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Advancement of DarwinCore postponed on standards track
by Stan Blum 28 Sep '05

28 Sep '05

Advance of DarwinCore postponed. A surprise at the recent TDWG annual meeting was the withdrawal of DarwinCore2 from the ballot of standards up for recommendation. This was done because recent changes need more time for review and explanation; it does NOT mean that support for the DarwinCore has been withdrawn, nor does it mean that we have to wait until next year to finalize the schema. With some diligent work over the next two to three months, we can finalize the DarwinCore2, test it, and begin broader deployment. If you are a current or potential user of the DarwinCore, please note that additional work needs to be done and your participation would be appreciated. The longer version of what transpired in St. Petersburg follows below. On July 10th, more than 60 days before the annual meeting as prescribed by the TDWG bylaws, John Wieczorek and I posted a revised version of the DarwinCore2 on the review web site (http://darwincore.calacademy.org/Documentation/DarwinCore2Draft_v1-4_HTML). This draft incorporated the advisable changes proposed since the draft of October, 2004. We then informed the TDWG Executive Committee, that the DarwinCore2 was ready to be considered for recommendation as a full TDWG standard. On September 12th at the annual meeting, conveners of the respective subgroups presented their proposed standards in a plenary session. I summarized the current state of the DarwinCore2, the changes made since last year, and the rationale behind them. The most significant change was to remove the geospatial elements from the core and place them in a geospatial extension. We did this for two reasons: 1) to follow the emerging best practice of constructing schemas to be interoperable across domains; and 2) to improve the stability of the core by making it smaller. Unfortunately, this change caught many people unaware, and serious questions were raised in the discussion period. These questions and my responses to them are summarized here. 1) Geospatial elements are critical to many users of the DarwinCore, so why remove them? Response: There is broad agreement among data architects, within TDWG and beyond, that the best way to achieve interoperability across domains is to import external schemas (and thereby the elements they contain), for example GML, rather than redundantly defining conceptually equivalent elements in our own namespace, as we have done in the past. An alternative we did not discuss, but will consider in the coming weeks, is whether a better strategy would be to import the GML elements directly into the core rather than putting them into an extension. In any case, we are certain that the DarwinCore, or application schemas based on the DarwinCore, will import their geospatial elements from GML. 2) These critical geospatial elements are now relegated to a specification that is not at the same level of maturity as the DarwinCore. Is this a good thing to do? Response: This will be inevitable if we develop our information domain by solidifying the areas with greatest commonality and defer more specialized elements to subsequent work by appropriate stakeholders. [A point I didn't make at the meeting, but would like to make now is that GML is actually more mature, or at least more broadly deployed, than any TDWG standard. So the elements in the geospatial extension are more stable than the DarwinCore, not less stable.] 3) Can the geospatial extension include the GML elements for lines and polygons as well as those for points? Response: This will need further investigation, but would certainly be desirable in the long run. Another cautionary marker appeared the next day among the contributed papers. Roger Hyam gave a presentation about managing change among interdependent schemas. He described a situation in which version dependencies among schemas could require them to be upgraded simultaneously, which effectively eliminates the main benefit of separating them in the first place. Gregor Hagedorn challenged the generality of Roger's point saying that proper referencing of schemas could ensure the required flexibility. The issue was left open and obviously requires further study and resolution, preferably in the form of a recommendation from a group of technical architects to the groups constructing references among schemas. As the deadline approached to open the vote on standards up for recommendation, both Adrian Rissone and Walter Berendsohn approached me (Stan) separately and asked me to withdraw the DarwinCore from the ballot. Both of them said that people had expressed to them the opinion that the recent changes to the DarwinCore were too large relative to the earlier draft, and too recent to warrant putting the schema up for recommendation as a standard. Although I believe the DarwinCore would have received at least the required simple majority of votes, in the interest of broader consensus I agreed to withdraw it from the ballot. Therefore, at the beginning of the final session on Tuesday I "announced" that we had agreed to take the DarwinCore off the ballot while the larger architectural issues were settled. I went on to explain that in my judgement the best course of action would include the following tasks: 1) convene technical experts to develop an explicit recommendation about how to incorporate elements from one schema into another (i.e., to address the issue Roger Hyam raised); 2) work with the various DarwinCore user communities to determine the most appropriate allocation of elements to the core and its extensions, producing explicit lists of elements that would be available to each specialist community by constructing their schema from the core, GML, and their own extensions; 3) resolve these issues as quickly as possible (2-3 months), and fix the resulting draft as version 2.0; 4) Develop explicit instructions for upgrading providers with DarwiCore2 and begin testing. At the end of the discussion I asked for vocal expressions with agreement or disagreement for withdrawing the darwincore from the ballot. About 10 people voiced support for withdrawing it from the ballot, no one expressed disagreement, and most were silent (perhaps stunned). It was done, and now the work goes on. An architecture interest group is being established and will be announced on the main TDWG mailing list. Roger Hyam will lead that group until more formal arrangements are made. Finally, I want to point out some problems we have had with group dynamics. I was too busy this last year to devote sufficient time to promoting discussion and developing consensus. Things are only going to get worse for me with the need to revise the general TDWG standards development process. Therefore, John Wieczorek and Renato de Giovanni are going take over managing the DarwinCore, though I will do my best to continue to participate. I think passive publishing (e.g., via a web site or wiki) is ineffective if the tempo of contributions is episodic. People stop visiting the web site when activity drops off, and they don't come back unless something is pushed into their inbox. Therefore I would like to encourage stakeholders in the DarwinCore to subscribe to the email list. Instructions can be found at http://circa.gbif.net/tdwg. We will do our best to respond to your concerns and keep the discussion moving. Sincerely, Stan Blum

