The Proceedings of TDWG Abstracts of the 2007 Annual Conference of the Taxonomic Databases Working Group 16-22 September 2007 Bratislava, Slovakia (Hosted by the Faculty of Natural Science, Comenius University) Edited by Anna Weitzman and Lee Belbin Published by Biodiversity Information Standards (TDWG) and the Missouri Botanical Garden St. Louis, 2007 TDWG 2007 sponsored by: © Taxonomic Databases Working Group, 2007 © Missouri Botanical Garden, St. Louis, Missouri, U.S.A., 2007 © Cover design: Adrian Rissoné, 2007 To be cited as: Weitzman, A.L., and Belbin, L. (eds.). Proceedings of TDWG (2007), Bratislava, Slovakia. This book contains abstracts of the papers, posters and computer demonstrations presented at the Annual Conference of the Taxonomic Databases Working Group held 16-22 September 2007 at the SÚZA (Správa účelových zariadení) Conference Centre in Bratislava, Slovakia, hosted by the Faculty of Natural Science of the Comenius University. The meeting attracted more than 141 participants from 25 countries and 88 prestigious scientific research institutions, museums and companies. The editors acknowledge with thanks the contribution of Arturo Ariño, Reed Beaman, Lee Belbin, Walter Berendsohn, Stan Blum, Alex Chapman, Renato de Giovanni, Stinger Guala, Gregor Hagedorn, Donald Hobern, Roger Hyam, Gail Kampmeier, Jessie Kennedy, Éamonn O Tuama, Ricardo Pereira, Rich Pyle, Adrian Rissoné, Annie Simpson and Neil Thomson towards the editing of this publication, and also the numerous peer reviewers. Published and distributed as an Adobe® Portable Document Format (PDF) document for free download from the Conference web site at http://www.tdwg.org/conference2007/ ISBN 978-1-930723-71-9 Contents Session 1. Client's Perspectives: User Needs 1.1. EDIT needs Biodiversity Information Standards Walter G. Berendsohn, Markus Döring, Malte C. Ebach ........................................................ 9 1.2. Biodiversity Heritage Library: Progress & Potential Chris Freeland ....................................................................................................................... 10 1.3. One million species in the Catalogue of Life – a triumph for Species 2000 and ITIS, or for TDWG standards? Frank A. Bisby....................................................................................................................... 10 1.4. User Needs - The alpha and omega of system design Charles J.T. Copp .................................................................................................................. 11 1.5. Exploring the Brave New World of eTaxonomy Chuck Miller.......................................................................................................................... 12 Session 2. Client's Perspectives: Examples of TDWG Standards in Use 2.1. TDWG Standards in use within the Global Biodiversity Information Facility (GBIF) Data Portal Tim Robertson....................................................................................................................... 13 2.2. Assessing the Threat of Invasive Species in South America: an ensemble modeling approach in support of data standards, integration, and dissemination Miguel Fernandez, Wendy Tejeda, Guillermo Duran, Adriana Rico, Christian Arias, Maria Laura Quintanilla, Alberto Pareja, Juan Carlos Chive, Monica Rivera, Healy Hamilton ................................................................................ 13 2.3. Results of a Needs Assessment Survey of the Global Invasive Species Information Network (GISIN) Annie Simpson, Jim Graham, Michael Browne, Hannu Saarenmaa, Elizabeth Sellers .................................................................................................................... 14 2.4. When Taxonomies Meet Observations: An Examination of Taxonomic Concepts used by the Observation Systems eBird and the Avian Knowledge Network Paul Edward Allen................................................................................................................. 16 2.5. Taxonomists at work: relationships of process and data Anna Weitzman, Christopher Lyal ........................................................................................ 16 Session 3. Needed Technologies: Introductions and Demos 3.1. TDWG Standards Architecture - What and Why Roger Hyam........................................................................................................................... 18 3.2. Life Sciences Identifiers (LSID) and the Biodiversity Information Standards (TDWG) Ricardo Scachetti Pereira.......................................................................................................19 3.3. Nala: A Semantic Data Capture Extension for Mozilla Firefox Ben Szekely, Ricardo Scachetti Pereira................................................................................. 19 3.4. Key Enabling Technologies: Transfer Protocols Donald Hobern ...................................................................................................................... 20 Session 4. Ontologies and Vocabularies: Atomizing biodiversity information 4.1. The Role of Ontologies in the TDWG Architecture Roger Hyam........................................................................................................................... 22 4.2. Integrating TDWG standards with EDIT’s Common Data Model Markus Döring, Andreas Müller, Ben Clark, Marc Geoffroy................................................ 23 Proceedings of TDWG (Biodiversity Information Standards) – 2007, Bratislava, Slovakia 3 4.3. ALTER-Net: A Data Ontology for LTER Observations and Measurements Kathi Schleidt ........................................................................................................................ 23 4.4. An ontological approach to describing and synthesizing ecological data, using a generalized model for “scientific observations” Mark Schildhauer, Matthew Jones, Joshua Madin, Shawn Bowers ...................................... 24 Session 5. LSIDs: Gluing it together to meet users' needs 5.1. LSIDs for Taxon Names: The ZooBank Experience Richard Pyle .......................................................................................................................... 26 5.2. LSID and TCS deployment in the Catalogue of Life Richard John White, Andrew C Jones, Ewen R Orme .......................................................... 26 5.3. An LSID authority for specimens and an LSID browsing client Kevin James Richards ........................................................................................................... 27 5.4. LSID policy and implementation in Australia Greg Whitbread, Alex R. Chapman, Ben Richardson ........................................................... 28 5.5. LSID Mashup Daniel Miranker..................................................................................................................... 29 Session 6. Enabling Technologies: Protocols 6.1. TapirLink: Facilitating the transition to TAPIR Renato De Giovanni ..............................................................................................................30 6.2. RDF over TAPIR Roger Hyam........................................................................................................................... 30 6.3. TAPIR networks in Australia’s Virtual Herbarium and the Atlas of Living Australia Greg Whitbread, Shunde Zhang, Paul Coddington ............................................................... 31 6.4. Checklist Provider Tool: a GBIF Application for Sharing Taxonomic Checklists Using TAPIR and TCS Wouter Addink, Jorrit van Hertum........................................................................................ 32 6.5. Shibboleth, a potential security framework for the TDWG architecture Lutz Suhrbier, Andreas Kohlbecker ...................................................................................... 32 Session 7. Models for Integrating TDWG: Species Profile Model 7.1. Main aspects of the Species Profile Model and the TDWG architecture Andreas Kohlbecker, Markus Döring, Andreas Müller......................................................... 33 7.2. Species Profile Model: Data integration lessons from GBIF Donald Hobern ...................................................................................................................... 33 7.3. SPM from an SDD perspective: Generality and extensibility Gregor Hagedorn ................................................................................................................... 34 7.4. Coming to Terms with SPM Robert A. Morris ................................................................................................................... 35 Session 8. Models for Integrating TDWG: Literature Model 8.1. Linking Bibliographic Data to Library Content Julius Welby .......................................................................................................................... 36 8.2. Use cases from taxonomists, conservationists, and others Cynthia Sims Parr, Christopher Lyal..................................................................................... 36 8.3. Progress in making literature easily accessible: schemas and marking up Terry Catapano, Anna Weitzman .......................................................................................... 37 8.4. Literature & interoperability: a working example using Ants Donat Agosti, Terry Catapano, Guido Sautter....................................................................... 38 8.5. Taxonomic Literature: