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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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iDigBio announces open registration for July 12 workshop
by Austin Mast 24 Apr '12

24 Apr '12

iDigBio announces open registration for the Specimen Digitization Tools and Practices Workshop at the Botany 2012 Conference (http://www.botanyconference.org/). The workshop is designed to introduce current and future biological and paleontological specimen collections staff to resources and workflows that can lead to greater efficiencies in the digitization of their collections. The workshop is organized by iDigBio, the National Resource for Advancing Digitization of Biological Collections. It will be held from 8:00 AM – 5:30 PM on Thursday, July 12, the day after the conference at the conference facility in Columbus, OH. Breakfast, lunch, and dinner for registered workshop participants will be provided. To register for the workshop, send an email by June 15 to Cathy Bester (cbester(a)flmnh.ufl.edu) that includes your name and institution as you would like them to appear on your name tag. iDigBio will accommodate as many participants as the budget permits. For a schedule and additional information visit https://www.idigbio.org/content/idigbio-botany-2012-digitization-workshop-o… iDigBio has also organized a symposium entitled “Building a High-Resolution, Specimen-Based Picture of Life: Possibilities and Challenges” for the Botany 2012 conference. It will be held on the afternoon of Wednesday, July 11, from 1:30-5:45. More details on the symposium are available at http://www.botanyconference.org/engine/search/?func=AbstractTitle&section=3…. iDigBio is the National Resource for Advancing Digitization of Biological Collections (ADBC) funded by the National Science Foundation. The mission of iDigBio is to develop a national infrastructure that supports the vision of ADBC by overseeing implementation of standards and best practices for digitization; building and deploying a customized cloud computing environment for collections; recruiting and training personnel, including underserved groups; engaging the research community, collections community, citizen scientists, and the public through education and outreach activities; and planning for long-term sustainability of the national digitization effort. For more information, visit http://www.idigbio.org. With best regards, Austin Austin Mast Associate Professor Director of the Robert K. Godfrey Herbarium Member of the Steering Committee of iDigBio, The National Resource for Advancing Digitization of Biological Collections Department of Biological Science 319 Stadium Drive Florida State University Tallahassee, FL 32306-4295 U.S.A. Office: King Life Science Building, room 4065 Lab: King Life Science Building, rooms 4068 and 4084 Herbarium: Biological Science Unit One, room 100 Voice: 1 (850) 645-1500 Fax: 1 (850) 645-8447 amast(a)bio.fsu.edu

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tdwg 2012 in inappropriate venue
by Bob Morris 22 Apr '12

22 Apr '12

Dear fellow TDWG members, As I said publicly at TDWG 2011, I feel that it is inappropriate for an organization devoted to the open exchange of scientific data and information to hold a meeting in a country where there is routine governmental suppression of internet connectivity on political grounds. I personally would attend any scientific meeting in such a country except one by an organization like TDWG which should be taking a position about openness of access to information, and I hope others will join me in this position and publicly decline to attend TDWG 2012. Sometimes an argument is made in such cases that participation is a way to support the hosting organization, which in this case is eminent. But often just the opposite can result: the authorities will proudly say to themselves: "See, they come anyway." Bob Morris -- 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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Five years on: major conference on libraries and the Semantic Web, 27 April 2012 - Final announcement
by DCMI Announce 10 Apr '12