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International Recorder Conference - Luxembourg, 2-3 December 2005
by Adrian Rissone 27 Sep '05

27 Sep '05

A TDWG member has asked me to circulate this information to the membership: We would like to invite you to the 1st International Recorder Conference - Collating and managing natural science field and collection records in Europe which will be held in Luxembourg on the 2nd and 3rd of December 2005. Please check the homepage of the conference for more information and a download of the 1st circular: http://www.symposium.lu/recorder Theme: European-funded projects such as ENHSIN and BioCASE have helped develop techniques and standards for biodiversity data sharing but there is still a great need for software and standards that can capture, manage and integrate the original natural sciences collection and field data. The theme of this meeting is to introduce field biologists, earth scientists and natural science museum curators across Europe to software and standards that can meet this need. <http://www.nbn.org.uk/information/info.asp?Level1ID=1&Level2ID=1> The meeting will include presentations on the development of Recorder software in the UK and Luxembourg and its associated applications, including 'Thesaurus' software, to collate and manage their data and link to both GIS and web-based delivery systems. The emphasis will be on the development and use of data standards and how Recorder can help build integrated systems for the collation, management and dissemination of information in the natural sciences across Europe. The conference will cover the conceptual model upon which Recorder is based and give examples of how this is implemented in the application, with examples of Recorder use at different levels from the individual naturalist through local, regional and national collation centres. Examples of working systems will be demonstrated and current development work will be described. The scope and potential of the BioCASE / Luxembourg Thesaurus will be discussed with examples of how it is being utilised in Recorder and other applications, including (hopefully) its use for terminology control in the London Natural History Museum. The problems of developing, disseminating and sustainably supporting an international version of Recorder and associated software will be discussed and proposals made for future action. We hope to see you soon in Luxembourg Best wishes For the organising committee Guy Colling and Tania Walisch

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Ballot on proposed standards (September 2005)
by Adrian Rissone 22 Sep '05

