Open Journal System
Proceedings of TDWG
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2009

2009 Pre-conference Provisional

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Table of Contents

e-Biosphere 09-Outcomes

UK Roadmap for delivery of Internet-based Taxonomy Abstract
Frank Bisby, Malcolm Scoble, Norman MacLeod, Colin Miles, Amanda Read, Walter Berendsohn, Mark Costello, Thomas Orrell
e-Biosphere and TDWG Abstract
Walter G. Berendsohn, et al.

Sharing e-knowledge on agricultural diversity worldwide

CONABIO’s experience: Sharing e-knowledge, solutions and lessons learned Abstract
Patricia Koleff, Cecilio Mota, Francisca Acevedo, Oswaldo Oliveros, Claudia Sánchez, Israel Martínez
Biodiversity Informatics and co-Operation in Taxonomy for Interactive shared Knowledge base (BIOTIK) Abstract
B.R. Ramesh, N. Ayyappan, D. Balasubramanian, P. Grard
Agropolis global presentation of Pl@ntNet Abstract
Daniel Barthélémy, Nozha Boujemaa, Daniel Mathieu, Jean-François Molino, Pierre Bonnet, Raffi Enficiaud, Elise Mouysset
Landscape of the information standards for plant genebanks Abstract
Theo van Hintum
Value of a coordinate: geographic analysis of agricultural biodiversity Abstract
Andy Jarvis, Julian Ramirez, Nora Castañeda, Samy Gaiji, Luigi Guarino, Hector Tobón, Daniel Amariles

Global networks

The GBIF Global Names Architecture Abstract
David P Remsen, Markus Döring,
The Global Invasive Species Information Network: Its latest advances and its barriers Abstract
Michael Browne, Jim Graham, Christine Fournier, Annie Simpson
The Global Biodiversity Information Facility (GBIF): The decentralised architecture Abstract
Samy Gaiji, Éamonn Ó Tuama, David Remsen, Vishwas Chavan, Tim Robertson
EDIT: experience and impact Abstract
Dave Roberts
The Global Biodiversity Information Facility – strategic objectives and perspectives on building the biodiversity informatics commons Abstract
Nick King

Ontology and Life Science Identifiers: The state of the play

Vocabularies - Managing Them Abstract
Kehan Tristam Harman, Roger Hyam, David P Remsen
The TDWG Life Sciences Identifiers Applicability Statement Abstract
Ben Richardson
Persistent Identifiers for Biodiversity Informatics: Status and Likely Directions Abstract
Greg Riccardi, Richard White, Phil Cryer, Roger Hyam, Chuck Miller, Nicola Nicolson, Éamonn Ó Tuama, Rod Page, Jonathan Rees, Kevin Richards
Linked Data Abstract
Roger Hyam

EDIT Cyberplatform

ENHANCING THE VISUALIZATION OF BIOLOGICAL DATA: EDIT GEOGRAPHIC TOOLS Abstract
Pere Roca, P. Sastre, J. M. Lobo, B. Meganck, Franck Theeten, P. Mergen, Andreas Müller, A. Kohlbecker, S. Dusan, D. Mikiewicz
The Introduction of EDIT's Community Single Sign-On System Abstract
Lutz Suhrbier, Andreas Kohlbecker, Andreas Müller
Crossmedia publishing with the CDM Abstract
Niels Hoffmann
Fieldwork today with data acquisition tools Abstract
Alexander Kroupa
The Taxonomic workflow in the EDIT Platform for Cybertaxonomy Abstract
Andreas Kohlbecker, Pepe Ciardelli, Niels Hoffmann, Katja Luther, Andreas Müller
e-Taxonomy with CATE and EDIT Abstract
Benjamin Richard Clark
Using the CDM to build Europe’s largest species database Abstract
Marc Geoffroy, Anton Güntsch, Andreas Kohlbecker
The EDIT Taxonomic Editor - More Features, Less Code Abstract
Pepe Ciardelli
The EDIT Platform for Cybertaxonomy - User Workshop Abstract
Pepe Ciardelli, Niels Hoffmann, Andreas Kohlbecker, Alexander Kroupa

Agriculture including Biocuration, Disease

Semantic Web for Ecosystem Approach applied to Fisheries Abstract
Julien Barde, Pascal Cauquil, Abdel Dkhissi
Integrating Animal Health and Biodiversity Informatics Standards Abstract
James Case
Catalogue of Life Phase 2 and the new 4D4Life Project Abstract
Richard J White, Frank A Bisby, Meirion Jones, Wouter Addink

Identifying Biodiversity for Food and Agriculture

Impact of Citizen Science projects on biodiversity policies :Tela Botanica conference results Abstract
VIOLETTE ROCHE
Plant diversity, functional traits and ecoinformatics Abstract
Eric Garnier
Data integration and its impact on genebank management Abstract
Christopher Richards, Gayle Volk
Semantic Standards for Genomic Analyses of the South and Mediterranean Plants: the Generation Challenge Program Use Case Abstract
Manuel Ruiz
Sketches from an anthropologist’s fieldnotes on local knowledge about agrobiodiversity: a primer for biodiversity information specialists Abstract
Eric Garine
New challenges for visual information retrieval in biodiversity applications Abstract
Raffi Enficiaud, Nozha Boujemaa
The concept of "Networked collection" or "Virtual collection":
revisiting the classical delineation between "in situ" and "ex situ" conservation and its consequences on database management Abstract
Roland Bourdeix, S F Weise, S Planes, L Guarino, T Bambridge, C Lusty

Accessing information on Agricultural genetic resources and crop wild relatives

ACCESSING INFORMATION ON PLANT GENETIC RESOURCES Abstract
Elizabeth Arnaud, