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Birds-of-a-Feather gatherings for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 14 Jun '10

14 Jun '10

In anticipation of the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), we solicit all attendees to propose and discuss Birds-of-a-Feather gatherings. See below for details. Birds-of-a-Feather gatherings (BoFs) are informal, ad-hoc, focused face-to-face discussion groups that form around a shared interest. BoFs have a leader (usually, but not necessarily, the proposer) who initiates or moderates the discussion, but typically not a preset agenda. The topics of BoFs can range widely, including general cultural or computational infrastructure issues, or narrower questions such as how to make the best use of a particular software tool or how to solve a particular computational challenge. Anyone willing to lead such a group can propose a BoF. iEvoBio will provide space that can accommodate up to 8-10 BoFs. Sign-up sheets will be provided on-site on the first day of the conference where attendees can propose a BoF or sign up for one proposed by someone else. BoFs will be about 1 hr in duration and take place in the afternoon of the second day of the conference. In line with their informal nature, there is no official prior call for or submission of BoFs. However, we encourage those intending to propose one to sound out or rally potential attendees ahead of time. We suggest to employ Twitter (http://twitter.com) for this, using the #ievobioBof tag to mark BoF proposals and comments. Birds-of-a-Feather gatherings are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Lightning talks (waiting list only), 3) Challenge entries, and 4) Software Bazaar entries. The Calls for Challenge entries (http://ievobio.org/challenge.html) and Software Bazaar entries (http://ievobio.org/ocs/index.php/ievobio/2010/) remain open. 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)

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Deadline for Call for Challenge entries for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Hilmar Lapp 08 Jun '10

08 Jun '10

This is a reminder that the Call for Challenge entries for the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) closes in two weeks on June 21, 2010. The theme of the 2010 iEvoBio conference challenge is "New visualization methods for evolutionary data". Visualizing evolution is a key part of our discipline and presents opportunities as much as it does obstacles. The iEvoBio Challenge is deliberately wide ranging: entries could range from geophylogenies to visualizing extremely large phylogenetic trees, to mashups showing relationships between lineages and other types of data (e.g. conservation status). 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 . Selected candidates will make short oral presentations to demonstrate their visualization in a "Challenge session" at the conference, and will automatically be entered into the Software Bazaar if suitable. The winners of the Challenge will be judged collectively by the iEvoBio participants. There will be cash prizes for the first place ($1,000) and runner up entries. Challenge entries 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) Software Bazaar entries, and 4) Birds-of-a-Feather gatherings. The Calls for Lightning Talks and Software Bazaar entries remain open (see http://ievobio.org/ocs/index.php/ievobio/2010/), 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. Continuous updates can also be found 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)

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a science metadata and standards wiki
by Jim Croft 04 Jun '10

04 Jun '10

this was established over a year ago, but with traditional slackness I missed it. The Dublin Core bods posted this today: http://dublincore.org/groups/sam/ which has a link to this: http://ils.unc.edu/spaces/sam/index.php/Main_Page which includes a link to this: http://ils.unc.edu/spaces/sam/index.php/Standards chunks of our biodiv stuff are covered and referenced. apologies to those for whom this is boring old stuff... jim -- _________________ Jim Croft ~ jim.croft(a)gmail.com ~ +61-2-62509499 ~ http://www.google.com/profiles/jim.croft 'A civilized society is one which tolerates eccentricity to the point of doubtful sanity.' - Robert Frost, poet (1874-1963)

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string literals vs. uris for dwc:recordedBy, dwc:identifiedBy, and dwc:georeferencedBy in RDF
by Steve Baskauf 01 Jun '10

01 Jun '10

The definition for the Darwin Core term recordedBy http://rs.tdwg.org/dwc/terms/index.htm#recordedBy says "A list (concatenated and separated) of names ...". The examples given are string literals. However, when using this term as a predicate in RDF, it would seem preferable to use a URI to an RDF representation of the entity (if one exists) rather than a string literal. For example, can I use: <dwc:recordedBy rdf:resource="http://people.vanderbilt.edu/~steve.baskauf/foaf.rdf#me"/> rather than <dwc:recordedBy>Steven J. Baskauf</dwc:recordedBy> ? 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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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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Darwin Core generic XML with attributes
by Steve Baskauf 21 May '10

