February 2009 - tdwg - lists.tdwg.org

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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