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Test Example of Occurrence RDF with DarwinCore/TDWG (might not be correct :-\)
by Peter DeVries 08 May '09

08 May '09

I thought I would try to start using the DarwinCore vocabulary in my observation RDF. I thought it might be easiest to start with the SimpleDarwinCore. The following URL takes you to an RDF file that combines my older vocabulary with my attempt at the SimpleDarwinCore. There is some redundancy in this version but it looks like I can probably replace a number of my terms with DarwinCore terms. The DarwinCore representation appears at the bottom of the RDF. http://species.geospecies.org/observations/a3c39dad-6756-4129-9a61-fbd32883… I would appreciate comments or suggestions. Thanks! Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

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Test Example of Occurrence RDF with DarwinCore/TDWG (might not be correct :-\)
by Peter DeVries 08 May '09

08 May '09

I thought I would try to start using the DarwinCore vocabulary in my observation RDF. I thought it might be easiest to start with the SimpleDarwinCore. The following URL takes you to an RDF file that combines my older vocabulary with my attempt at the SimpleDarwinCore. There is some redundancy in this version but it looks like I can probably replace a number of my terms with DarwinCore terms. The DarwinCore representation appears at the bottom of the RDF. http://species.geospecies.org/observations/a3c39dad-6756-4129-9a61-fbd32883… I would appreciate comments or suggestions. Thanks! Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

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Call for Nominations for a GBIF LSID-GUID Task Group
by Eamonn O Tuama (GBIF) 24 Apr '09

24 Apr '09

Dear TDWG Members and Friends, The Call for Nominations to a GBIF LSID-GUID Task Group is attached. Please observe the deadline of 10 May 2009 for nominating candidates. Kindly send your nominations directly to Éamonn Ó Tuama (eotuama(a)gbif.org) Best regards, Éamonn _______________________________________________ Éamonn Ó Tuama, M.Sc., Ph.D. ( <mailto:eotuama@gbif.org> 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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Consolidating TDWG work
by Donald.Hobern＠csiro.au 06 Apr '09

06 Apr '09

Dear TDWG Members and Friends, Those of you who attended the conference in Perth last year will remember Annie Simpson's explanation of how hard it still is for a group like the Global Invasive Species Information Network (GISIN) to take TDWG's work and apply it directly to solve data integration issues in their community. As I have previously suggested, I believe we should look closely at GISIN's requirements and make sure that those in a similar situation have all the tools and documentation required to start connecting data easily in ways that are compatible with TDWG standards. We have most of the pieces in place. We just need to organise and document them better. Invasive species are of great significance to many countries. This means that addressing GISIN's requirements is directly relevant to a large number of TDWG participants. However their scenario is also a template for data sharing in many other biodiversity-related projects. They need to aggregate information from many sources to populate several inter-related data models (BioStatus, Occurrences, ProfileURLs, ImpactStatus, ManagementStatus and DispersalStatus). Several of these are very close to existing data models based on TDWG standards (for example, the Occurrence model can be considered to be extended Darwin Core). Others are examples of the kind of community-specific data which all biodiversity projects need to share. TDWG's goal should be to ensure that GISIN and similar groups can follow a simple set of instructions (a "cook book") and use standard tools to build a network of this kind, and that they can do so in a way which ensures that related communities can also benefit from the data they share. For example, if GISIN members use the GISIN toolkit to share data, we ought to make sure that no further steps are required for GBIF, OBIS and others to integrate GISIN Occurrence data into their own indexes of species occurrences, or for EOL, ALA and others to integrate GISIN ImpactStatus, ManagementStatus and DispersalStatus data into their species profiles. I am therefore writing this email as an appeal for TDWG members to step forward and help to complete the work we have started. I am setting a challenge for us to do whatever still needs to be done to our standards, tools and data sharing recommendations so that we can produce such a cook book by the end of 2009. I don't believe this is an unrealistic goal. We can start work now on identifying and resolving issues. We can plan activities at the 2009 TDWG conference in November to resolve any issues still outstanding at that point and to hold hackathon activities to fill any gaps in our tool set. This work also aligns well with the e-Biosphere conference's plan to develop a roadmap for biodiversity informatics for the next 10 years. We have added a page to the TDWG Invasive Species wiki to seed discussion of what we need to do - http://wiki.tdwg.org/twiki/bin/view/InvasiveSpecies/GisinRequirements. Please take the time to look at this page (and at the information on GISIN's requirements at http://wiki.tdwg.org/twiki/bin/view/InvasiveSpecies/WebHome and http://www.niiss.org/cwis438/websites/GISINDirectory/Tech/ProtocolSpecifica…) Append comments and suggestions on what else we may need to do to the wiki, or simply reply to this message. In particular, if you are interested in being involved with the relevant TDWG Interest Groups in addressing some of the listed requirements, please contact me or the relevant Interest Group leaders. I believe this is the most significant thing that TDWG can do right now to support the work of biodiversity informatics worldwide. Please consider making your own contribution to make it happen. Best wishes, Donald [cid:736345722@24032009-2DA9] 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<mailto:Donald.Hobern@csiro.au> Web: http://www.ala.org.au/

