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Semantic Web: What is a species?
by Peter DeVries 25 Jan '09

25 Jan '09

An interesting side discussion started up from my earlier post and I thought it might beworth discussion on the general list. I expect there will be a number of different opinions on this subject which might prove enlightening. What is a species? The way I have constructed my system I consider species to be real things too which different taxonomic hypothesis are applied. A collector or curator would then decide which species concept they believe is the best match for their specimen or group of specimens. Those individuals would then be tied to a particular species concept. (Not necessarily a specific genus species) Statements or properties could then be associated with particular species concepts. For instance: This Culicidoid species concept is a member of the Anophelinoid Group and thereby inherits the following properties: Maxillary palps about as long as proboscus, not strongly recurved Scutellum evenly rounded Scutellum seta more or less evenly distributed Most like diagram http://..... I am not sure that you could make useful statements like this if specimens are abstracted as an array of names, and if species are not real things that are separate from individual taxonomic hypothesis. Note I use Anophelinoid rather than Anophelinae to avoid tying this group of morphological characters to a specific taxonomic hypothesis. Under this model genera, families and subspecies (as they are now used) are thought of as human constructed clades and are not real in the same sense as species are real. A species exists whether or not a human has chosen to describe and name it. There also seems to be a difference in how ecologists, medical entomologists and taxonomists think of species. The former tend to view species as real things while the later see them as a human constructed grouping, where the taxonomic hypothesis is the species concept. >From the perspective of the semantic web, species concepts defined in these different ways have different meanings and may not be able to be merged directly. At least that is my current thinking .... How do others think of species? --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

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Semantic Web Linked Data Validator
by Peter DeVries 22 Jan '09

22 Jan '09

For those interested in making their data available on the Semantic Web, check out Vapour http://validator.linkeddata.org/vapour It provides a way to test if your URI's properly resolve. - Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries(a)wisc.edu Insects of Wisconsin <http://insects.entomology.wisc.edu/> Spiders of Wisconsin <http://spiders.entomology.wisc.edu/> ------------------------------------------------------------

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FW: Database job
by Lee Belbin 08 Jan '09

08 Jan '09

Lee Belbin TDWG Secretariat From: Gary Rosenberg [mailto:rosenberg@ansp.org] Sent: Thursday, 8 January 2009 9:21 AM To: Lee Belbin Subject: Database job Hi Lee, I don't know if you've heard that the Academy of Natural Sciences is looking for a biodversity database manager. The ad was posted on taxacom, but some TDWG members might not have seen it. Could you circulating the link to the TDWG distribution list? http://www.ansp.org/about/employment.php#983 People can contact me if they have questions about the position. Best wishes, Gary Rosenberg """""""""""""""""""""""""""""""""""""""""""""""""""""""" Gary Rosenberg, Ph.D. Pilsbry Chair of Malacology Academy of Natural Sciences 1900 Benjamin Franklin Parkway Philadelphia, PA 19103-1195 USA Phone: 215-299-1033, Fax: 215-299-1170 Email: rosenberg(a)ansp.org http://clade.acnatsci.org/rosenberg http:///www.malacolog.org/ <http://www.malacolog.org/>

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Reminder: deadline for abstract submission to EGU Biodiversity Informatics Session
by Eamonn O Tuama (GBIF) 06 Jan '09

06 Jan '09

Dear Colleagues, We kindly remind you that the deadline for submitting an abstract to the European Geosciences Union (EGU) General Assembly 2009 is 13 January 2009! We cordially invite you to submit an abstract for the Biodiversity Informatics session, the main objective of which is to highlight the value of adopting informatics standards for both Biodiversity and Earth and Space Science disciplines thereby promoting interoperability across heterogeneous systems and, in particular, demonstrating how the kinds of observational data mobilised by the Global Biodiversity Information Facility network can be integrated with other geospatial data to address issues relating to climate change, protected area management, invasive species, etc. General information: http://meetings.copernicus.org/egu2009/index.html Biodiversity Informatics Session: http://meetingorganizer.copernicus.org/EGU2009/session/380 Guidance on abstract submission: http://meetings.copernicus.org/egu2009/abstract_management/index.html If you have any questions, please do not hesitate to contact one of the organisers: Convenor: Eamonn O Tuama; eotuama at gbif.org Co-convenor: Hannu Saarenmaa; hannu.saarenmaa at helsinki.fi Co-convenor: Jeremy Kerr; Jeremy.Kerr at uottawa.ca _______________________________________________ Éamonn Ó Tuama, Ph.D. (eotuama(a)gbif.org) Senior Programme Officer, Inventory, Discovery, Access (IDA), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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The Club of Rome: biodiversity / technology: call for contributions
by Lee Belbin 15 Dec '08

