March 2012 - tdwg - lists.tdwg.org

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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Re: [tdwg] Whitepaper consultation on Biodiversity Informatics
by Roderic Page 30 Mar '12

30 Mar '12

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

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Whitepaper consultation on Biodiversity Informatics
by Dave Roberts 29 Mar '12

29 Mar '12

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) --

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FW: Bioversity International - Vacancy Announcement
by Lee Belbin 25 Mar '12

25 Mar '12

Bioversity International is currently recruiting for a Research Leader, Genetic Resources Informatics. Please see http://www.bioversityinternational.org/about_us/job_opportunities.html From: Ingrid Lambert Human Resources Manager Bioversity International (Bioversity) Via dei Tre Denari, 472/a 00057 Maccarese Rome, Italy Tel: +39 066118 335 Fax: +39 066118 341 Email: <mailto:i.lambert@cgiar.org> i.lambert(a)cgiar.org < <http://www.bioversityinternational.org> http://www.bioversityinternational.org> Announcement: Bioversity International, Bioversity for short, is the operating name of the International Plant Genetic Resources Institute (IPGRI) and the International Network for Improvement of Banana and Plantain (INIBAP). With our partners, we undertake research aimed at improving people's lives through the use and conservation of agricultural biodiversity.

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Call for student applications for PhyloSoC 2012
by Karen Cranston 24 Mar '12

24 Mar '12

*** Please disseminate widely at your local institutions, including *** *** posting to message and job boards, so that we reach as many *** *** students as possible *** Are you a student interested in evolutionary biology and open-source software development? PHYLOINFORMATICS SUMMER OF CODE 2012 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2012 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/ ). Students in the program receive a stipend from Google (and the coveted T-shirt upon completion!), and work from their home, or home institution, for the duration of the 3 month program. You will have to opportunity to collaborate with our enthusiastic mentor community, and will have at least one dedicated mentor to help you complete your project. We are particularly targeting students interested in both evolutionary biology and software development. Our website, above, lists potential projects. Projects include many programming languages (e.g. C/C++, Java, Perl, R) and cover subjects ranging from visualization to algorithm implementation to data interoperability. You don't need to be an expert in either evolutionary biology or software development - find a project idea that interests you, and we can work with you to develop a proposal that fits your skills. We also welcome novel project ideas apart from those already on the list. INTERESTED? Contact us 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. Admission is competitive, and we want plenty of time to work with you to develop a great project proposal. TO APPLY: Apply online at the Google Summer of Code website: http://www.google-melange.com/gsoc/homepage/google/gsoc2012 where you will also find GSoC program rules and eligibility requirements. The 14-day application period for students opens on Monday March 26th and runs through Friday, April 6th, 2012. Google Summer of Code FAQ: http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc20… Karen Cranston and Jim Proctor National Evolutionary Synthesis Center http://nescent.org -- ~~~~~~~~~~~~~~~~~~~~~~~ karen.cranston(a)gmail.com ~~~~~~~~~~~~~~~~~~~~~~~

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Call for Challenge entries for conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Nico Cellinese 21 Mar '12

