.com>; <semantic-web(a)w3.org> Sent: Friday, December 01, 2006 7:19 PM Subject: Re: AW: ANN: RDF Book Mashup - Integrating Web 2.0 data sources like Amazon and Google into the Semantic Web > > On 1 Dec 2006, at 18:27, Richard Newman wrote: >> Systemone have Wikipedia dumped monthly into RDF: >> >> http://labs.systemone.at/wikipedia3 >> >> A public SPARQL endpoint is on their roadmap, but it's only 47 million >> triples, so you should be able to load it in a few minutes on your >> machine and run queries locally. > > Unfortunately this only represents the hyperlink structure and basic > article metadata in RDF. It does no scraping of data from info boxes or > article content. Might be interesting for analyzing Wikipedia's link > structure or social dynamics, but not for content extraction. > > Richard > > > >> >> -R >> >> >> On 1 Dec 2006, at 4:30 AM, Chris Bizer wrote: >> >>>> I wish that wikipedia had a fully exportable database >>>> http://en.wikipedia.org/wiki/Lists_of_films >>>> >>>> For example, being able to export all data of this movie as RDF, >>>> maybe a templating issue at least for the box on the right. >>>> http://en.wikipedia.org/wiki/2046_%28film%29 >>> >>> Should be an easy job for a SIMILE like screen scraper. >>> >>> If you start scraping down from the Wikipedia film list, you should get >>> a >>> fair amount of data. >>> >>> To all the Semantic Wiki guys: Has anybody already done something like >>> this? >>> Are there SPARQL end-points/repositories for Wikipedia-scraped data? >> >> >> > > _______________________________________________ General mailing list General(a)simile.mit.edu http://simile.mit.edu/mailman/listinfo/general

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Call: Technical Author for GBIF Data Portal documentation
by Donald Hobern 01 Dec '06

01 Dec '06

Call: Technical Author for GBIF Data Portal documentation --------------------------------------------------------- The GBIF Data Portal (http://www.gbif.net/) is a central component of the GBIF network and is currently being replaced with a new implementation (test version on-line at http://newportal.gbif.org) which will offer richer functionality for users. GBIF is seeking the services of a technical author who has an understanding of biodiversity data to develop online documentation and tutorial materials for this portal. In addition, this person will contribute to the development of an explanatory video loop based on the documentation materials. The following deliverables are required (all as on-line web pages): 1. Quick introduction to using the portal (includes GBIF data use agreement, http://www.gbif.org/DataProviders/Agreements/DUA). 2. A set of three to five short “how-to” guides to performing useful tasks with the portal (portions of these will also be used for demonstration videos). 3. Instructions for other web sites on making links to the portal or embedding elements from the portal. 4. Guidance for new data providers (includes GBIF data sharing agreement, http://www.gbif.org/DataProviders/Agreements/DSA). 5. Technical documentation for software developers that explains how to use the web service interfaces offered by the portal, and develop new visualization and analysis tools to be linked to the portal. The key skills required for this role are: 1. Capability to explain technical tasks and instructions in clear, simple, highly understandable English. 2. Experience in developing online documentation and text for demonstration videos. 3. Understanding of biodiversity data (in particular, species occurrence data and taxonomic information). A pre-existing working background knowledge of the GBIF mission would be a significant benefit. The GBIF Secretariat expects to place a contract for a total of approximately four months’ work (the majority in late 2006/early 2007, but part-time throughout the first half of 2007), including some time working with staff at the GBIF Secretariat in Copenhagen. How to apply ------------ Interested applicants should send the following by e-mail to Donald Hobern, GBIF Deputy Director for Informatics (dhobern(a)gbif.org) by 30 November 2006: 1. Curriculum vitae 2. Description of relevant experience and skills 3. Details on availability through June 2007 4. Expected remuneration ------------------------------------------------------------ Donald Hobern (dhobern(a)gbif.org) Deputy Director for Informatics Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 ------------------------------------------------------------

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Biodiversity Informatics References
by Eduardo Dalcin 27 Nov '06

27 Nov '06

Dear Taxacom friends, It's just to inform a URL where I've put together a bunch of Biodiversity Informatics references, with emphasis on Data Quality: http://www.taxondata.org/referencias/ Contributions are very welcome. Regards, -- Eduardo Dalcin eduardo(a)taxondata.org

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Call: Taxonomic Data Provider Tool Developer
by Donald Hobern 10 Nov '06

