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Call: Taxonomic Data Provider Tool Developer
by Donald Hobern 10 Nov '06

10 Nov '06

Call: Taxonomic Data Provider Tool Developer -------------------------------------------- GBIF is seeking to simplify the integration of data relating to nomenclature (scientific names) and taxonomy (classification of organisms using scientific names) by developing tools to connect such data more easily to the GBIF network. GBIF is addressing this issue in several ways: 1. Working with the Species 2000 & ITIS Catalogue of Life partnership (http://www.sp2000.org/) to promote the development of a network of global species databases 2. Enhancing the GBIF data portal (http://www.gbif.net/) to index nomenclatural and taxonomic resources served over the web as tab-delimited data sets 3. Developing a data provider tool based on TDWG (http://www.tdwg.org/) data standards to support dynamic query of nomenclatural and taxonomic data sets over the web (more complex for data providers than 2. above, but offering a search interface) GBIF is seeking the services of a software developer to develop the data provider tool (item 3 above). The tool should have the following features: 1. Relational database (two version of same model in Access and MySQL) corresponding to TDWG Taxon Concept Schema (TCS) v. 1.01 (http://www.tdwg.org/subgroups/tnc/tcs-schema-repository/) 2. Customised provider tool using either the Python implementation (pyWrapper, http://trac.pywrapper.org/) or the PHP implementation (forthcoming) of the TAPIR protocol, with five endpoints configured, one for each class of data obect in TCS (Specimen, Publication, TaxonName, TaxonConcept, TaxonRelationshipAssertion) 3. Customisation of TAPIR configuration interfaces as required 4. Interface to import tab-delimited file formats adopted by GBIF (see item 2, above) into the TCS relational database The developer should have the following skills: 1. Experience in web development using PHP or Python. 2. Experience in modeling data structures using a relational database (specifically MySQL and/or Access) 3. Familiarity with TAPIR or one of the earlier TDWG data access protocols (DiGIR, http://digir.sourceforge.net/, or BioCASe, http://www.biocase.org/products/protocols/index.shtml) 4. Ability to plan and organise development work Familarity with the TDWG Taxon Concept Schema and general understanding of the principles of nomenclature and taxonomy will be an advantage. The GBIF Secretariat expects to place a contract for a period of approximately four months’ work. How to apply ------------ Interested applicants should send the following by e-mail to Donald Hobern, GBIF Deputy Director for Informatics (dhobern(a)gbif.org) by 30 November 2006: 1. Curriculum vitae 2. Description of relevant experience and skills 3. Details on availability 4. Expected remuneration ------------------------------------------------------------ Donald Hobern (dhobern(a)gbif.org) Deputy Director for Informatics Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 ------------------------------------------------------------

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Call for participation in the Agents Interest Group
by Neil Thomson 06 Nov '06

06 Nov '06

Dear TDWG'ers At the recent 2006 Conference of TDWG the new structure of Interest Groups and Task Groups was accepted. One of the proposed new Interest Groups was for Agents, which is the term used to cover persons, organisations and software acting in some specific role or roles. These are generic, in that information about agents is useful in conjunction with many of the other TDWG standards and making this available in a standard way that can be picked up by any of them would be a valuable aid to consistency. At the moment, there is only one Task Group that may be attached to the AIG and that is the one developing Natural Collections Descriptions (NCD). This emerging standard can already be used to describe organisations, in a "level 1" sort of way by viewing them as "collections of collections". It also acknowledges the strong link between collections and persons by providing hooks to biographical databases which provide rich information about persons and may be based on BiogML or EAC. Providing information about agents in a standard form, in effect building a directory of organisations and persons engaged in natural history activity, could be one of the objectives of the AIG. If you are interested in joining (or leading) an Agents Interest Group and helping to define the relationship between agents and the TDWG data standards and ontology then please send me an email at mailto:n.thomson@nhm.ac.uk With thanks, Neil ------- Neil Thomson Head of Data & Digital Systems The Natural History Museum, Cromwell Road, London SW7 5BD Tel: +44 (0)20 7942 5294, Fax: +44 (0)20 7942 5559, Email: n.thomson(a)nhm.ac.uk http://www.nhm.ac.uk

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Position at the Acad. Nat. Sciences in Philadelphia: Biodiversity Information Manager
by freirefierro 12 Oct '06

12 Oct '06

Dear all: Your help distributing this post will be greatly appreciated. Sincerely, Alina. ****** Alina Freire-Fierro Collection Manager Herbarium PH, Botany Deptartment Academy of Natural Sciences of Philadelphia 19th and Parkway Philadelphia, PA 19103 U.S.A. *** Tel: 1-215-299-1157 freirefierro(a)ansp.org http://www.acnatsci.org/research/jessupinfo.html http://espanol.groups.yahoo.com/group/Anunciosbotanicos/ ******************************** Biodiversity Information Manager (Position Announcement # 938) Issue Date: October 12, 2006 Closing Date: Open Until Filled The Academy of Natural Sciences of Philadelphia seeks an administrator for the databases of its specimen collections who can develop database-driven desktop and web applications. The collections encompass 17 million specimens in areas spanning botany, entomology, herpetology, ichthyology, malacology, mammalogy, ornithology, paleontology and general invertebrates. The databases hold more than 1 million records in several platforms. More information about science at the Academy is available at http://www.ansp.org/research. The information manager will be responsible for maintaining the integrity of the databases, and will work closely with curatorial staff to develop informatics tools for efficient capture of biodiversity data and images, quality control, data visualization and analysis, GIS, web-based data access, and internet collaboration. Duties will include development of information models, database documentation, information security, code, user interfaces, quality control, and database life cycle management. Other duties will include assisting collections and research staff in developing informatics support sections of grant proposals. Good communication skills are essential. There is the possibility of some time for independent research in biodiversity informatics depending on qualifications. Requirements: Degree in biology (with strong computer programming/database skills) or a degree in computer science (with extensive knowledge of biology). Experience with web-database programming in a LAMP environmental (Linux, Apache, MySQL or PostgreSQL, PHP) and with MS Access and Visual Basic. Desirable: Advanced degree (Master’s or Ph.D.); experience with biodiversity databases; experience with some of the following: Linux/Unix system administration; Perl or Bash scripting; FileMaker Pro; qmail/ezmlm; ImageMagick; MapServer; DiGIR/TAPIR. Salary is commensurate with experience. The position is available immediately. The Academy of Natural Sciences offers a competitive benefits package. TO APPLY: Send resume, statement of interest, and the names, addresses and telephone numbers of three references to: Maria Eife, Asst. Office Manager Announcement: Biodiversity Information Manager #938 The Academy of Natural Sciences 1900 Benjamin Franklin Parkway Philadelphia, PA 19103-1195

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Announce: Proposal for "microformat" for marking-up taxonomic names in HTML: comments and contributions sought
by Andy Mabbett 24 Sep '06

24 Sep '06

Hello - my first post to this mailing list. I'm not a taxonomist, but I've been told by one that you might be interested in recent proposals for a formula (a "microformat" <http://microformats.org>) for marking-up, in HTML, the names of species (and other ranks, varieties, hybrids, etc.). Microformats are a way of adding additional, simple markup to human-readable data items on web pages, using common and open HTML standards, so that the information can be extracted by software and indexed, searched for, saved, cross-referenced or aggregated. Microformats are also open standards, freely available for anyone to use. The proposed format respects all existing biological taxonomies, and is not intended to change or supplant any of them - it merely provides webmasters with a method of either: 1) marking-up a taxonomical name (or taxon-common name pair) in such a way that its components can be recognised by computers or 2) marking up a common name, so as to associative with it a taxonomical name, in such a way that the latter's components can be recognised by computers For instance, if I mark up a list of common names on a page I maintain: <http://www.westmidlandbirdclub.com/staffs/tittesworth/latest.htm> using that microformat, a visitor might have browser tool which lists all the species on the page, sorted into alphabetical order within taxonomic class, or in taxonomic order, and then creates links to, say (for Joe Public) their entries in Wikipedia, or the British Trust for Ornithology, or (for scientists) some academic database of the users choosing. Early thoughts on the format are on an editable "wiki", here: <http://microformats.org/wiki/species> Please feel free to participate - the proposal needs both messages of support (particularly from people or organisations who have websites on which they might use them) and, especially, comments and constructive criticisms - does the proposal understand and use taxonomy correctly; is the terminology right, are there any omissions or overlooked, unusual naming conventions? You can use the above wiki, or the microformats mailing list: <http://microformats.org/wiki/mailing-lists> and/ or please feel free to pass this e-mail to other interested parties. Thank you. -- Andy Mabbett Birmingham, England