21 Mar '12

Many trees enter. Fresh analysis ensues. New insights emerge. The conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) is again holding a Challenge competition in 2012, on the theme "Synthesizing Phylogenies". Somewhere, buried in large sets of trees, lies a stunning new revelation, a baffling discovery, the answer to a longstanding controversy, or simply something not obvious to the naked eye. The mission of the 2012 iEvoBio challenge is to find those revelations, discoveries and answers within your own data and/or within one of the datasets provided by the challenge. What new scientifically interesting results can you pull from these trees, using any combination of techniques at your disposal? Further information on the nature of challenge entries and how to submit them can be found on the iEvoBio website athttp://ievobio.org/challenge.html. Submissions are due by June 25, 2012. Selected candidates will make short oral presentations to demonstrate their work in a "Challenge session" at the conference, and if suitable will automatically be entered into the Software Bazaar track of the conference. 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. 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 Geneious Challenge has the same open and closing dates as the iEvoBio Challenge. See http://ievobio.org/geneious_challenge.html for more information. Separate from iEvoBio, the Encyclopedia of Life (EOL) is leading a Phylogenetic Tree challenge to encourage not only the development of large phylogenies, but their practical use. Together with the Global Names project they will choose two winning entries: one for the best large tree and one for the most promising but not necessarily large tree -- both in Darwin Core Archive format suitable for use in major biodiversity websites such as EOL. The two winners will receive paid trips to the 2012 iEvoBio conference. See http://eol.org/info/tree_challenge for more information. More details about the iEvoBio conference and program are available at 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 athttp://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 <><><><><><><><><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Assistant Curator, Botany & Informatics Adjunct Assistant Professor, Department of Biology Florida Museum of Natural History University of Florida 354 Dickinson Hall, PO Box 117800 Gainesville, FL 32611-7800, U.S.A. Tel. 352-273-1979 Fax 352-846-1861 http://cellinese.blogspot.com/

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Deadline to apply for funds for iDigBio workshop approaching
by Austin Mast 14 Mar '12

14 Mar '12

This is a reminder that the application for funds (up to $500!) to attend iDigBio's Specimen Digitization Tools and Practices Workshop at the Botany 2012 Conference is due by midnight on Monday, March 19. The workshop will be held from 8:00AM – 5:00PM on Thursday, July 12, the day after the conference at the conference facility in Columbus, OH. For more information on the workshop and how to apply for financial assistance to attend, visit https://www.idigbio.org/content/workshop-and-symposium-botany-2012 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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Applications open for iEvoBio 2012 Travel Awards
by Nico Cellinese 13 Mar '12

13 Mar '12

The 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) is offering limited funds for travel expenses for the 2012 iEvoBio meeting in Ottawa, Canada. Preference will be given to participants lacking sources of funding for meeting attendance, such as graduate students, emerging professionals, and participants from underrepresented groups and countries. Please explain in an attached document the need for funding, the benefit that attending iEvoBio will afford you and how you will contribute to the meeting (max 350 words). We are looking for do-ers! A brief letter of support from your advisor, supervisor, or professional mentor should be submitted to the organizing committee (electronically), together with the application headed by the information below, to travelaward(a)ievobio.org by the deadline of 15 April 2012. Participants are required to make all their own travel arrangements, including visas and lodging, if required. Application format: Name: Contact information (address/phone/email): Academic Institution: Role (student, researcher, etc.): Origination of travel (if different from home institution) and estimated travel expenses: Explain the benefit that attending iEvoBio will afford you and what you will bring to the meeting (350 words or less):

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DC-2012 EXTENDED CfP DEADLINE: International Conference on Dublin Core and Metadata Applications
by DCMI Announce 12 Mar '12