10 Nov '06

Call: Taxonomic Data Provider Tool Developer -------------------------------------------- GBIF is seeking to simplify the integration of data relating to nomenclature (scientific names) and taxonomy (classification of organisms using scientific names) by developing tools to connect such data more easily to the GBIF network. GBIF is addressing this issue in several ways: 1. Working with the Species 2000 & ITIS Catalogue of Life partnership (http://www.sp2000.org/) to promote the development of a network of global species databases 2. Enhancing the GBIF data portal (http://www.gbif.net/) to index nomenclatural and taxonomic resources served over the web as tab-delimited data sets 3. Developing a data provider tool based on TDWG (http://www.tdwg.org/) data standards to support dynamic query of nomenclatural and taxonomic data sets over the web (more complex for data providers than 2. above, but offering a search interface) GBIF is seeking the services of a software developer to develop the data provider tool (item 3 above). The tool should have the following features: 1. Relational database (two version of same model in Access and MySQL) corresponding to TDWG Taxon Concept Schema (TCS) v. 1.01 (http://www.tdwg.org/subgroups/tnc/tcs-schema-repository/) 2. Customised provider tool using either the Python implementation (pyWrapper, http://trac.pywrapper.org/) or the PHP implementation (forthcoming) of the TAPIR protocol, with five endpoints configured, one for each class of data obect in TCS (Specimen, Publication, TaxonName, TaxonConcept, TaxonRelationshipAssertion) 3. Customisation of TAPIR configuration interfaces as required 4. Interface to import tab-delimited file formats adopted by GBIF (see item 2, above) into the TCS relational database The developer should have the following skills: 1. Experience in web development using PHP or Python. 2. Experience in modeling data structures using a relational database (specifically MySQL and/or Access) 3. Familiarity with TAPIR or one of the earlier TDWG data access protocols (DiGIR, http://digir.sourceforge.net/, or BioCASe, http://www.biocase.org/products/protocols/index.shtml) 4. Ability to plan and organise development work Familarity with the TDWG Taxon Concept Schema and general understanding of the principles of nomenclature and taxonomy will be an advantage. The GBIF Secretariat expects to place a contract for a period of approximately four months’ work. How to apply ------------ Interested applicants should send the following by e-mail to Donald Hobern, GBIF Deputy Director for Informatics (dhobern(a)gbif.org) by 30 November 2006: 1. Curriculum vitae 2. Description of relevant experience and skills 3. Details on availability 4. Expected remuneration ------------------------------------------------------------ Donald Hobern (dhobern(a)gbif.org) Deputy Director for Informatics Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 ------------------------------------------------------------

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Call for participation in the Agents Interest Group
by Neil Thomson 06 Nov '06

06 Nov '06

Dear TDWG'ers At the recent 2006 Conference of TDWG the new structure of Interest Groups and Task Groups was accepted. One of the proposed new Interest Groups was for Agents, which is the term used to cover persons, organisations and software acting in some specific role or roles. These are generic, in that information about agents is useful in conjunction with many of the other TDWG standards and making this available in a standard way that can be picked up by any of them would be a valuable aid to consistency. At the moment, there is only one Task Group that may be attached to the AIG and that is the one developing Natural Collections Descriptions (NCD). This emerging standard can already be used to describe organisations, in a "level 1" sort of way by viewing them as "collections of collections". It also acknowledges the strong link between collections and persons by providing hooks to biographical databases which provide rich information about persons and may be based on BiogML or EAC. Providing information about agents in a standard form, in effect building a directory of organisations and persons engaged in natural history activity, could be one of the objectives of the AIG. If you are interested in joining (or leading) an Agents Interest Group and helping to define the relationship between agents and the TDWG data standards and ontology then please send me an email at mailto:n.thomson@nhm.ac.uk With thanks, Neil ------- Neil Thomson Head of Data & Digital Systems The Natural History Museum, Cromwell Road, London SW7 5BD Tel: +44 (0)20 7942 5294, Fax: +44 (0)20 7942 5559, Email: n.thomson(a)nhm.ac.uk http://www.nhm.ac.uk

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Position at the Acad. Nat. Sciences in Philadelphia: Biodiversity Information Manager
by freirefierro 12 Oct '06

12 Oct '06

Dear all: Your help distributing this post will be greatly appreciated. Sincerely, Alina. ****** Alina Freire-Fierro Collection Manager Herbarium PH, Botany Deptartment Academy of Natural Sciences of Philadelphia 19th and Parkway Philadelphia, PA 19103 U.S.A. *** Tel: 1-215-299-1157 freirefierro(a)ansp.org http://www.acnatsci.org/research/jessupinfo.html http://espanol.groups.yahoo.com/group/Anunciosbotanicos/ ******************************** Biodiversity Information Manager (Position Announcement # 938) Issue Date: October 12, 2006 Closing Date: Open Until Filled The Academy of Natural Sciences of Philadelphia seeks an administrator for the databases of its specimen collections who can develop database-driven desktop and web applications. The collections encompass 17 million specimens in areas spanning botany, entomology, herpetology, ichthyology, malacology, mammalogy, ornithology, paleontology and general invertebrates. The databases hold more than 1 million records in several platforms. More information about science at the Academy is available at http://www.ansp.org/research. The information manager will be responsible for maintaining the integrity of the databases, and will work closely with curatorial staff to develop informatics tools for efficient capture of biodiversity data and images, quality control, data visualization and analysis, GIS, web-based data access, and internet collaboration. Duties will include development of information models, database documentation, information security, code, user interfaces, quality control, and database life cycle management. Other duties will include assisting collections and research staff in developing informatics support sections of grant proposals. Good communication skills are essential. There is the possibility of some time for independent research in biodiversity informatics depending on qualifications. Requirements: Degree in biology (with strong computer programming/database skills) or a degree in computer science (with extensive knowledge of biology). Experience with web-database programming in a LAMP environmental (Linux, Apache, MySQL or PostgreSQL, PHP) and with MS Access and Visual Basic. Desirable: Advanced degree (Master’s or Ph.D.); experience with biodiversity databases; experience with some of the following: Linux/Unix system administration; Perl or Bash scripting; FileMaker Pro; qmail/ezmlm; ImageMagick; MapServer; DiGIR/TAPIR. Salary is commensurate with experience. The position is available immediately. The Academy of Natural Sciences offers a competitive benefits package. TO APPLY: Send resume, statement of interest, and the names, addresses and telephone numbers of three references to: Maria Eife, Asst. Office Manager Announcement: Biodiversity Information Manager #938 The Academy of Natural Sciences 1900 Benjamin Franklin Parkway Philadelphia, PA 19103-1195

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