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Announcement: New edition of Terms Used in Bionomenclature
by David Remsen (GBIF) 27 May '10

27 May '10

Dear TDWG-ers FYI I'd like to announce the publication of an updated edition of Terms Used in Bionomenclature, compiled by Prof. David Hawksworth. This is a glossary of over 2,100 terms used in biological nomenclature - the naming of whole organisms of all kinds. The glossary is available in print-ready PDF format as well as via an online web application that can be browsed, searched, and output in HTML, JSON and RDF to support re-use and referencing. GBIF is also producing a limited number of paper copies of the glossary which will be available at GBIF-supported meetings and events. The web application supports the development of controlled vocabularies using resolvable identifiers for nomenclatural terms. More information and links to the PDF and web versions can be found on the glossary home page at http://www.gbif.org/communications/resources/print-and-online-resources/bio… The web application is online at http://bionomenclature-glossary.gbif.org/ I'm happy to field comments on the implementation and pass on comments regarding the content to David Hawksworth. Kind regards, David Remsen ---------------------------------------------------------------------------- David Remsen, 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 Mobile +45 28751472 Skype: dremsen ----------------------------------------------------------------------------

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[tdwg-phylo] Call for Software Bazaar entries open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 26 May '10

26 May '10

The Call for Software Bazaar entries is now open for the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs/index.php/ievobio/ 2010. See below for instructions. The Software Bazaar features presenters demonstrating their software live on a laptop. At iEvoBio, this session takes the place of a poster session, and will be between 1.5-2 hours in duration. Conference attendees will be able to walk from one demonstration to the next and open a conversation with the presenters. Please also see our FAQ for this information (http://ievobio.org/faq.html#software). The Software Bazaar is part of the interactive afternoon program on the first conference day. Entries should be software aimed at advancing research in phylogenetics, evolution, and biodiversity, and can include interactive visualizations that have been pre-computed (such as SVGs, or Google Earth-compatible KML files). Submissions consist of a title, which will typically be the name of the software (or visualization method) being presented, the URL of a website where more information about the software can be obtained, and the license under which the source code is available. The provided website must contain a link to where the source code (and possibly binaries) can be downloaded. If it is not obvious from the provided website, the submission must describe what the software does. Reviewers will judge whether a submission is within scope of the conference (see above), and need to be able to verify whether the open- source requirement(*) is met. Presenters are expected to bring their own laptops for presentation, and any auxiliary devices necessary (such as a mouse). Power will be available at the presentation tables (110V/60Hz, US-style plugs; international presenters need to bring a suitable adaptor). Please let the organizing committee know as much in advance as possible if you expect to have unusually high demands for wireless network bandwidth. Note that commercial marketing activities are not permitted - presenters wishing to promote commercial or proprietary services or products should contact the Evolution conference about exhibitor space. Review and acceptance of Software Bazaar submissions will be on a rolling basis. The deadline for submission is the morning of the first day of the conference (June 29). As the number of Software Bazaar presentation slots is finite, we cannot guarantee the availability of slots up until the day of the conference. We cannot accept submissions until the open-source requirements are met. We ask all submitters of Software Bazaar presentations to be willing to also serve as reviewers of such, as described above. Softwar Bazaar demonstrations are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Lightning talks, 3) Challenge entries, and 4) Birds-of-a- Feather gatherings. The Calls for Challenge entries (http://ievobio.org/challenge.html ) and Lightning Talks (same submission URL as above) remain open, and information on the Birds-of-a-Feather session is forthcoming. More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona) (*) iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software development (see http://www.opensource.org/docs/definition.php) and reuse within the research community. For this reason, software to be demonstrated to conference attendees must be licensed with a recognized Open Source License (see http://www.opensource.org/ licenses/), and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial. Authors are advised that non-compliant submissions must be revised to meet the requirement by June 27 at the latest, and in the event that presentation slots run out, precedence is established by the date they are first found in compliance, not the date of submission.

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Missing Synonymy document
by David Remsen (GBIF) 19 May '10

19 May '10

Several TDWG related sites, lists, and mails have referenced a document houses at Yale illustrating zoological and botanical synonymy http://code.google.com/p/gbif-ecat/wiki/GNAsynonymsExample Anyone have a copy of this file? I've got a mail to the webmaster but just in case I thought I might ask here. Best, David

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Comment about the definition of the Darwin Core class Occurrence
by Steve Baskauf 02 May '10

02 May '10

I have posted a comment regarding the meaning of the Darwin Core class Occurrence and its relationship to other Darwin Core and Dublin Core terms. I would appreciate responses either on the Google Code darwincore site or via the tdwg-tag list (tdwg-tag(a)lists.tdwg.org) which I think is the appropriate venue for the discussion (I am cross-posting here because I'm not sure how many people are actually on the tag list). The comment is at: http://code.google.com/p/darwincore/issues/detail?id=70 Steve Baskauf -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

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[tdwg-phylo] Call for Lightning Talks open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 26 Apr '10