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TDWG motto
by Lee Belbin 05 Apr '09

05 Apr '09

Dear TDWG Members and Friends We need a 'pithy' (brief, punchy, memorable) motto for TDWG for use on a banner, web site, stationary etc. All suggestions and comments would be appreciated at http://wiki.tdwg.org/twiki/bin/view/Executive/TdwgMotto before April 18. Thanks Lee Lee Belbin TDWG Secretariat

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FW: Cyberinfrastructure Summer Traineeships for repository interoperability
by Donald.Hobern＠csiro.au 30 Mar '09

30 Mar '09

We have received the following notice, which may be of interest to some TDWG participants. Best wishes, Donald *** Please disseminate widely to students at your institution *** CYBERINFRASTRUCTURE SUMMER TRAINEESHIPS 2009 VIRTUAL DATA CENTER FOR BIODIVERSITY, EARTH, ECOLOGICAL, AND EVOLUTIONARY SCIENCE DATA http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_200 9 Summer traineeships are available for up to four students and postdocs interested in informatics as applied to scientific data ranging from the fields of biodiversity, ecology, and evolutionary biology. The program provides a unique opportunity for undergraduate, masters, and PhD students as well as postdocs to obtain hands-on experience writing and extending open-source software as part of a distributed collaborative software development team building a Virtual Data Center (VDC) that includes major data and metadata repositories in those fields. Trainees accepted into the program will receive a stipend ($4,500), and with the exception of attending one meeting near the beginning and one near the end of the 3-month program period may work from their home, or home institution. Travel costs incurred in connection with the meetings will be reimbursed. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. Initial project ideas are listed on the website. These range from validation of metadata and identifier resolution, to supporting LSID and semantic-web compliant PURLs for digital data objects, to implementing modern web-service APIs, to cataloging the diversity of metadata schemas. The project ideas are flexible and can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. The traineeships are supported by a National Science Foundation (NSF) grant to a consortium of major repositories for biodiversity, earth and environmental, ecological, and evolutionary science. The consortium includes the LTER Network Office, the U.S. Geological Survey, NASA and Oak Ridge National Laboratory, the Global Biodiversity Information Facility (GBIF), the National Evolutionary Synthesis Center(NESCent), and the National Center for Ecological Analysis and Synthesis (NCEAS). It aims to develop the cyberinfrastructure and technologies necessary to build a Virtual Data Center (VDC) based on a network of existing and new physical repositories ("nodes") that interoperate using open standards and protocols. The network will enable discovery of as well as open, stable, and secure access to data in any of its member nodes. TO APPLY: Students apply online. Instructions for applying are at the website (see "When you apply"), along with program rules and eligibility requirements. The 15-day application period for students opens on Monday March 30th and runs through Monday, April 13th, 2009. INQUIRIES: vdc-twg {at} ecoinformatics {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early as possible. Cyberinfrastructure Traineeships Website: http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_200 9 2009 NESCent Phyloinformatics Summer of Code (NESCent's participation in the Google Summer of Code; managed separately; postdocs not eligible; ***student application period ends April 3rd***) http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009 To sign up for quarterly NESCent newsletters: http://www.nescent.org/about/contact.php --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org

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e-Biosphere 09 Forum on standards
by Donald.Hobern＠csiro.au 25 Mar '09

25 Mar '09

Dear TDWG Members and Friends, The e-Biosphere conference to be held this June in London (http://www.e-biosphere09.org/) aims to develop a roadmap for biodiversity informatics for the next 5-10 years. As part of this, the conference organisers have established an "Online Conference Community" (OCC - see http://www.e-biosphere09.org/page/22/online-conference-community) to host a range of discussion groups, each of which is intended to produce a position paper to feed into the roadmap discussions. One of these communities is for "Standards development and management" - see http://forum.e-biosphere09.org/viewforum.php?f=60. I have just posted two messages to this group to try to foster some discussion on the future of standards development within our community. Clearly this is all core business to TDWG and I would encourage you to participate in this forum and make your views known. Many thanks, Donald [cid:127130500@26032009-2E97] 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<mailto:Donald.Hobern@csiro.au> Web: http://www.ala.org.au/

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TAPIR and Darwin Core submitted to the TDWG Standards Track
by Lee Belbin 17 Feb '09

17 Feb '09

Dear Members and Friends TAPIR and Darwin Core have recently been submitted to the TDWG Standards Track for review. Gail Kampmeier has agreed to be the Review Manager for Darwin Core and Piers Higgs will be the Review Manager for TAPIR. Please support Gail and Piers as they manage the review process. [They were both overloaded before they very kindly took on this role.] You may be called on to review one of the submissions or to provide advice at some stage in the process (see http://www.tdwg.org/about-tdwg/process/) The TDWG Executive Committee congratulates and thanks Renato, John, their Task Groups and many supporters for the wonderful work they have all done over the last few years. Lee Lee Belbin TDWG Secretariat

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TDWG in 2009
by Donald.Hobern＠csiro.au 12 Feb '09

12 Feb '09

Dear TDWG Members and Friends, TDWG 2009 will be help in Montpellier France from November 9-13. I thought I would take this opportunity to outline the activities I see as important for TDWG this year leading up to the conference this November. There are many important things for us to be doing in the lead up to the meeting. Consolidation of past work We have made much progress over the last few years in reworking our standards for greater interoperability. The LSID work and the associated LSID vocabularies have been a major part of this. These changes make it much easier to reuse TDWG standards with different technologies, to embed TDWG data elements in other structures, and to map other data formats into forms which can be interpreted as TDWG-compliant data. However this work is still incomplete. We need to formalise the vocabularies as an agreed high-level ontology or data model to support cross-project data integration. Many of our projects are awaiting a clear lead in this area. Please contact me if you are interested in leading some of this work or contributing to the discussion. One obvious example of the importance of this work comes from Annie Simpson's comments during her presentation in Perth. It should not be difficult for a group like GISIN to adopt TDWG standards and be able quickly to build a network to share data using those standards. I reiterate the challenge for us to solve this problem this year, using GISIN's requirements as a benchmark. It is encouraging to see that NCD nears the end of its public review and that TAPIR has just been submitted to the TDWG standards track. It would appear that the submission of Darwin Core is not far off either. Please help to ensure that we end up with effective standards that can be easily adopted by a wide audience. e-Biosphere 2009 The e-Biosphere 2009 conference (http://www.e-biosphere09.org/) will take place in London in June. This goals of this conference are to: * Present and discuss the extraordinary progress made in Biodiversity Informatics over the past decade, * Provide participants with demonstrations of current capabilities in this field, and * Bring stakeholders together to create a roadmap for the next decade. The main meeting (1-3 June) has a programme of invited speakers who will provide an overview of what is happening in biodiversity informatics and promote a vision for the importance of this work. These sessions will address the first and second of the goals above. At the end of the week, there will be a smaller two-day workshop with representatives from a range of biodiversity informatics projects discussing synergies and efficient collaboration (the third goal). e-Biosphere is significant to TDWG for several reasons: 1. The opening session on 2 June will present the benefits of data standards and integration, and we expect that many of the other sessions will directly or indirectly highlight TDWG work. We are also organising a booth to publicise the work of TDWG and hope that this will be an opportunity to demonstrate the value of our role to a wider audience. 2. The e-Biosphere organisers have established an "Online Conference Community" (http://forum.e-biosphere09.org/) to engage the wider community in pre-conference discussions. One of the categories (to be added soon) will be on the role of standards and tools in biodiversity informatics. We encourage TDWG members to contribute to this and to the other conference discussions. 3. TDWG will be represented in the roadmap discussions on 4-5 June. We trust that this session will help us all to clarify priorities for the next few years and will feed into discussions at TDWG 2009 and beyond. TDWG 2009 In recent years TDWG conferences have moved away from their earlier format, with significant emphasis on working group meetings, to become more of a reporting conference on the activities of TDWG-related projects. This has had some benefits, but has also in some ways weakened the organisation by reducing our focus on the core activity of developing and promoting standards. The vitality of our working groups in large measure depends on the conference providing a focus for their activity. For this reason, TDWG 2009 will be structured differently. Monday and Friday of the conference have been reserved for plenary sessions, but for the rest of the conference we plan to run three parallel (and, I hope, intersecting) streams of activities. One of these will be on the use of biodiversity informatics to support agriculture and crop diversity. Another stream will be for TDWG to initiate activity in response to the roadmap developed at e-Biosphere 2009. The third stream is still be be selected. Each stream will include a range of activities (e.g. symposia, seminars, task group sessions, hackathons) planned to address key issues and to result in real deliverables to progress biodiversity informatics in the area. We are establishing a Program Committee to plan the conference in detail and will keep you informed of progress. Best wishes, Donald [cid:669132404@13022009-14D8] 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<mailto:Donald.Hobern@csiro.au> Web: http://www.ala.org.au/