12 Mar '12

*** Please excuse the cross-posting *** CfP DEADLINE EXTENSION for DC-2012, Malaysia =========================================================== DC-2012 Call for Participation (EXTENSION) to 30 March 2012 =========================================================== International Conference on Dublin Core and Metadata Applications: "Metadata for Meeting Global Challenges" 3-7 September 2012, Kuching, Sarawak, Malaysia DC-2012 will explore the global, national and regional roles of metadata in addressing global challenges such as food security, the digital divide, and sustainable development. Metadata plays a significant role globally in information systems shaping how we know, monitor and change social and governmental systems affecting everything from the environment, human rights and justice to education and peace. DC-2012 will bring together in Kuching the community of metadata scholars and practitioners to engage in the exchange of knowledge and best practices in developing languages of description to meet these global challenges. DC-2012 is part of Knowledge Technology Week 2012 in Malaysia. For more information, see http://dcevents.dublincore.org/index.php/IntConf/index/pages/view/ktw2012. Collocated events include: --DC-2012 International Conference on Dublin Core and Metadata Applications --PRICAI 2012 The 12th Pacific Rim International Conference on Artificial Intelligence --PRIMA 2012 The 15th International Conference on Principles and Practice of Multi-Agent Systems --Artificial Intelligence Workshops (AIW2012) ---------------------------------- DEADLINES & IMPORTANT DATES: --SUBMISSION **DEADLINE EXTENSION**: 30 March 2012 --AUTHOR NOTIFICATION: 25 May 2012 --FINAL COPY: 29 June 2012 ---------------------------------- IMPORTANT URLS: --SUBMISSION URL: http://dcevents.dublincore.org/index.php/IntConf/dc-2012/author/submit?requ… --ONLINE CFP: http://dcevents.dublincore.org/index.php/IntConf/dc-2012/schedConf/cfp --CONFERENCE WEBSITE: http://purl.org/dcevents/dc-2012 --ORGANIZING COMMITTEE: http://dcevents.dublincore.org/index.php/IntConf/dc-2012/about/organizingTe… ---------------------------------- Beyond the conference theme, submissions are welcome on a wide range of metadata topics, such as: -- Metadata principles, guidelines, and best practices -- Metadata quality (methods, tools, and practices) -- Conceptual models and frameworks (e.g., RDF, DCAM, OAIS) -- Application profiles -- Metadata generation (methods, tools, and practices) -- Metadata interoperability across domains, languages, time, structures, and scales. -- Cross-domain metadata uses (e.g., recordkeeping, preservation, curation, institutional repositories, publishing) -- Domain metadata (e.g., for corporations, cultural memory institutions, education, government, and scientific fields) -- Bibliographic standards (e.g., RDA, FRBR, subject headings) as Semantic Web vocabularies -- Accessibility metadata -- Metadata for scientific data, e-Science and grid applications -- Social tagging and user participation in building metadata -- Usage data (paradata/attention metadata) -- Knowledge Organization Systems (e.g., ontologies, taxonomies, authority files, folksonomies, and thesauri) and Simple Knowledge Organization Systems (SKOS) -- Ontology design and development -- Integration of metadata and ontologies -- Search engines and metadata -- Linked data and the Semantic Web (metadata and applications) -- Vocabulary registries and registry services ---------------------------------- SUBMISSIONS --All submissions for papers, reports, extended poster abstracts, community workshop and special sessions must do so through the DCMI Peer Review System at http://dcpapers.dublincore.org/index.php/pubs/. Author registration with the peer review system and instructions for the submission process appear under the "Information for Authors" link. --All submissions must be in English. --All submissions will be peer-reviewed by the International Program Committee. --Unless previously arranged, accepted papers, project reports and posters must be presented in Kuching by at least one of their authors. Submissions for Asynchronous Participation: With prior arrangement, a few exceptional papers, project reports and extended poster abstracts will be accepted for asynchronous presentation by their authors. Submissions accepted for asynchronous presentation must follow both the general author guidelines for submission as well as additional instructions located at http://purl.org/dcevents/dc-2012/remote. ---------------------------------- PUBLICATION -- Accepted papers, project reports and poster abstracts will be published in the permanent online conference proceedings and in DCMI Publications ( http://dcpapers.dublincore.org/) -- Special session and community workshop session abstracts will be published in the online conference proceedings. -- Papers, research reports and poster abstracts must conform to the appropriate formatting template available through the DCMI Peer Review System. -- Unless previously arranged, accepted papers, project reports and posters must be presented at The Hague by at least one of their authors. -- Submitting authors in all categories must provide basic information regarding current professional positions and affiliations as a condition of acceptance and publication. ---------------------------------- SUBMISSION CATEGORIES FULL PAPERS (8-10 pages; Peer reviewed): Full papers either describe innovative work in detail or provide critical, well-referenced overviews of key developments or good practice in the areas outlined above. PROJECT REPORTS (4-5 pages; Peer reviewed): Project reports describe a specific model, application, or activity in a concise presentation. POSTERS (1-2 pages; Peer reviewed): Posters are for the presentation of projects or research under development or late-breaking results. Poster submission should consist of a one-two page extended abstract. One or more sessions will be scheduled for display and discussion of posters at the conference venue. Instructions on the preparation of the display poster can be found at http://dcevents.dublincore.org/index.php/IntConf/index/pages/view/posterAut… . SPECIAL & PANEL SESSIONS: Special and panel sessions are organized by experts in a specific area of metadata. Each special session serves as a focused exchange of the latest research and/or best practice in the area. A proposal for a special session consists of a single document of approximately 800-1,200 words in length containing: --Session title --35-50 word abstract for use in promoting the session --Brief description of the scope and motivation for the session --Names and brief CVs of session facilitators, presenters, or panelists --Brief CVs of the organizers DCMI COMMUNITY & TASK GROUP WORKSHOP SESSIONS: DCMI Community Workshop & Task Group Sessions are intended to: (1) advance the specific work of DCMI entities as defined at http://dublincore.org/groups/#communities; and (2) to set the work agenda for the Community or Task Group for the coming year. Note: Communities wanting to present a special session or a panel in the area of the Community's interest should submit a proposal under Special & Panel Sessions above. ---------------------------------- PROGRAM COMMITTEE CO-CHAIRS --Schubert Foo, Professor and Associate Dean, Wee Kim Wee School of Communication and Information, Nanyang Technological University, Singapore --Hans Overbeek, Ministry of Internal Affairs, The Hague, Netherlands