10 Apr '12

There are still places available for the Seminar “Five years on”, marking the five years of progress in library linked data since the “London Meeting” of 2007. The Seminar takes place on Friday 27 April 2012, 09.00/30 to 17.00. The venue for the Seminar is the British Library, St. Pancras, London. The final list of speakers for the Seminar includes: * Mikael Nilsson, Google * Edmund Chamberlain, Cambridge University Library * Alan Danskin, British Library * Barbara Tillett, Joint Steering Committee for the Development of RDA (JSC) * Robina Claphan, Europeana * Mirna Willer, IFLA ISBD Review Group * Pat Riva, IFLA FRBR Review Group * Thomas Baker, DCMI * Gordon Dunsire, IFLA Namespaces Technical Group and DCMI * Diane Hillmann, DCMI and Metadata Management Associates * Owen Stephens, JISC The London Meeting of 31 April/1 May 2007 stimulated significant development of Semantic Web representations of the major international bibliographic metadata models, including IFLA’s Functional Requirements family and the International Standard Bibliographic Description (ISBD), and MARC as well as RDA itself. Attention is now beginning to focus on the management and sustainability of this activity, and the development of high-level semantic and data structures to support library applications. Registration for the Seminar has been set at USD 190 (including VAT), which includes lunch and refreshments for two breaks. Further information and online registration is available at: http://dcevents.dublincore.org/index.php/BibData/fyo Please note that registration for the DCMI meetings on Thursday 26 April has now closed, as all places have been taken. Cheers, and apologies for cross-posting.

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NISO/DCMI Webinar with Dan Brickley: Schema.org and Linked Data
by DCMI Announce 03 Apr '12

03 Apr '12

***Please excuse the cross-posting*** =============================================================== NISO/DCMI Webinar: Schema.org and Linked Data: Complementary Approaches to Publishing Data PRESENTER: Dan Brickley DATE: April 25, 2012 TIME: 1:00pm - 2:30pm Eastern (17:00-18:30 UTC) INFORMATION & REGISTRATION: http://www.niso.org/news/events/2012/dcmi/linked_data/ =============================================================== ABOUT THE WEBINAR Schema.org--a collaboration of the Google, Yahoo!, and Bing search engines--provides a way to include structured data in Web pages. Since its introduction in June 2011, the Schema.org vocabulary has grown to cover descriptive terms for content such as movies, music, organizations, TV shows, products, locations, news items, and job listings. The goal of Schema.org is "to improve the display of search results, making it easier for people to find the right web pages." The Schema.org initiative has emerged as a focal point for publishers of structured data in Web pages, especially but not exclusively in the commercial sector. This webinar will explore how the publication methods of Schema.org relate to the methods used to publish Linked Data. Must data providers commit to one or the other, or can the two approaches exist side-by-side, even reinforcing each other? TOPICS AND SPEAKERS Dan Brickley is best known for his work on Web standards in the W3C community, where he helped create the Semantic Web project and many of its defining technologies. Dan is currently working on outreach activities related to the Schema.org initiative. Previous work included six years on the W3C technical staff, establishing ILRT's Semantic Web group at the University of Bristol, and more recently at Joost, an Internet TV start-up, and at the Vrije University Amsterdam. He has been involved with resource discovery metadata since 1994 when he published the first HTML Philosophy guide on the Web, and has been exploring distributed, collaborative approaches to "finding stuff" ever since. Thomas Baker, Chief Information Officer of the Dublin Core Metadata Initiative, has recently co-chaired the W3C Semantic Web Deployment Working Group and the W3C Incubator Group on Library Linked Data. REGISTRATION Registration is per site (access for one computer) and closes at 12:00 pm Eastern (16:00 UTC) on April 25, 2012. Discounts are available for NISO and DCMI members and students. Can't make it on the webinar date/time? Register now and gain access to the recorded archive for one year. NISO/DCMI are holding four joint webinars in 2012. Register for three and receive the 4th for free. For more information and to register, visit the event webpage: http://www.niso.org/news/events/2012/dcmi/linked_data/

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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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species group - Dwc interpretations?
by Peter Oboyski 01 Apr '12

01 Apr '12

Hi all, Forgive me if this has been discussed already. I am trying to decide how to deal with species groups in our database. Here are some real life examples. Eg. Terellia sp. (virens group) option 1: Genus: Terellia SpecificEpithet: virens TaxonCertainty: species group option 2: Genus: Terellia SpecificEpithet: sp. (virens group) Eg. Oecetis new sp.? inconspicua group option 1: Genus: Oecetis SpecificEpithet: new sp. TaxonCertainty: "?" how do I incorporate the group? option 2: Genus: Oecetis SpecificEpithet: n.sp. (inconspicua group) TaxonCertainty: "?" --------------------------------------------------- Peter T Oboyski University of California http://nature.berkeley.edu/~poboyski/ ---------------------------------------------------

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Re: [tdwg] [Taxacom] Whitepaper consultation on Biodiversity Informatics
by Peter Stevens 30 Mar '12

30 Mar '12

Mmm, I don't see that one can have useful content sans questions. Maybe this is part of the problem, assuming that taonomic literature has useful data? P. On Mar 30, 2012, at 7:59 AM, Chris Thompson wrote: > Thanks, Rod, > > for the great comment on the focus should be on "questions," not > technologies. > > BUT I would add the basic focus should FIRST be on content. The > information > that can be used to answer questions. > > In the half century, I have been in the "biodiversity" business, > what has > been the clear trend is the continued re-invention of the > "infrastructure > technologies," investing big bucks in "new and better" software, > etc., but > virtually nothing on content. The old "taxonomy is free" paradigm. > People > have questions, they want answer, so the critical component is > content, the > information necessary to answer those question. Not so new > technology to > simply re-scuffle the old information. > > We run the Systema Dipterorum (see us at www.diptera.org), an online > nomenclator and species database for more than 10% of the known > biodiversity, flies (Insecta: Diptera), which are critical as they > have one > of this highest impact on human society, as disease vectors, > pollinators, > crop pests, biological control agents, model organisms (Drosophila), > forensics indicators, etc. We provide basic information on more > than 160,000 > species and a quarter of million names, with simple obsolete software > (FileMakerPro version 6), but as we have a budget of only some 50K > per year > we focus on content, trying to keep up with the thousands of new > species > being added annually, etc. And enhancement of our basic content. > > What we need is support to improve our content, to enhance it, to > have it > "peer-reviewed," etc. No some new software to simply re-format it. > > Oh, well ... > > back to the data ... > > Sincerely, > > Chris > > see us at www.diptera.org > > -----Original Message----- > From: Roderic Page > Sent: Friday, March 30, 2012 3:43 AM > To: Dave Roberts > Cc: Norman Morrison ; Peter van Tienderen ; Hannu Saarenmaa ; Alex > Hardisty > ; tdwg(a)lists.tdwg.org ; taxacom > Subject: Re: [Taxacom] Whitepaper consultation on Biodiversity > Informatics > > Dear Dave, > > This sounds like a great opportunity. > > That said, I little part of me dies when I read "infrastructure" > documents. > The focus is invariably on technologies rather than questions, and > I don't > think people actually want "infrastructure", they want things to > help them > do the things they're trying to do (as opposed to cool things that > could be > built for them). > > I've made some comments on the topics, but rather than pollute your > own > outline with my grumpiness, I've made a copy and scribbled some > thoughts on > that. The annotated document is at > https://docs.google.com/document/d/ > 1VLvysjbm6IUhceAEgkAWSQ9yc71YK-9_48bPNZACZPo/edit > or http://bit.ly/H17nLs if that link gets mangled. > > Regards > > Rod > > > On 29 Mar 2012, at 12:31, Dave Roberts wrote: > >> Dear Colleague, >> >> we need funding to pursue biodiversity research, but funding is >> under huge >> pressure. One area for which there is potential is in biodiversity >> informatics because we are witnessing a paradigm shift in the way we >> handle data. Now it is expected that data will be openly accessible, >> presenting huge opportunities if only the data can be found when >> needed. >> >> There is a strong need for a community voice to present the >> funders with a >> set of priorities. We have successfully built a number of >> infrastructural >> components, such as INSDC, GBIF, Catalogue of Life, but we lack the >> bridges to allow users to integrate elements from these resources to >> address a simple question. >> >> With the encouragement of the European Commission, we are launching a >> consultation to write a White Paper on biodiversity informatics. >> We have >> made a list of potential chapters with a brief outline of what >> they might >> cover here: >> >> http://is.gd/WhitePaperChapters >> >> This document is a public Google doc. The approach we propose is >> to ask >> for volunteers to lead the development of each chapter. >> >> * If you can identify a new chapter, please add it to the Chapters >> list >> >> * If you are prepared to lead a chapter, put your name against the >> chapter, open a new public googledoc and past the link into the >> chapters >> list. >> >> * Please do not create chapters dedicated to specific disciplines, >> such as >> molecular biology, because there is no way to prioritise one >> discipline >> against another. >> >> * Three funded EU projects will administer the production of the >> white >> paper. agINFRA, BioVeL and ViBRANT will supply. We will edit the >> chapters >> for continuity and will produce an executive summary. >> >> * If you are able to join the editorial group, email one of the >> organisers. We expect this to work by self-nomination. >> >> The European Commission would like access to such a community view in >> forming the funding calls under Horizon2020. It is possible that >> other >> funders may pay similar attention. It makes no sense to do this >> over just >> Europe. We recognise that biodiversity is global and we need global >> priorities. >> >> Timetable >> 27 April: initial draft chapters; propose group meetings with >> dates in May >> >> 1 June: refined chapters merged by editorial group >> >> 22 June: draft executive summary and edited chapters >> >> July: public meeting >> >> 1st Sept: Publication of white paper >> >> This timetable is tight because the Horizon2020 funding calls will be >> drafted in the last quarter of 2012. To have real benefit in >> Europe, we >> need to move quickly. >> >> Organising Group: >> Alex Hardisty <hardistyAR_at_cardiff_dot_ac_dot_uk> >> Dave Roberts <dmr_at_nomencurator_dot_org> >> Hannu Saarenmaa <hannu_dot_saarenmaa_at_uef_dot_fi> >> Norman Morrison <norman_at_nmorrison_dot_info> >> Peter van Tienderen <P_dot_H_dot_vanTienderen_at_uva_dot_nl> >> -- >> Dr D.McL. Roberts, Tel: +44 (0)20 7942 5086 >> Dept. Zoology, >> The Natural History Museum, >> Cromwell Road, >> London SW7 5BD >> Great Britain Email: dmr(a)nomencurator.org >> Web page: >> http://scratchpads.eu >> http://www.nhm.ac.uk/research-curation/projects/euk-extreme/ >> -- >> "The intent of [bureaucratic] language is not to deceive, it is to >> preserve one's interpretive latitude so that if context changes a >> new more >> approporiate meaning can be attached to the language already used." >> Matthew Crawford (The case for working with your hands, Penguin 2010) >> -- >> >> >> >> >> _______________________________________________ >> >> Taxacom Mailing List >> Taxacom(a)mailman.nhm.ku.edu >> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom >> >> The Taxacom archive going back to 1992 may be searched with either of >> these methods: >> >> (1) by visiting http://taxacom.markmail.org >> >> (2) a Google search specified as: >> site:mailman.nhm.ku.edu/pipermail/taxacom your search terms here >> > > --------------------------------------------------------- > Roderic Page > Professor of Taxonomy > Institute of Biodiversity, Animal Health and Comparative Medicine > College of Medical, Veterinary and Life Sciences > 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 > Skype: rdmpage > 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 > > _______________________________________________ > > Taxacom Mailing List > Taxacom(a)mailman.nhm.ku.edu > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom > > The Taxacom archive going back to 1992 may be searched with either > of these > methods: > > (1) by visiting http://taxacom.markmail.org > > (2) a Google search specified as: site:mailman.nhm.ku.edu/ > pipermail/taxacom > your search terms here > > > _______________________________________________ > > Taxacom Mailing List > Taxacom(a)mailman.nhm.ku.edu > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom > > The Taxacom archive going back to 1992 may be searched with either > of these methods: > > (1) by visiting http://taxacom.markmail.org > > (2) a Google search specified as: site:mailman.nhm.ku.edu/ > pipermail/taxacom your search terms here