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How Species Concepts and Taxonomic Hypothesis are different as it relates to the Semantic Web
by Peter DeVries 02 Feb '09

02 Feb '09

I started this note based on Rod Page's Blog thoughts on Wiki Modeling, which got me thinking. http://iphylo.blogspot.com/2009/02/wiki-modelling-part-1.html Also, if you go back to the 2006 tdwg list I tried to make this point earlier, but did not seem to succeed and that is why I ended up creating my own species concept identifiers. The NCBI taxon id works in a way similar to the GeoSpecies ID's in that the ID stays the same despite changes in nomenclature. I would use this except that there is no NCBI ID for most species. There needs to be a sequence for there to be an NCBI ID. In this sense, the NCBI ID and GeoSpecies ID are compatible types of OTU's. It seems that the genomics/proteomics people are already using forms of the NCBI ID as Species identifiers (URI's) For example, these are similar concepts, in that the meaning is similar and they stay the same despite changes in nomenclature. They are being used as Species Concept identifiers. http://species.geospecies.org/spec_concept_uuid/0fcb5b7e-bcfc-4b56-b565-e1e… http://bio2rdf.org/taxon:7163 http://purl.uniprot.org/taxonomy/7163 These are names or taxonomic hypothesis: http://lsid.tdwg.org/urn:lsid:ubio.org:namebank:2593981 <- name Aedes vexans , taxonomic hierarchy (hypothesis), changes with changes in nomenclature http://lsid.tdwg.org/urn:lsid:ubio.org:classificationbank:11149341 <- taxonomic hierarchy (hypothesis) http://lsid.tdwg.org/urn:lsid:ubio.org:classificationbank:2463176 <- taxonomic hierarchy (hypothesis) This gets into what makes a good species concept URI. (identifier) The first set of identifiers can represent a Species Concept independent of a particular taxonomic hypothesis The second set of identifiers represent various taxonomic hypotheses, that might apply to a specific species concept. Was I able to clearly demonstrate the differences between these two type of identifiers? Under this model, the species hypothesis i.e. name is not the Species Concept. Comments, suggestions and disagreements are welcome :-) - Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

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