21 May '10

This recent discussion reminds me of a question that I have been wondering about for several months and hadn't gotten around to bringing up: can you have a Darwin Core XML representation where an element has a literal value and an attribute? If the XML is RDF, then I think the answer is pretty much "no" as I just found out with the W3C Validator. However, in generic XML I don't think there is any rule that says that one can't have any attribute that one wants. The only guidance I know of on the subject is: http://rs.tdwg.org/dwc/terms/guides/xml/index.htm#implement It states that the value of a Darwin Core property should be the content of the element rather than stating the value as an attribute. However, I have the situation where I want to store or transfer two somewhat equivalent representations of the value of a property: a string literal form and a URI form. In the example we've been talking about, I would like my generic (non-RDF) XML to do something like this: <?xml version="1.0" encoding="UTF-8"?> <dwr:SimpleDarwinRecordSet xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dwc="http://rs.tdwg.org/dwc/terms/" xmlns:dwr="http://rs.tdwg.org/dwc/xsd/simpledarwincore/" > <dwr:SimpleDarwinRecord> <dwc:occurrenceID rdf:resource="http://herbarium.org/hb123456">http://herbarium.org/hb123456</dwc:occurrenceID> <dwc:recordedBy rdf:resource="http://people.vanderbilt.edu/~steve.baskauf/foaf.rdf#me">Steve Baskauf</dwc:recordedBy> <dwc:basisOfRecord rdf:resource="http://rs.tdwg.org/dwc/dwctype/PreservedSpecimen">PreservedSpecimen</dwc:basisOfRecord> ... more elements, mostly with string literal values... </dwr:SimpleDarwinRecord> </dwr:SimpleDarwinRecordSet> This would meet the basic guidelines of the Darwin Core XML Guide in that the literal values would be the contents of the elements. What I don't know is if the inclusion of the rdf:resource attributes would invalidate the XML if it were validated against someone's schema that was silent about attributes or if the schema would have to explicitly say that having an rdf:resource attribute was a valid option. I think I don't know enough about XML schemas ... The reason why I would like to maintain/transfer both types of values (literal and URI) is so that I could use the XML data to generate both HTML and RDF if I wanted. The HTML would tell humans that the occurrence was a PreservedSpecimen, but the RDF would tell a linked data client that the occurrence was a http://rs.tdwg.org/dwc/dwctype/PreservedSpecimen . I realize that for my own internal use, the XML can have any format I want, but if I were exporting XML for general public use, would it be bad to use the approach above? Steve As an aside, I wanted to see exactly what the definition was for rdf:resource However, the usual namespace for rdf: (http://www.w3.org/1999/02/22-rdf-syntax-ns#) doesn't seem to include "resource" in the defined properties. Very odd! Maybe I'm just missing something... -- 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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Fwd: Mountain Biodiversity Portal online!
by Javier de la Torre 13 May '10

13 May '10

Hi all, I am forwarding this email because I think you might find it interesting. Soon we will be posting more info about the project on the biodivertido blog. All source code is Open Source. Javier. Begin forwarded message: > From: Global Mountain Biodiversity Assessment <GMBA(a)unibas.ch> > Date: May 10, 2010 12:29:51 PM GMT+02:00 > To: gmba(a)unibas.ch > Subject: Mountain Biodiversity Portal online! > > Dear colleagues, > > we are very happy to announce that the GMBA/GBIF Mountain Biodiversity Portal is now online! > > You can now explore and download GBIFs biodiversity data (http://www.gbif.org) for the mountains of the world, and search mountain areas from region to globe, or select by mountain life zones (such as the treeless alpine zone) on an interactive map. > > You are welcome to visit the Mountain Biodiversity Portal at http://www.mountainbiodiversity.org > See the demo video on how to use it: (http://vimeo.com/11552863). > > The Mountain Biodiversity Portal is a contribution to the Mountain Programme of the Convention on Biological Diversity disussed today in Nairobi (http://www.cbd.int/sbstta14/) and is GMBA/DIVERSITAS contribution the the International Year of Biodiversity 2010. > > We are looking forward to receive your feedback on this new tool. > > With kind regards, > Eva Spehn > -- > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > Global Mountain Biodiversity Assessment (GMBA) > Dr. Eva Spehn, GMBA office > > Institute of Botany, University of Basel > Schoenbeinstr.6, 4056 Basel, Switzerland > Tel: ++41 (0)61 267 35 11, Fax: ++41 (0)61 267 35 04 > > email: gmba(a)unibas.ch > GMBA network: http://www.gmba.unibas.ch/ > GMBA Mountain Portal: http://www.mountainbiodiversity.org

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Referring to GBIF distribution map in RDF
by Roderic Page 11 May '10

11 May '10

Dear All, I'm interested in referring to a GBIF distribution map in RDF, and am having fun figuring out how to do it. One way is to use a c-squares- based URI, see http://iphylo.blogspot.com/2010/05/referring-to-one-degree-s quare-in-rdf.html (http://tinyurl.com/33ba4kt). The idea is that each 1° × 1° square in a GBIF map has it's own c- squares-based URI, e.g. http://bioguid.info/csquare:3317:364 , and hence a distribution would be a list of these URIs (perhaps with the number of records from each square). Any thoughts on this approach, and whether we have an existing vocabulary to describe these relationships? Regards Rod --------------------------------------------------------- Roderic Page Professor of Taxonomy DEEB, FBLS Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r.page(a)bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962(a)aim.com Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html

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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 this 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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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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