26 Apr '10

The Call for Lightning Talks is now open for the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs/index.php/ievobio/2010. See below for instructions. Lightning talks are short presentations of 5 minutes. They are ideal for drawing the attention of the audience to new developments, tools, and resources, or to subsequent events where more in-depth information can be obtained. Please also see our FAQ for more information (http://ievobio.org/faq.html#lightning ). Lightning talks will be part of the more interactive afternoon program on both conference days. Submitted talks should be in the area of informatics aimed at advancing research in phylogenetics, evolution, and biodiversity, including new tools, cyberinfrastructure development, large-scale data analysis, and visualization. Submissions consist of a title and an abstract at most 1 page long. The abstract should provide an overview of the talk's subject. Reviewers will judge whether a submission is within scope of the conference (see above). If applicable, the abstract must also state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met. Review and acceptance of lightning talks will be on a rolling basis. The deadline for submission is the morning of the first day of the conference (June 29). Note that the number of lightning talk slots is finite, and given the high volume of submissions we experienced for full talks, the Lightning Talks track may fill up early. We cannot accept lightning talks until the open-source requirements are met, and so waiting with that until the deadline risks that the track is full by that time. We ask all submitters of lightning talks to be willing to also serve as reviewers of such, as described above. Lightning talks are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of- a-Feather gatherings. The Call for Challenge entries remains open (see http://ievobio.org/challenge.html) , and information on the Software Bazaar and Birds-of-a-Feather sessions is forthcoming. More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona) (*) iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software development (see http://www.opensource.org/docs/definition.php) and reuse within the research community. For this reason, if a submitted talk concerns a specific software system for use by the research community, that software must be licensed with a recognized Open Source License (see http://www.opensource.org/licenses/), and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial.

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[tdwg-phylo] Deadline extension for full talk abstracts for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 07 Apr '10

07 Apr '10

The deadline for submitting abstracts for full talks to the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) has been extended by one week to Thursday, April 15, 2010. We hope that this will give those interested in contributing sufficient time to do so. Please see http://bit.ly/iEvoBio_CfA for the full Call for Abstracts and author instructions. We still expect to be able to notify accepted talks in time for the early registration deadline of iEvoBio (and Evolution). More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/ iEvoBio, and there is a Google group you can join at http://groups.google.com/group/ievobio-announce to receive announcements. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona)

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[tdwg-phylo] Student application deadline approaching for Google Summer of Code
by Hilmar Lapp 05 Apr '10

05 Apr '10

Reminder: Student applications are due by April 9, 19:00 UTC (3pm EDT, 12pm PDT, 21:00 CEST), which is only a few days away. PHYLOINFORMATICS SUMMER OF CODE 2010 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). NESCent is particularly targeting students interested in both evolutionary biology and software development. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. Full details about the 2010 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2010 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2010/faqs --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org

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[tdwg-phylo] Reminder: Deadline for full talk abstracts for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 03 Apr '10

03 Apr '10

This is a reminder that the deadline for submitting abstracts for full talks to the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) is Thursday, April 8, 2010, which less than 1 week away. Please see http://bit.ly/iEvoBio_CfA for the full Call for Abstracts and author instructions. As another reminder, full talks are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Lightning talks (5 mins long), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of-a-Feather gatherings. The Call for Challenge entries is also open (see http://ievobio.org/ challenge.html). Tentative submission deadlines are listed on the conference website (http://ievobio.org/program.html#dates). More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/ iEvoBio, and there is an announcment-only Google group at http://groups.google.com/group/ievobio-announce . You can use the group's RSS feed (see above URL), or join the group to receive announcements by email. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona)

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Re: [tdwg-content] tdwg-content Digest, Vol 13, Issue 1
by Nicolson, David 02 Apr '10

02 Apr '10

Roger et al., As was suggested by others, the >3-part "name" bit is resolved by looking at ICBN Article 24.1 (with my emphasis): "The *NAME* of an infraspecific taxon is a combination of the name of a species and an infraspecific epithet. A connecting term is used to denote rank." The Example right under it notes that such taxa "may be referred to" by the many-part strings... but while those convey information about the classification of the taxon they do not qualify as "names" under the Code. Note that you could have a 7-part monster like: Aus bus subsp. cus var. dus subvar. eus f. fus subf. gus But no matter how you slice it this would convey classification information, but is not technically a scientific "name" under the Code. It is rather more simple in zoology, since there is only one rank below species that can be used for valid/accepted names: subspecies... ...so nothing more than trinomial for either of these Codes. Cheers! ________________________________________ From: tdwg-content-bounces(a)lists.tdwg.org [tdwg-content-bounces(a)lists.tdwg.org] On Behalf Of tdwg-content-request(a)lists.tdwg.org [tdwg-content-request(a)lists.tdwg.org] Sent: Thursday, April 01, 2010 6:00 AM To: tdwg-content(a)lists.tdwg.org Subject: tdwg-content Digest, Vol 13, Issue 1 Send tdwg-content mailing list submissions to tdwg-content(a)lists.tdwg.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.tdwg.org/mailman/listinfo/tdwg-content or, via email, send a message with subject or body 'help' to tdwg-content-request(a)lists.tdwg.org You can reach the person managing the list at tdwg-content-owner(a)lists.tdwg.org When replying, please edit your Subject line so it is more specific than "Re: Contents of tdwg-content digest..." Today's Topics: 1. subvarieties and subformas in DwC (Roger Hyam) ---------------------------------------------------------------------- Message: 1 Date: Thu, 01 Apr 2010 10:55:45 +0100 From: Roger Hyam <rogerhyam(a)mac.com> Subject: [tdwg-content] subvarieties and subformas in DwC To: tdwg-content(a)lists.tdwg.org Message-ID: <05FAD862-9F58-405D-96F1-60EDF4A9C28E(a)mac.com> Content-Type: text/plain; charset=us-ascii Hi All, Is there a standard way of including 4 word names in DwC for the sub sub ranks such as subvarieties and subformas. I don't condone the use of these ranks but if we have to express them what do people normally do? Have I missed something in the docs? Many thanks, Roger ------------------------------ _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content End of tdwg-content Digest, Vol 13, Issue 1 *******************************************

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subvarieties and subformas in DwC
by Roger Hyam 01 Apr '10

01 Apr '10

Hi All, Is there a standard way of including 4 word names in DwC for the sub sub ranks such as subvarieties and subformas. I don't condone the use of these ranks but if we have to express them what do people normally do? Have I missed something in the docs? Many thanks, Roger

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