22 Sep '05

TDWG ANNUAL MEETING 2006 NOTIFICATION OF BALLOT The following proposed standards were recommended for ratification at the TDWG Annual Meeting in St. Petersburg, Russian Federation, during the week beginning 11 September 2005. In accordance with the TDWG Constitution and By-Laws a vote by all members in good standing on final ratification of each proposed standard is required. Ballot papers have been sent electronically to all current members in good standing. If you are a member who is in arrears of current dues but who wishes to vote in this ballot, please contact Stan Blum (sblum(a)calacademy.org) as soon as possible to renew. Othewise, your vote may not be counted at the close of the ballot on 23 October 2005. If you have any other questions please contact me as soon as possible. Regards, Adrian Rissone TDWG Secretary ---------------------------------------- Proposed Standard: ABCD (Access to Biological Collections Data): The Access to Biological Collections Data (ABCD) Schema 2.0 is a comprehensive standard for access to and the exchange of data about specimens and observations (a.k.a. primary biodiversity data). It is based on information models such as ASC and BioCISE and incorporates many existing exchange standards. Further information at http://www.bgbm.org/TDWG/CODATA/Schema/. Proposed Standard: SDD (Structured Descriptive Data) Major changes are incorporated in the latest version of SDD: All object types are derived from abstract base type. ExternalDataInterface grouping given up, all object types, including SDD ones treated symmetrically. Multilingual representation was simplified (one level of nesting less than previous version). The text character facility was redesigned to be expressed differently in xml, the previous solution was considered unintuitive. This involves element name and structural changes, but no essential changes in functionality. The expression of measurement units was simplified, rather than allowing multiple units within a character (which required structures to define units and their conversion methods), only one unit may be defined, which may be accompanied with different scientific prefix letters (k, c, m, µ) in different descriptions. http://160.45.63.11/Projects/TDWG-SDD/index.html http://wiki.cs.umb.edu/twiki/bin/view/SDD/WebHome Proposed Standard: TCS (Taxonomic Concept Transfer Schema) The Taxon Concept Schema (TCS) was developed to enable the transfer of taxonomic name and concept data using an abstract model of taxonomic concepts which can capture the range of models represented and understood by the various taxonomic data providers. The model, presented as an XML schema document, has been through several revisions which have been presented in different fora and discussed on the tcs-lc(a)ecoinformatics.org mailing list and the TCS Wiki at http://tdwg.napier.ac.uk where all previous versions of the schema can be obtained along with related documentation. At TDWG 2005 TCS v1.0 was voted to be recommended as a TDWG standard. Minor issues were discussed and proposals for minor changes to TCS are being accepted until 30th September at which point TCS v1.0 will be fixed for the ballot. Discussion on minor changes continues on tcs-lc mailing list and the final version 1.0 will be posted on the Wiki.

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TDWG/GBIF Call for Participation: Globally Unique Identifiers for Biodiversity Informatics
by Donald Hobern 09 Sep '05

