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Citizen Science Interest Group home
by andrea thomer 31 May '12

31 May '12

Hello all, Over the last few months Arthur Chapman and I have been (unfortunately rather slowly) pulling together a charter for a Citizen Science Interest Group (CSIG); this charter (available at http://bit.ly/JPQpal) was ratified on March 9. We've had a bit of trouble pulling a wiki together, so until we get that figured out, we're using a Google Group for messages and other information. If you'd like to join, please request an invitation through the Google Group: https://groups.google.com/group/tdwg-CSIG If you have any questions, comments, or concerns, please don't hesitiate to post to the group's forums, or email me or Arthur directly. Thanks, Andrea Thomer RA, Center for Informatics Research in Science and Scholarship Graduate School of Library and Information Science University of Illinois at Urbana-Champaign

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Semantics of Biodiversity Webcast/Voice access
by John Deck 16 May '12

16 May '12

Yes, we were able to get web/voice access running for semantics of biodiversity workshop which is happening right now! 9am-5pm Central time, US -- Agenda: https://docs.google.com/document/d/1Z-RytvBlinIcSD3ctK1kiWUs2rr4TOxijT2TQb9… You can follow along and provide feedback via the chat window (which i'll monitor) using the following instructions *********** Anyone can join the meeting during scheduled meeting times and listen/view slides using the access code below. The audio portion is via phone conference and visuals via web-conference. Step 1: Dial-In U.S. & Canada: 866.740.1260 Germany: 08006645316 (Toll Free) United Kingdom: 08004960576 (Toll Free) List of global toll-free numbers: http://www.readytalk.com/legacy/an.php?tfnum=8667401260 Access Code: 8585349 Step 2: Web Login https://cc.readytalk.com/r/osfex4x22ka6 -- John Deck (541) 321-0689

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BioJS
by Bob Morris 13 May '12

13 May '12

http://www.ebi.ac.uk/~jgomez/biojs/registry/index.html describes an object-oriented library (and mechanisms for extending it) of JavaScript components that can probably be easily extended to other biodiversity informatics concerns than the ones in the library. This could make it quite easy to have common look-and-feel web apps within and between projects. Further details and participation at http://code.google.com/p/biojs/ --Bob -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Harvard University Herbaria Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram === The content of this communication is made entirely on my own behalf and in no way should be deemed to express official positions of The University of Massachusetts at Boston or Harvard University.

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W3C best practices for publishing RDF vocabularies
by Bob Morris 12 May '12

12 May '12

http://www.w3.org/TR/swbp-vocab-pub/ Although it is 4 years old, I don't recall having seen this before. Sorry for duplication if it is already on the radar of the tdwg rdf best practices task group. -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Harvard University Herbaria Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram === The content of this communication is made entirely on my own behalf and in no way should be deemed to express official positions of The University of Massachusetts at Boston or Harvard University.

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Call for Challenge entries for iEvoBio conference
by Cellinese,Nico 10 May '12

10 May '12

Many trees enter. Fresh analysis ensues. New insights emerge. As a reminder, the iEvoBio conference is again holding a Challenge competition in 2012, this time on the theme, "Synthesizing Phylogenies." Further information on the nature of challenge entries and how to submit them can be found on the iEvoBio website at http://ievobio.org/challenge.html. Submissions are due by June 25, 2012. Cash prizes will be awarded for first place (USD 1,500) and runner-up entries. The winning entries will be selected by a vote of the iEvoBio meeting participants. Also, alongside the iEvoBio Challenge, 2012 iEvoBio sponsor Biomatters Ltd is running the Geneious Challenge. The goal of this challenge is to develop a new plugin to Geneious Pro, using the public API, that enables a new and exciting visualization or analysis. The winning entry will receive a $1000 cash prize, and all entrants who submit by the deadline will receive a 12-month subscription license. The deadline for the Geneious Challenge is the same as for the iEvoBio Challenge. Seehttp://ievobio.org/geneious_challenge.html for more information. More details about the iEvoBio conference and program are available at http://ievobio.org<http://ievobio.org/>. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign

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Fwd: First Draft of Core Open Annotation Specification (Community Draft 1) published by Open Annotation Community Group [via Open Annotation Community Group]
by Bob Morris 05 May '12

05 May '12

Also see the Community Draft of the associated Extension Specification ---------- Forwarded message ---------- From: Search Team <webmaster(a)w3.org> Date: Fri, May 4, 2012 at 2:18 PM Subject: First Draft of Core Open Annotation Specification (Community Draft 1) published by Open Annotation Community Group [via Open Annotation Community Group] To: public-openannotation(a)w3.org On 2012-05-04 the Open Annotation Community Group published the first draft of the following specification: Core Open Annotation Specification (Community Draft 1). Participants contribute material to this specification under the W3C Community Contributor License Agreement (CLA). If you have any questions, please contact the group on their public list: public-openannotation(a)w3.org. Learn more about the Open Annotation Community [...] ---------- This post sent on Open Annotation Community Group 'First Draft of Core Open Annotation Specification (Community Draft 1) published by Open Annotation Community Group' https://www.w3.org/community/openannotation/2012/05/04/first-draft-of-core-… Learn more about the Open Annotation Community Group: http://www.w3.org/community/openannotation -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Harvard University Herbaria Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram === The content of this communication is made entirely on my own behalf and in no way should be deemed to express official positions of The University of Massachusetts at Boston or Harvard University.

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Call for Software Bazaar entries open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity
by Cellinese,Nico 24 Apr '12

24 Apr '12

The Call for Software Bazaar entries is now open for the 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs2/index.php/ievobio/2012. 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 approximately 2.0 hours in duration. Conference attendees will be able to walk from one demonstration to the next and talk with the presenters. Please also see our FAQ (http://ievobio.org/faq.html) 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). 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 (http://www.confersense.ca/Evolution2012) 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 can be obtained, and the license under which the source code is available. The website must contain a link to where the source code (and possibly binaries) can be downloaded. If it is not obvious from the 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, a large display, or other hardware. 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 (July 10), but, because space for Software Bazaar presentations is finite, we cannot guarantee the availability of slots for late submissions. We cannot accept submissions until the open-source requirements are met. Software 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 the Birds-of-a-Feather call is forthcoming. More details about the conference and program are available at http://ievobio.org<http://ievobio.org/>. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida and Florida Museum of Natural History Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign (*) 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 July 8 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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Semantics of Biodiversity Workshop
by John Deck 06 Apr '12

06 Apr '12

Following is a workshop of broad interest to many of you. If you are interested in attending or have further questions, please contact John Deck (jdeck(a)berkeley.edu) Note that there is a limited time in which to make your guaranteed hotel reservations at the The Oread hotel in Lawrence, under the "Biodiversity Semantics Workshop", which must be done before April 15th to get the reserved rate. Feel free to forward or post. Cheers, John ******* Google Doc link describing workshop and agenda: https://docs.google.com/document/d/1Z-RytvBlinIcSD3ctK1kiWUs2rr4TOxijT2TQb9… Text Description of above google doc link: Semantics of Biodiversity Workshop May 16 - 18, 2012 University of Kansas Biodiversity Institute -- Lawrence, Kansas Sponsored by RCN4GSC, Morphbank, Kansas University Biodiversity Informatics Center, and BiSciCol in collaboration with the National Center for Biomedical Ontology ** ABOUT THE SPEAKER ** Barry Smith is a prominent contributor to ontology research in biomedical and other domains. He is one of the principal scientists of the NIH National Center for Biomedical Ontology, a Scientific Advisor to the Gene Ontology Consortium, a PI on the Protein Ontology and Infectious Disease Ontology projects, and one of the founders of the Open Biomedical Ontologies (OBO) Foundry initiative. TOPICS ** The Semantics of Biodiversity Workshop will explore terms used to describe biological collection objects and their derivatives using the Darwin Core standard as a starting point. The goal is to enable linking data across domains and to produce a deeper understanding of our planet’s biodiversity. For example, by linking information about the ecosystem (both gross and micro-habitat) and the geospatial environment to tissue samples and derived sequences, we can better understand population dynamics, ecosystem gene expression, and the significance of biodiversity in different environments. While the biodiversity informatics community has made much progress in standardizing terms over the last 20 years, specific problem areas are encountered both within and between relevant standards domains. Drawing on community discussions from the TDWG and GSC communities, and using the experiences of OBO in integrating information, Smith will guide a discussion of term clarification for the Darwin Core standard. Some example discussion topics are: - How do samples and occurrences relate to each other? - How can we best distinguish between collection objects, observations, and individuals? - What is the nature of the relationship between habitats, environments, and environmental materials? - What is the difference between a set, a lot, and a collection? - How to deal with taxonomic names associated with collection objects? Much of the workshop will be devoted to these and other discussion topics that will be introduced by attendees. Come prepared with your topics and/or important darwin core terms and be able to introduce them. It will be helpful to indicate before the workshop what topic you can introduce at the meeting by emailing jdeck(a)berkeley.edu. ** ** Day 1 (Wednesday, May 16th) 9am - 5:30pm Coffee & treats Wednesday and Thursday hosted by KU Breakfast at Hotel all 3 days Lunch and dinner on your own, with plenty of options within walking distance Background and problem statement (Wednesday) - Review successful examples from other communities - Getting clear on the distinctions between objects, data, and metadata - Contrasting annotation with metadata - Relationship expressions. - Tracking Identifiers to refer to objects or classes uniquely. Applying ontological principles to our subject domain (Wednesday and Thursday) - Interactive review of 10 or so of the most important Darwin core terms from the ground up. Participants will be describing terms and the intention behind their original formation. Come prepared to discuss your term(s) of interest. 6pm- 7:30pm Reception hosted by Kansas University’s Biodiversity Institute Day 2 (Thursday, May 17th) 9am - 5:30pm Solutions for the future (Thursday) - Enabling linked data - Pitfalls, traps, and planning - Creating a sociology so people can re-use ontologies Planning the 3rd Day discussions (4-5:30pm on Thursday) - Barry will be departing at 4pm on Thursday and so we will use the remainder of day to plan our discussion for Friday. ** Day 3 (Friday, May 19th) 9am - Noon We will be collecting discussion topics on Thursday afternoon for our Friday discussion. Some possible topics include: - Develop concrete proposals for Darwin Core term clarification - Do we need a new namespace for Darwin Core (for enforcing URIs)? - Implications for MIxS Standard - Implications for the Darwin Core Archive Format - Recommendations to the TDWG-RDF Group -- John Deck (541) 321-0689

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Deadline extension for full talk abstracts for Conference on Informatics
by Cellinese,Nico 03 Apr '12

03 Apr '12

The deadline for submitting abstracts for full talks to the 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) has been extended to Monday, April 9, 2012. We hope that this will give those interested in contributing sufficient time to do so. Please see http://bit.ly/iEvoBio2012_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 athttp://ievobio.org<http://ievobio.org/>. You can also find continuous updates on the conference's Twitter feed (http://twitter.com/iEvoBio) or Google Plus page (http://bit.ly/iEvoBio-on-Gplus) and there is a Google group you can join at http://groups.google.com/group/ievobio-announce to receive announcements. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Society of Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida and Florida Museum of Natural History Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign

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Change genus definition or introduce genericName?
by Peter Desmet 22 Mar '12

22 Mar '12

Hi everyone, A spin-off of the discussion regarding canonicalScientificName (and possibly a solution to it as well) concerns the term "genus". As mentioned before, most people probably interpret this term as "The name of the genus of the scientificName." - scientificName: *Aster* simplex var. ramosissimus (Torrey & A. Gray) A. Cronquist - acceptedNameUsage: Symphyotrichum lanceolatum (Willdenow) G.L. Nesom subsp. lanceolatum var. lanceolatum - genus: *Aster* - specificEpithet: simplex - infraspecificEpithet: ramosissimus Even though it is defined as "The full scientific name of the genus in which the taxon is classified.", which leads to this for synonyms: - scientificName: Aster simplex var. ramosissimus (Torrey & A. Gray) A. Cronquist - acceptedNameUsage: *Symphyotrichum* lanceolatum (Willdenow) G.L. Nesom subsp. lanceolatum var. lanceolatum - genus: *Symphyotrichum Nees* - specificEpithet: simplex - infraspecificEpithet: ramosissimus For more background on this issue, please read: http://code.google.com/p/darwincore/issues/detail?id=151 & http://lists.tdwg.org/pipermail/tdwg-content/2012-March/002877.html There are now two possible solutions on the table (by Markus Döring, http://code.google.com/p/darwincore/issues/detail?id=151#c7) for sharing the genus name part we have 2 options: A) consistent dwc approach: We keep the dwc:genus definition as it is to be inline with the other classification terms including subgenus. All of these should contain the accepted classification, not necessarily the part of the name. Two new terms genericName and infragenericEpithet are then proposed to hold the genus part of a name and the infra generic part. This approach keeps the dwc terms consistent and does not mix classification terms with terms for atomized names. B) least change approach: Taking into account that many people already use dwc:genus for the name part we alter the definition of the term as proposed here. This results in the least impact on existing publishers and probably consumers too. But it has the drawback of i) dwc terms are inconsistent with family & subgenus being the classification, not the name part, ii) no option anymore to share the genus classification, iii) no way to share all infra generic names I would hope we can start a vote around those 2 options with A) being my clear favorite We need your opinion and input to move this issue forward. Thanks, Peter -- Peter Desmet Biodiversity Informatics Manager Canadensys - www.canadensys.net Université de Montréal Biodiversity Centre 4101 rue Sherbrooke est Montreal, QC, H1X2B2 Canada Phone: 514-343-6111 #82354 Fax: 514-343-2288 Email: peter.desmet(a)umontreal.ca / peter.desmet.cubc(a)gmail.com Skype: anderhalv Public profile: http://www.linkedin.com/in/peterdesmet

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