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DCMI-UK REGIONAL MEETING: Registration Open for "Five Years ON" Seminar at British Library
by DCMI Announce 30 Mar '12

30 Mar '12

******Excuse the cross-posting****** ======================================================================== SEMINAR: "Five Years On" (Library Linked Data) A DCMI-UK Regional Meeting VENUE: The British Library, London DATE: Friday, 27 April 2012 WEBSITE: http://dcevents.dublincore.org/index.php/BibData/fyo REGISTRATION OPEN: http://dcevents.dublincore.org/index.php/BibData/fyo/about/registration (***Limited to 70 participants***) Meetings co-endorsed by DCMI and DCMI-Member JISC ======================================================================== This seminar marks five years of progress in library linked data since the “London Meeting” of 2007 London Meeting of 31 April/1 May 2007 between DCMI and Joint Steering Committee for the Development of RDA stimulated significant development of Semantic Web representations of the major international bibliographic metadata models, including IFLA’s Functional Requirements family and the International Standard Bibliographic Description (ISBD), and MARC as well as RDA itself. Attention is now beginning to focus on the management and sustainability of this activity, and the development of high-level semantic and data structures to support library applications. The DCMI Bibliographic Metadata Task Group [1] and the DCMI Vocabulary Management Community [2] will hold inaugural meetings the day before the seminar. The venue for both days is the British Library, St. Pancras, London. The planning committee is pleased to announce a preliminary list of speakers for the Seminar including: --Barbara Tillett, Joint Steering Committee for the Development of RDA (JSC) --Robina Claphan, Europeana --Mirna Willer, IFLA ISBD Review Group --Pat Riva, IFLA FRBR Review Group --Thomas Baker, DCMI --Gordon Dunsire, IFLA Namespaces Technical Group and DCMI --Diane Hillmann, DCMI and Metadata Management Associates --Owen Stephens, JISC [1] http://wiki.dublincore.org/index.php/Bibliographic_Metadata_Task_Group [2] http://dublincore.org/groups/vocabulary-management/ ======================================================================== DATES/TIMES/REGISTRATION: THURSDAY, 26 APRIL: --Bibliographic Metadata Task Group - 9:30-12:30 --Vocabulary Management Community - 14:00-17:00 --The DCMI meetings on Thursday, 26 April are free and open to anyone -- but space is very limited (36) and advanced registration is required. FRIDAY, 27 April: --Seminar: "Five Years On" - 9:00-17:00 --Registration for the Seminar on Friday, 27 April has been set at US$190 (app. Euro 120) (including VAT), which includes lunch and two refreshment breaks. ======================================================================== Please address questions to the meeting planners, Gordon Dunsire and Diane Hillmann. Diane Hillmann (metadata.maven(a)gmail.com) --(Moderator, DCMI Vocabulary Management Community; Co-Chair, DCMI Bibliographic Metadata Task Group) Gordon Dunsire (gordon(a)gordondunsire.com) --(Co-Chair, DCMI Bibliographic Metadata Task Group)

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Re: [tdwg] [Taxacom] Whitepaper consultation on Biodiversity Informatics
by Dave Roberts 30 Mar '12

30 Mar '12

Dear Chris, you are not the first to point out the issue of content. The question, though, that bothers me is that if you had, say $5M for a grant call, what could you do by way of content creation that would make an appreciable difference? Taxonomists would argue that you could, say, bid to get the other half of the plants into CoL, but how much impact would that have? In comparison to wikipedia? This is a complicated landscape. Taxonomists have largely driven biodiversity informatics and, over a couple of decades, have not delivered effective, joined-up services for the life sciences. That was the motivation that prompted the commission to suggest the white paper. Basically they're asking the question "where can we put funding so that we can see the impact?". Where are the road-blocks? Don't get me wrong. If someone can make a convincing argument that we can make a breakthrough in usage and linkage of our existing information by the creation of a certain body of content, that would be fabulous. For your diptera example, I think we need a different approach to make that kind of resource sustainable and scaleable. One possible solution is to follow the open source model and break the problem into small enough bites that can be funded by individual institutions, e.g. as individual server as we do with the Scratchpads. Its no good, though, if they're silos. We also need the tools to join the data together. Finally, this is not a grant proposal. We're trying to identify priority points for which we need solutions, not propose the solutions themselves. Rod has proposed any number of such bottlenecks in his blogs over the years. Which ones are most important? Make them the basis of a call and see who can devise a good solution. Cheers, Dave -- On 30 Mar 2012, at 13:59, Chris Thompson wrote: > Thanks, Rod, > > for the great comment on the focus should be on "questions," not technologies. > > BUT I would add the basic focus should FIRST be on content. The information that can be used to answer questions. > > In the half century, I have been in the "biodiversity" business, what has been the clear trend is the continued re-invention of the "infrastructure technologies," investing big bucks in "new and better" software, etc., but virtually nothing on content. The old "taxonomy is free" paradigm. People have questions, they want answer, so the critical component is content, the information necessary to answer those question. Not so new technology to simply re-scuffle the old information. > > We run the Systema Dipterorum (see us at www.diptera.org), an online nomenclator and species database for more than 10% of the known biodiversity, flies (Insecta: Diptera), which are critical as they have one of this highest impact on human society, as disease vectors, pollinators, crop pests, biological control agents, model organisms (Drosophila), forensics indicators, etc. We provide basic information on more than 160,000 species and a quarter of million names, with simple obsolete software (FileMakerPro version 6), but as we have a budget of only some 50K per year we focus on content, trying to keep up with the thousands of new species being added annually, etc. And enhancement of our basic content. > > What we need is support to improve our content, to enhance it, to have it "peer-reviewed," etc. No some new software to simply re-format it. > > Oh, well ... > > back to the data ... > > Sincerely, > > Chris > > see us at www.diptera.org > > -----Original Message----- From: Roderic Page > Sent: Friday, March 30, 2012 3:43 AM > To: Dave Roberts > Cc: Norman Morrison ; Peter van Tienderen ; Hannu Saarenmaa ; Alex Hardisty ; tdwg(a)lists.tdwg.org ; taxacom > Subject: Re: [Taxacom] Whitepaper consultation on Biodiversity Informatics > > Dear Dave, > > This sounds like a great opportunity. > > That said, I little part of me dies when I read "infrastructure" documents. The focus is invariably on technologies rather than questions, and I don't think people actually want "infrastructure", they want things to help them do the things they're trying to do (as opposed to cool things that could be built for them). > > I've made some comments on the topics, but rather than pollute your own outline with my grumpiness, I've made a copy and scribbled some thoughts on that. The annotated document is at https://docs.google.com/document/d/1VLvysjbm6IUhceAEgkAWSQ9yc71YK-9_48bPNZA… or http://bit.ly/H17nLs if that link gets mangled. > > Regards > > Rod > > > On 29 Mar 2012, at 12:31, Dave Roberts wrote: > >> Dear Colleague, >> >> we need funding to pursue biodiversity research, but funding is under huge pressure. One area for which there is potential is in biodiversity informatics because we are witnessing a paradigm shift in the way we handle data. Now it is expected that data will be openly accessible, presenting huge opportunities if only the data can be found when needed. >> >> There is a strong need for a community voice to present the funders with a set of priorities. We have successfully built a number of infrastructural components, such as INSDC, GBIF, Catalogue of Life, but we lack the bridges to allow users to integrate elements from these resources to address a simple question. >> >> With the encouragement of the European Commission, we are launching a consultation to write a White Paper on biodiversity informatics. We have made a list of potential chapters with a brief outline of what they might cover here: >> >> http://is.gd/WhitePaperChapters >> >> This document is a public Google doc. The approach we propose is to ask for volunteers to lead the development of each chapter. >> >> * If you can identify a new chapter, please add it to the Chapters list >> >> * If you are prepared to lead a chapter, put your name against the chapter, open a new public googledoc and past the link into the chapters list. >> >> * Please do not create chapters dedicated to specific disciplines, such as molecular biology, because there is no way to prioritise one discipline against another. >> >> * Three funded EU projects will administer the production of the white paper. agINFRA, BioVeL and ViBRANT will supply. We will edit the chapters for continuity and will produce an executive summary. >> >> * If you are able to join the editorial group, email one of the organisers. We expect this to work by self-nomination. >> >> The European Commission would like access to such a community view in forming the funding calls under Horizon2020. It is possible that other funders may pay similar attention. It makes no sense to do this over just Europe. We recognise that biodiversity is global and we need global priorities. >> >> Timetable >> 27 April: initial draft chapters; propose group meetings with dates in May >> >> 1 June: refined chapters merged by editorial group >> >> 22 June: draft executive summary and edited chapters >> >> July: public meeting >> >> 1st Sept: Publication of white paper >> >> This timetable is tight because the Horizon2020 funding calls will be drafted in the last quarter of 2012. To have real benefit in Europe, we need to move quickly. >> >> Organising Group: >> Alex Hardisty <hardistyAR_at_cardiff_dot_ac_dot_uk> >> Dave Roberts <dmr_at_nomencurator_dot_org> >> Hannu Saarenmaa <hannu_dot_saarenmaa_at_uef_dot_fi> >> Norman Morrison <norman_at_nmorrison_dot_info> >> Peter van Tienderen <P_dot_H_dot_vanTienderen_at_uva_dot_nl> >> -- >> Dr D.McL. Roberts, Tel: +44 (0)20 7942 5086 >> Dept. Zoology, >> The Natural History Museum, >> Cromwell Road, >> London SW7 5BD >> Great Britain Email: dmr(a)nomencurator.org >> Web page: >> http://scratchpads.eu >> http://www.nhm.ac.uk/research-curation/projects/euk-extreme/ >> -- >> "The intent of [bureaucratic] language is not to deceive, it is to preserve one's interpretive latitude so that if context changes a new more approporiate meaning can be attached to the language already used." Matthew Crawford (The case for working with your hands, Penguin 2010) >> -- >> >> >> >> >> _______________________________________________ >> >> Taxacom Mailing List >> Taxacom(a)mailman.nhm.ku.edu >> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom >> >> The Taxacom archive going back to 1992 may be searched with either of these methods: >> >> (1) by visiting http://taxacom.markmail.org >> >> (2) a Google search specified as: site:mailman.nhm.ku.edu/pipermail/taxacom your search terms here >> > > --------------------------------------------------------- > Roderic Page > Professor of Taxonomy > Institute of Biodiversity, Animal Health and Comparative Medicine > College of Medical, Veterinary and Life Sciences > 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 > Skype: rdmpage > 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 > > _______________________________________________ > > Taxacom Mailing List > Taxacom(a)mailman.nhm.ku.edu > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom > > The Taxacom archive going back to 1992 may be searched with either of these methods: > > (1) by visiting http://taxacom.markmail.org > > (2) a Google search specified as: site:mailman.nhm.ku.edu/pipermail/taxacom your search terms here -- Dr D.McL. Roberts, Tel: +44 (0)20 7942 5086 European Distributed Institute of Taxonomy Project, Coordinator WorkPackage 6 (Unifying Revisionary Taxonomy), Dept. Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD Great Britain Email: dmr at nomencurator dot org Web page: http://scratchpads.eu Web page: http://www.editwebrevisions.info/ -- "You can't just ask customers what they want and then try and give it to them. By the time you get it built, they'll want something new." [Steve Jobs, quoted in The Guardian, Technology Section, 25 June 09]. --

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