09 Sep '05

TDWG/GBIF Call for Participation: Globally Unique Identifiers for Biodiversity Informatics -------------------------------------------------------- Background ---------- The Taxonomic Databases Working Group (http://www.tdwg.org/) and the Global Biodiversity Information Facility (http://www.gbif.org/) have received funding from the Gordon and Betty Moore Foundation (http://www.moore.org) to strengthen the infrastructure supporting the interchange of biodiversity data. A TDWG Infrastructure Project Team has now been established and is seeking requirements for globally unique identifiers (GUIDs) for biodiversity informatics, and to establish infrastructure to support their use. This review will consider how GUIDs could benefit all communities exchanging biodiversity data. TDWG and GBIF are therefore seeking input from institutions with an interest in organismal biodiversity data (including, but not limited to: natural history museums, herbaria, culture collections, gene banks, zoological and botanical gardens, and biological monitoring projects). Process ------- The planned process is as follows: * Survey the requirements: an open call for input from all areas of biodiversity informatics (using mailing lists and/or Wikis to support public discussion). * First workshop to review requirements, to evaluate candidate technologies and to establish working groups. The workshop will be limited to around 25 participants is planned to take place 1-3 February 2006 at the National Evolutionary Synthesis Center, Durham, North Carolina, USA (http://www.nescent.org/). Our thanks go to Cliff Cunningham at NESCent for hosting this workshop. * Working groups will address identified tasks using mailing lists and/or Wikis to support public discussion and provide recommendations. * Second workshop to review working group recommendations and to define models and processes for initial implementation. The workshop will be limited to around 25 participants for 3 days and take place in mid-2006 at a location to be announced. * Publication of TDWG standards for GUIDs and an initial implementation of any associated services and support tools. How to participate ------------------ Provide input to the survey of requirements through one of the following: * Add comments or edit pages in the wiki at http://wiki.gbif.org/guidwiki. If you wish to become actively involved and attend the workshops please add content describing your experience and interests to a wiki page associated with your name. * Subscribe to the mailing list TDWG-GUID(a)listserv.nhm.ku.edu at http://listserv.nhm.ku.edu/archives/tdwg-guid.html - your comments may then be added to the Wiki. Your input is particularly sought if: * You are involved in a project that is experimenting with or using some form of GUID technology (LSID, DOI, etc.). We would value comments on strengths and weaknesses of the approach and your experience in deploying solutions (see http://wiki.gbif.org/guidwiki/wikka.php?wakka=ExistingProjects). * You can describe ways in which GUIDs could be used to solve problems within your domain of interest (see http://wiki.gbif.org/guidwiki/wikka.php?wakka=GUIDUseCases). Send an expression of interest to participate in the GUID workshops. Please send such applications to guids(a)gbif.org, providing the following information: 1. Name and contact details 2. Institutional affiliation 3. Specific area(s) of interest within biodiversity informatics 4. Reasons for interest in participation in GUID standards development 5. Would you be able to devote time to web-based discussions as part of a working group between the two workshops? 6. Would you require support to attend the workshops? If so, to what extent? Please also include items 1-5 on your wiki page Workshops --------- * The first workshop will take place at the National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, USA, 1-3 February 2006. * The workshops are intended to be focused working sessions, and therefore attendance will be limited * Participants will be selected on the basis of expertise, experience, contributions to discussions, willingness to devote time to a working group, and diversity of attendees' backgrounds and institutions. Contacts -------- For further information, please send messages to guids(a)gbif.org. The TDWG Infrastructure Project Team is: * Lee Belbin, Australia - Project Manager * Roger Hyam, United Kingdom - Technical Architect * Ricardo Pereira, Brazil - Senior Software Engineer The GBIF contact is: * Donald Hobern, Programmer Officer for Data Access and Database Interoperability (dhobern(a)gbif.org) --------------------------------------------------------------- Donald Hobern (dhobern(a)gbif.org) Programme Officer for Data Access and Database Interoperability Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 ---------------------------------------------------------------

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TDWG 2005 Annual Meeting - much new and updated information on web site
by Adrian Rissone 08 Sep '05

08 Sep '05

TDWG 2005 Annual Meeting - much new and updated information on web site Apologies for cross-posting. If you are attending the meeting please visit the web site at: http://www.tdwg.org/2005meet/TDWG_2005_Intro.html to view important new and updated information (follow the Menu links). The Meeting Programme is now available, with links to presentation, poster and computer demonstration abstracts. Also available are arrangements for arriving at St. Petersburg Airport, details of local travel and departure. Looking forward to seeing you in Russia. Regards, Adrian Rissone TDWG 2005 Meeting Co-ordinator and TDWG Secretary

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TDWG memberships
by Stan Blum 08 Sep '05

08 Sep '05

Dear past present and future members of TDWG, This year I am very late in sending out the usual membership application and renewal form. This is due in part to the fact that I am also very late in (re-)establishing a bank account for TDWG in the US. I have filed the necessary papers with State and Local governments, but I have not yet received the authorization from the State of California. Without a bank account, I cannot accept checks or electronic transfers. Fortunately, we do have our account with RegOnline, which allows us to collect funds with credit cards. TDWG membership dues sustain the organization and entitle members to receive a free copy of any printed TDWG Standard, the TDWG Newsletter, and to vote at meetings. As we have moved into the age of electronic communications, TDWG standards have been published electronically, and the TDWG web site and email lists have replaced the newsletter. Voting rights remain the primary benefit of TDWG membership, which is important this year as several proposed standards will be put before the membership for adoption. What I propose to do in the mean time is to encourage everyone who can to use the RegOnline account to pay dues with a credit card. Even if you are not attending this year's meeting, you can pay membership dues by registering for the meeting at http://www.regonline.com/25832 and selecting the "membership only" registration type. If you cannot use a credit card, please send me an email indicating that you promise to pay annual membership dues (170 Euros - Institutional; 60 Euros - Individual) for the year 2005 via check or electronic transfer after the TDWG bank account has been established (expected in October). With that promise, you will have voting rights at this year's meeting. If you are sending delegates to the annual meeting in St. Petersburg, paying in cash is also an option. With humble apologies for any inconvenience,. Stan Blum TDWG Treasurer, 2005

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URGENT: TDWG 2005 - Registration
by Adrian Rissone 06 Sep '05

06 Sep '05

TDWG 2005 Registration URGENT MESSAGE FOR DELEGATES NOT REGISTERED There are a number of people who have indicated that they are attending the TDWG Meeting in St. Petersburg (some of whom have booked hotels) who have not registerd on the Registration web site. If this includes YOU it is VERY important that you register NOW. Lack of proper registration is causing us great problems with local organisation in Russia. The registration site is at: http://www.regonline.com/25832 Thank you for your co-operation. Regards, Adrian Rissone TDWG 2005 Meeting Co-ordinator

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TDWG Subgroup: Observation-based monitoring of biological organisms
by Steve Kelling 06 Sep '05

06 Sep '05

Dear All, At the 2004 TDWG meeting in Christchurch NZ, a new subgroup was formed to explore avenues that incorporate observation-based monitoring of biological organisms data into existing federation mechanisms of the bioinformatics community. Our goal is to develop methods that facilitate interoperability with existing metadata standards, external portals, and data harvesting structures, without loosing the inherent value of these data. A potential outcome of this subgroup is to develop a rich description standard for observational and monitoring data. For this to occur the standard must be extensible to allow the incorporation of a diversity of data types. Furthermore, the standard should incorporate variables from more general resource discovery standards (e.g. from Dublin Core or Darwin Core). Background information on the observational data subgroup may be found at: http://www.avianknowledge.net/tdwg At the Christchurch meeting a number of TDWG'ers expressed interest in helping with our efforts to integrate observational data into TDWG, and we will have a subgroup meeting at this year's TDWG meeting in St. Petersburg. For those of you that are able to attend this year's meeting and are interested in our efforts, you are very welcome to attend the subgroup meeting. If you are interested in helping with the observational data subgroup but are unable to attend the St Petersburg meeting, please let me know and I will updated on our efforts. All comments are welcome, Thanks, Steve Kelling Director of Information Sciences Cornell Lab of Ornithology 607-254-2478 (work) 607-342-1029 (cell)

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Call for Contractors for GBIF Data Portal: Java Developers and Data Administrator
by Donald Hobern 31 Aug '05