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TDWG 2006: last chance to register without late registration penalty
by Adrian Rissone 12 Sep '06

12 Sep '06

Annual Meeting and Symposium of the Taxonomic Databases Working Group Missouri Botanical Garden 15 - 22 October 2006 http://tdwg2006.tdwg.org/ REGISTRATION AND HOTEL REDUCED RATES ENDING SOON Register now for TDWG 2006. 1. It's cheaper to register A late registration penalty fee of 50 $US will apply after 13 September 2006. 2. It's cheaper for a room at the Recommended Hotel The deadline for hotel discount is 13 September 2006. 3. We, the meeting Organisers, really do need to know NOW how many delegates to expect. It strains the relationship with our hosts (Missouri Botanical Garden) if we keep on reserve meeting rooms and facilities we don't need. If you register late it makes the local Organiser's job much more difficult arranging catering, transport and administration assistance. 4. We keep TDWGs standing costs down if we can plan early. Regards, Adrian Rissone Executive Secretary, TDWG Apologies to subscribers to whom this message is irrelevant and to delegates who have registered already. Unfortunately there is no way to send to a subset of the list.

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8 DAYS REMAINING: Taxonomic Databases Working Group (TDWG) Annual Meeting 2006
by Adrian Rissone 05 Sep '06

05 Sep '06

Annual Meeting and Symposium of the Taxonomic Databases Working Group Missouri Botanical Garden 15 - 22 October 2006 http://tdwg2006.tdwg.org/ SAVE $100! - BUT ONLY IN THE NEXT 8 DAYS REGISTRATION AND HOTEL REDUCED RATES ENDING SOON! Why should you register now for TDWG 2006? 1. It's cheaper to register! A late registration penalty fee of 50 $US will apply after 13 September 2006. 2. It's cheaper for a room at the Recommended Hotel The deadline for hotel discount is 13 September 2006. A number of registered delegates have indicated their intention to use the Recommended Hotel but have not yet made their hotel booking. Please do so as soon as possible. You MUST do so by 13 September to receive the discounted rate. You are not required to pay up front (but you must guarantee the booking with a credit card) and can cancel if necessary without penalty up to 15:00 local time on the day before you booked to arrive. The hotel booking URL is now being given on your Meeting registration confirmation e-mail. If you have an older version of the confirmation please contact me for the URL. 3. We, the meeting Organisers, really do need to know NOW how many delegates to expect. It strains the relationship with our hosts (Missouri Botanical Garden) if we keep on reserve meeting rooms and facilities we don't need. If you register late it makes the local Organiser's job 10 times more difficult arranging catering, transport and administration assistance. 4. If insufficient delegates register early for the Banquet we may have to cancel it completely - remember what a great social occasion it was in St. Petersburg? - it will be too bad if you are disappointed when you arrive in St. Louis because you did not book early enough. 5. We keep TDWGs standing costs down (and so YOUR membership & registration fees!) if we can plan early. What are you waiting for? Why not register TODAY? Questions? Ask me NOW. Please accept our apologies for cross-posting if you receive this message more than once. Regards, Adrian Rissone Executive Secretary You are receiving this message because you have registered for TDWG 2006, expressed interest in attending the Meeting, or have attended previous TDWG meetings. If you are receiving this message in error, or do not wish to be contacted in the future, please accept our apologies for intruding and send a request to be removed from future mailings to A.Rissone(a)nhm.ac.uk with Subject line "TDWG Direct Mail Removal Request".

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FINAL CALL: Taxonomic Databases Working Group (TDWG) Annual Meeting 2006 - Abstracts
by Adrian Rissone 01 Sep '06

01 Sep '06

This message contains FINAL time-critical information requiring immediate action. Please read it now. Annual Meeting and Symposium of the Taxonomic Databases Working Group Missouri Botanical Garden 15 - 22 October 2006 http://tdwg2006.tdwg.org/ ABSTRACTS FOR PRESENTATIONS - ** FINAL CALL ** The official deadline for Abstracts has been extended to 23:59 GMT on Saturday 2 September. THERE WILL BE NO FURTHER EXTENSION. PLEASE see the Abstracts Page for details and Instructions for Authors. Abstracts MUST be submitted in the required format. A number of abstracts have been received where the author has clearly not read the Instructions! In particular, please ensure the following: Be sure to state which Meeting Theme to which you think your Abstract is relevant. Be sure to suggest a Reviewer and their contact information. Be sure to add ALL co-authors with appropriate full details at the time of submitting the abstract into the system. If you wish to acknowledge a supporting agency, also add this as an acknowledgement in the Supporting Agency field when adding your abstract into the system. We have been asked why it is so important to submit abstracts correctly and why they will be peer reviewed. The reason is simple - the Abstracts will be published and correct presentation is seen as important in our current drive to make the TDWG a high profile, prestigious body. Please accept our apologies for cross-posting if you receive this message more than once. Regards, Adrian Rissone You are receiving this message because you have registered for TDWG 2006, expressed interest in attending the Meeting, or have attended previous TDWG meetings. If you are receiving this message in error, or do not wish to be contacted in the future, please accept our apologies for intruding and send a request to be removed from future mailings to A.Rissone(a)nhm.ac.uk with Subject line "TDWG Direct Mail Removal Request".

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LATEST UPDATE: Taxonomic Databases Working Group (TDWG) Annual Meeting 2006 - Abstracts and Registration
by Adrian Rissone 30 Aug '06

30 Aug '06

This message contains NEW time-critical information requiring immediate action. Please read it now. You are receiving this message because you have registered for TDWG 2006, expressed interest in attending the Meeting, or have attended previous TDWG meetings. If you are receiving this message in error, or do not wish to be contacted in the future, please accept our apologies for intruding and send a request to be removed from future mailings to A.Rissone(a)nhm.ac.uk with Subject line "TDWG Direct Mail Removal Request". Annual Meeting and Symposium of the Taxonomic Databases Working Group Missouri Botanical Garden 15 - 22 October 2006 http://tdwg2006.tdwg.org/ VISA TO ENTER THE UNITED STATES OF AMERICA We have been reminded that the process of obtaining a visa to enter the USA can be long for visitors from some countries. If you need a visa please ensure that you apply immediately. REGISTRATION AND HOTEL REDUCED RATES ENDING SOON! A late registration penalty fee of 50 $US will apply after 13 September 2006. The deadline for hotel discount is 13 September 2006. A number of registered delegates have indicated their intention to use the Recommended Hotel but have not yet made their hotel booking. Please do so as soon as possible. You MUST do so by 13 September to receive the discounted rate. You are not required to pay up front (but you must guarantee the booking with a credit card) and can cancel if necessary without penalty up to 15:00 local time on the day before you booked to arrive. The hotel booking URL is now being given on your Meeting registration confirmation e-mail. If you have an older version of the confirmation please contact me for the URL. ABSTRACTS FOR PRESENTATIONS The official deadline for Abstracts has been extended to 23:59 GMT on Saturday 2 September. THERE WILL BE NO FURTHER EXTENSION. PLEASE see the Abstracts Page for details and Instructions for Authors. Abstracts MUST be submitted in the required format. A number of abstracts have been received where the author has clearly not read the Instructions! In particular, please ensure the following: Be sure to state which Meeting Theme to which you think your Abstract is relevant. Be sure to suggest a Reviewer and their contact information. Be sure to add ALL co-authors with appropriate full details at the time of submitting the abstract into the system. If you wish to acknowledge a supporting agency, also add this as an acknowledgement in the Supporting Agency field when adding your abstract into the system. We have been asked why it is so important to submit abstracts correctly and why they will be peer reviewed. The reason is simple - the Abstracts will be published and correct presentation is seen as important in our current drive to make the TDWG a high profile, prestigious body. Please accept our apologies for cross-posting if you receive this message more than once. Regards, Adrian Rissone