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Call for Abstracts open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
by Nico Cellinese 03 Mar '12

03 Mar '12

The Call for Abstracts for full talks 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. Accepted talks will be 15 minutes in length and will be presented during the full talk session of the conference. Because the number of program slots for full talks is limited, some talks may be moved to the Lightning Talk session (5 minutes in length). 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 should be 1 page long at most and include a title, a list of contributors, and an abstract. The abstract should provide an overview of the talk's subject, and give enough detail to allow reviewers to decide whether the submission merits a full talk, or whether it should be moved to a Lightning Talk session. If the subject of the talk is a specific software component for use by the research community, the abstract must state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met. The deadline for submission is April 2, 2012. We intend to notify authors of accepted talks before early registration for iEvoBio (and Evolution) ends. Further instructions for submission are at the following URL: http://ievobio.org/ocs2/index.php/ievobio/2012/schedConf/cfp Full talks are one of the five kinds of contributed content that feature in iEvoBio. The other four 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 already open (see http://ievobio.org/challenge.html) The calls for contribution to the other three sessions will open later, and will remain open until shortly before the conference or until the respective track fills up. In addition, 2012 iEvoBio sponsor Biomatters Ltd will be running the Geneious Challenge alongside this year’s iEvoBio Challenge, see http://ievobio.org/geneious_challenge.html for more information. More details about the conference and program are available at 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, 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. Authors of full talks who cannot meet this requirement at the time of submission should state their intentions, and are advised that the requirement must be met by July 9, 2012, at the latest.

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iEvoBio conference, July 10-11, 2012
by Nico Cellinese 02 Mar '12

02 Mar '12

Dear All, The official website of iEvoBio 2012 is now open (www.ievobio.org) The 2 days conference will be held in conjunction with the annual Evolution meeting in Ottawa on the 10-11 July, 2012. Note that the program includes two exciting challenges and much more! We hope to see you in Canada! Cheers, NIco <><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Assistant Curator, Botany & Informatics Adjunct Assistant Professor, Department of Biology Florida Museum of Natural History University of Florida 354 Dickinson Hall, PO Box 117800 Gainesville, FL 32611-7800, U.S.A. Tel. 352-273-1979 Fax 352-846-1861 http://cellinese.blogspot.com/

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