31 Aug '05

Calls for Contractors for International Biodiversity Data Portal: Java Developers and Data Administrator Background ---------- The Global Biodiversity Information Facility (GBIF, http://www.gbif.org/) is an international organisation with a secretariat based in Copenhagen, Denmark. Its mission is to enable free and open international web-based exchange of data relating to ´ all living organisms (plants, animals, micro-organisms), in particular information on their biological classification and their geographic occurrence. GBIF brings together an international network of institutions and organisations which have set up web services with standard interfaces to share biodiversity data. The network includes a centrally-operated portal (http://www.gbif.net/) to assist users in discovering and selecting data from the network. This portal currently exists as a prototype and now needs to be redeveloped to provide a robust access point for biodiversity data (both XML web services and a browser interface). Further information can be found at the following links: http://circa.gbif.net/Public/irc/gbif/dadi/library?l=/architecture/ http://wiki.gbif.org/dadiwiki/wikka.php GBIF is seeking experienced Java developers and a data manager to work on this portal. These will be contract positions and will be based at the GBIF Secretariat in Copenhagen. All contractors will be expected to work in English. Call for Java Developers ------------------------ GBIF requires experienced Java web developers to work in Copenhagen through at least to the end of 2006. Applicants must be experienced in the following technologies: * Java (at least 3 years development experience) * XML (including XML Schema, XSLT, XPath) * Apache Tomcat Applicants should ideally also be familiar with the following technologies: * MySQL and/or PostgreSQL * Hibernate * JavaServer Faces and/or Struts * Log4J * Ant * Python Prior experience with the following technologies will be an advantage: * Data standards from the Taxonomic Databases Working Group (TDWG, http://www.tdwg.org/), in particular: - Darwin Core - ABCD Schema - Taxon Concept Schema ´ * Data exchange protocols from TDWG: - DiGIR - BioCASe - TAPIR * GML Web Feature Service * BioMOBY * XQuery Understanding of the principles of taxonomy and of biological collection management will be a significant advantage. Call for Data Administrator --------------------------- GBIF requires a Data Administrator to work in Copenhagen through at least to the end of 2006. The Data Administrator will provide helpdesk support to assist data providers in the following areas: * Configuration and use of standard software packages to share biodiversity data * Diagnosis of problems in mapping biodiversity data into XML formats * Use of controlled vocabularies for biodiversity data elements * Handling of taxonomic names The GBIF Data Portal includes a database which serves as an index to the biodiversity data records shared by participants in the GBIF network. The Data Administrator will also be responsible for administrative tasks relating to this database. Training will be provided in the use of tools for diagnosis of problems with biodiversity data and in the administration of the index database. Applicants must exhibit understanding of the principles of taxonomy and of biological collection management, and also of web-based data exchange using XML web services. Applicants must be able to demonstrate experience in some or all of the following technologies: * Data standards from the Taxonomic Databases Working Group (TDWG, http://www.tdwg.org/), in particular: - Darwin Core - ABCD Schema - Taxon Concept Schema * Data exchange protocols from TDWG: - DiGIR - BioCASe - TAPIR * XML (including XML Schema, XPath) * MySQL and/or PostgreSQL How to apply ------------ Interested applicants should send the following by e-mail to Donald Hobern, GBIF Programme Officer for Data Access and Database Interoperability (dhobern(a)gbif.org): * Curriculum vitae * Indication of the position to which the application relates * Description of how you fulfill the requirements for the position * Description of the strengths you can bring to the project * Confirmation of availibility to work in Denmark * Indication of when you would be available to start work in Copenhagen * Expected remuneration The closing date for applications is 30 September 2005. Interviews will take place early in October.

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TDWG early registration about to close
by Stan Blum 30 Aug '05

30 Aug '05

Anyone attending, but not yet registered for the TDWG meeting in St. Petersburg: We are finalizing arrangements for this year's TDWG meeting and need to get an accurate count of participants. Adjusting capacity for services later will incur greater expenses, so we will be increasing registration fees by 70 Euros on Friday, September 2, at midnight (GMT-6). At that time, member registration will become 200 EU, and non-member registration will become 230 EU. If you have made arrangements to attend this year's meeting and have not yet registered, please do so now and save yourself 70 Euros. Thanks, -Stan Blum TDWG Treasurer

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