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Guide to Best Practices for Georeferencing
by list.tdwg＠achapman.org 24 Aug '06

24 Aug '06

Apologies for cross-postings A Guide to Best Practices for Georeferencing has just been published on the GBIF (Global Biodiversity Information Facility) website. It can be downloaded from http://www.gbif.org/prog/digit/Georeferencing This publication is one of the outputs from the BioGeomancer project and discusses Best Practices for Georeferencing biological species (specimen and observational) data. The publication presents examples of how to georeference a wide range of different location types, and provides information and examples on how to determine the extent and maximum uncertainty distance for locations based on the information provided. A number of projects have been working for many years on the development of guidelines and tools for improving the georeferencing of primary biodiversity data. This document largely draws on those initiatives and attempts to bring the results of all this previous work into one comprehensive best practices document. It also draws upon new technologies and ideas developed through the current BioGeomancer project and existing projects such as MaNIS, HerpNet, MaPSTeDI, GEOLocate, INRAM, CRIA, ERIN and BioGeoMancer Classic. It is hoped that collections institutions, museums, herbaria and others, will adopt these guidelines to achieve consistency across the world in how locality data are georeferenced and documented, especially with regard to the recording of uncertainty. Citation information: Chapman, A.D. and J. Wieczorek (eds). 2006. Guide to Best Practices for Georeferencing. Copenhagen: Global Biodiversity Information Facility. Contributing authors: J.Wieczorek, R.Guralnick, A.Chapman, C.Frazier, N.Rios, R.Beaman, Q.Guo. Copyright © 2006 The Regents of the University of California. All rights reserved. The authors would appreciate any corrections or comments for future editions. regards Arthur D. Chapman Toowoomba, Australia

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URGENT UPDATE: Taxonomic Databases Working Group (TDWG) Annual Meeting 2006 - Reminder of late registration penalties
by Adrian Rissone 23 Aug '06

23 Aug '06

This message contains time-critical information requiring immediate action. Please read it now. You are receiving this message because you have registered for TDWG 2006, expressed interest in attending the Meeting, or have attended previous TDWG meetings. If you are receiving this message in error, or do not wish to be contacted in the future, please accept our apologies for intruding and send a request to be removed from future mailings to A.Rissone(a)nhm.ac.uk with Subject line "TDWG Direct Mail Removal Request". The 2006 Annual Meeting and Symposium of the Taxonomic Databases Working Group will be held at the Missouri Botanical Garden, St. Louis, Missouri, USA, from 15 - 22 October 2006. The meeting web site can be accessed here: http://tdwg2006.tdwg.org/ Registration is open now. There is an active link on the Registration Page to the RegOnline system which is handling registration for the meeting and has further links to discount booking at the recommended hotel and discount car rental. A PLEA FROM THE ORGANISERS From previous experience we know that delegates are slow to register and make hotel bookings. Anyone who attended the meeting in St. Petersburg in 2005 will know the possible consequences of late hotel bookings and late visa applications! Late registration is very disruptive to the smooth running of the meeting, making it difficult to plan meeting rooms, catering and transport. Late hotel bookings cause problems for the recommended hotel and may cost the TDWG money if we do not fulfill our advance booking commitment. This is a strong plea from the Meeting Organisers for ALL delegates to register and book your hotel room immediately. If you require help or further information please contact me without delay. PLEASE NOTE A late registration penalty fee of 50 $US will apply after 13 September 2006. The deadline for hotel discount is 13 September 2006. ABSTRACTS FOR PRESENTATIONS Abstracts for presentations by delegates were invited in June. Please see the Abstracts Page for details and Instructions for Authors. Abstracts MUST be submitted in the required format. The official deadline for Abstracts was 20 August 2006. This has been extended to 23:59 GMT on Saturday 2 September. There will be no further extension. Please accept our apologies for cross-posting if you receive this message more than once. Regards, Adrian Rissone

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