15 Dec '08

This looks like it should be a very interesting meeting and one where it would seem appropriate for TDWG to be 'raised'. Is anyone planning to attend? Would anyone consider representing TDWG and possibly reporting back (v.)briefly? We do have a number of prepared PowerPoint presentations on TDWG, a poster and brochures that could be used (see http://www.tdwg.org/about-tdwg/resources-for-outreach/) I'd be happy to help tailor a brief presentation. Help! Lee Lee Belbin TDWG Secretariat From: Club of Rome - ESC [mailto:agenda@clubofrome.at] Sent: Tuesday, 9 December 2008 1:52 AM To: agenda(a)clubofrome.at Subject: biodiversity / technology: call for contributions <http://www.clubofrome.at> The Club of Rome - European Support Centre Dear Ladies and Gentlemen, we are searching for contributions to an event which will discuss the usage of Information Technology for Biodiversity Conservation and Management and Information Technology in Agriculture. This implies database processing, sensor technologies, and also networking of organisations and activists. The event will be held on January 15th at UNESCO in Paris and is organized by the European Support Centre of the Club of Rome ( http://www.clubofrome.at ) and the project ICT Ensure ( http://ict-ensure.tugraz.at ). We would be very grateful if you forwarded this mail to persons in your organisation who are dealing with the topics and who might be interested to participate or to contribute with a statement. Please don't hesitate to contact us for further information. Best regards Thomas Schauer -- Dr. Thomas Schauer Director European Support Centre of the Club of Rome Tuchlauben 8/15, 1010 Vienna, Austria Tel.: +43-1-5125770 Fax: +43-1-5125770-10 http://www.clubofrome.at

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Biodiversity Informatics session at European Geosciences Union meeting: call for participation
by Eamonn O Tuama (GBIF) 08 Dec '08

08 Dec '08

Dear Colleagues, You are invited to submit an abstract for the Biodiversity Informatics session in the forthcoming Earth and Space Sciences Informatics programme of the European Geosciences Union General Assembly to be held in Vienna, 19-24 April 2009. The main objective of this session is to highlight the value of adopting informatics standards for both Biodiversity and Earth and Space Science disciplines thereby promoting interoperability across heterogeneous systems and, in particular, demonstrating how the kinds of observational data mobilised by the Global Biodiversity Information Facility network can be integrated with other geospatial data to address issues relating to climate change, protected area management, invasive species, etc. General information: http://meetings.copernicus.org/egu2009/index.html Biodiversity Informatics Session: http://meetingorganizer.copernicus.org/EGU2009/session/380 Guidance on abstract submission: http://meetings.copernicus.org/egu2009/abstract_management/index.html Authors are invited to submit abstracts by Tuesday 13 January 2009. If you have any questions, please do not hesitate to contact me or one of the co-convenors of the session, and please feel free to forward this message to others who may be interested. Convenor: Éamonn Ó Tuama; eotuama at gbif.org Co-convenor: Hannu Saarenmaa; hannu.saarenmaa at helsinki.fi Co-convenor: Jeremy Kerr; Jeremy.Kerr at uottawa.ca With regards, Éamonn Ó Tuama _______________________________________________ Éamonn Ó Tuama, Ph.D. (eotuama(a)gbif.org) Senior Programme Officer, Inventory, Discovery, Access (IDA), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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Project Officer Required
by Charles Hussey 21 Oct '08

21 Oct '08

Project Officer PESI project Fixed-term appointment, 22 months full-time. Based at the Natural History Museum, South Kensington, Salary £28,000 p.a. The Natural History Museum is leading a Work Package within a project funded through the EU Framework 7 Capacities Work Programme, entitled "A Pan-European Species-directories Infrastructure" (http://www.eu-nomen.eu/pesi <http://www.eu-nomen.eu/pesi> ). This 3-year project, which commenced in May 2008, is led by the University of Amsterdam and involves 40 partner organisations from 26 countries. PESI will integrate the infrastructural components of four major community networks on taxonomic indexing, namely those of marine life, terrestrial plants, fungi and animals, into a joint work programme. In addition, PESI will set up networks of both taxonomic experts and regional focal points and will work to address the issues of pooling resources, standardisation, sustainability, accessibility and international cooperation. Work Package 4, led by the NHM deals with the development, integration and application of taxonomic standards. We shall be working closely with relevant standards organisations and nomenclators (such as GBIF, ZooBank, IPNI, Index Fungorum and Algaebase). Work will include development of management classification schemes, a controlled terminology for species status and utilisation of globally unique identifiers for names (GUIDs). Required deliverables will take the form of four reports to the EU Commission. You will be working under the direction of the Work Package Leader and will have responsibility for undertaking the NHM programme of work. You will be liaising closely with the five other partners in the work package and with other work packages. There will be a small amount of foreign travel to attend meetings. You will be expected to have the ability both to work on your own initiative and as part of a collaborative team. You will be good at assessing facts and making reasoned judgements. A working knowledge of databases (preferably to do with biodiversity informatics), and of a European language, would be useful. You will have experience of producing technical reports. You will be able to demonstrate a familiarity with biological nomenclature and taxonomic classification. You must have a degree in a biological science or a computing discipline, preferably at PhD level, together with substantial experience as a professional or academic natural scientist or computer scientist. For a full job description and to apply online please visit the Natural History Museum website at www.nhm.ac.uk/jobs <http://www.nhm.ac.uk/jobs> Closing date: Sunday 16 November 2008. Posted by: Charles Hussey, Science Data Co-ordinator, UK Biodiversity Programme, Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD United Kingdom Tel. +44 (0)207 942 5213 Fax. +44 (0)207 942 5529 e-mail c.hussey(a)nhm.ac.uk Species Dictionary project: www.nhm.ac.uk/nbn/ <http://www.nhm.ac.uk/nbn/> Nature Navigator: www.nhm.ac.uk/naturenavigator/ <http://www.nhm.ac.uk/naturenavigator/>

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Metadata Discussion Meeting at TDWG 2008 Conference
by Eamonn O Tuama 30 Sep '08

30 Sep '08

Metadata Discussion Meeting at TDWG Conference 2008 Atlas of Living Australia and Global Biodiversity Information Facility are co-organisers of a special meeting on metadata to be held at the TDWG Conference in Fremantle, Australia, Sunday 19 October 2008, 14.00-17.00. We propose to open the discussion to any aspect of metadata but with a particular focus on metadata standards, major projects, systems in use, the role of ontologies, and certain key questions surrounding metadata. Key Questions The key questions needing discussion include, but are not limited to, the following: 1. What resources do we want to describe (all digital; some classes of digital; digital AND undigitised legacy; human experts, etc., record and dataset level)? 2. Can we make some preliminary core recommendations on metadata elements which all TDWG-related projects should maintain as a minimum? 3. How do we proceed to fuller recommendations on metadata standards and profiles, and web service interfaces, e.g., Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) - including appropriate use of PMH Sets - and Open Archives Initiative Object Reuse and Exchange (OAI-ORE)? 4. How do we handle natural language differences in metadata? 5. How can ontologies be effectively used with metadata? 6. How do we encourage production of good metadata? 7. How can a global, decentralised biodiversity network best share metadata? 8. Are there any other things we can do immediately to facilitate the interchange of metadata between our projects? 9. How should we avoid duplication of metadata records as they are harvested and aggregated in different locations? 10. Are there pilot activities around which we can test some of these ideas? 11. How should we establish ongoing collaboration within TDWG on this topic (wiki, mailing list, convenor, etc.)? To make effective use of the limited time for such a broad subject, we propose to offer a semi-open format for the discussion. This will revolve around a series of maximum-5-minute, 2-PowerPoint-slides presentations from represented projects on i) current metadata strategy and standards; ii) issues they need to see addressed. We require pre-submission and circulation of these slides to help build a sense of collaboration around a process and to create an "Introductory Statement" that will guide and inform our discussions on the day. A metadata wiki will be established prior to the meeting to aid our discussions. If you are interested in participating in the meeting, please contact the convenors Donald Hobern (Donald.Hobern(a)csiro.au) and Éamonn Ó Tuama (eotuama(a)gbif.org) If you wish to make a presentation, please submit your slides to the convenors by 1 September 2008. -- Éamonn Ó Tuama, Ms.C., Ph.D. (eotuama(a)gbif.org) Senior Programme Officer - Inventory, Discover, Access (IDA), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100, Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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Bioinformatician positions open with Australian phenomics networks
by Donald.Hobern＠csiro.au 03 Sep '08

03 Sep '08

The Australian government has funded three inter-related projects under the umbrella title, Integrated Biological Systems: * The Australian Phenomics Network (APN) - a network of research centres providing Australian and international researchers with mouse models for the study of human and animal disease. * The Australian Plant Phenomics Facility (APPF) - two nodes exploiting recent advances in robotics, imaging and computing to enable sensitive, high throughput analyses to be made of plant growth and function. * The Atlas of Living Australia (ALA) - a network of institutions and agencies working to develop tools and services for managing information on Australian biodiversity and research organisms. The ALA is providing some of the core information infrastructure to enable the APN and APPF to organise large quantities of data and images on their study organisms and to make these resources accessible to researchers in Australia and overseas. Two positions are now advertised for bioinformaticians to work with the APN and the APPF to explore their data management requirements and to work with the ALA to develop appropriate services to support these communities. The APN is seeking a bioinformatician to be based at Australian National University in Canberra. The closing date for applications is 24 September 2008. See the following materials: * Advertisement: http://www.ala.org.au/docs/ANUBioinformatician.pdf * Documentation: http://www.ala.org.au/docs/ANUBioinformatianDocumentation.doc The APPF is seeking a bioinformatician to be based at the University of Adelaide. The closing date for applications is 19 September 2008. See the following materials: * Advertisement: http://www.ala.org.au/docs/UABioinformatician.pdf * Documentation: http://www.ala.org.au/docs/UABioinformaticianDocumentation.doc I urge those who are interested to apply promptly. Donald Donald Hobern, Director, Atlas of Living Australia CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern(a)csiro.au Web: http://www.ala.org.au/

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Bioinformatician positions open with Australian phenomics networks
by Donald.Hobern＠csiro.au 03 Sep '08

03 Sep '08

The Australian government has funded three inter-related projects under the umbrella title, Integrated Biological Systems: * The Australian Phenomics Network (APN) - a network of research centres providing Australian and international researchers with mouse models for the study of human and animal disease. * The Australian Plant Phenomics Facility (APPF) - two nodes exploiting recent advances in robotics, imaging and computing to enable sensitive, high throughput analyses to be made of plant growth and function. * The Atlas of Living Australia (ALA) - a network of institutions and agencies working to develop tools and services for managing information on Australian biodiversity and research organisms. The ALA is providing some of the core information infrastructure to enable the APN and APPF to organise large quantities of data and images on their study organisms and to make these resources accessible to researchers in Australia and overseas. Two positions are now advertised for bioinformaticians to work with the APN and the APPF to explore their data management requirements and to work with the ALA to develop appropriate services to support these communities. The APN is seeking a bioinformatician to be based at Australian National University in Canberra. The closing date for applications is 24 September 2008. See the following materials: * Advertisement: http://www.ala.org.au/docs/ANUBioinformatician.pdf * Documentation: http://www.ala.org.au/docs/ANUBioinformatianDocumentation.doc The APPF is seeking a bioinformatician to be based at the University of Adelaide. The closing date for applications is 19 September 2008. See the following materials: * Advertisement: http://www.ala.org.au/docs/UABioinformatician.pdf * Documentation: http://www.ala.org.au/docs/UABioinformaticianDocumentation.doc I urge those who are interested to apply promptly. Donald Donald Hobern, Director, Atlas of Living Australia CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern(a)csiro.au Web: http://www.ala.org.au/

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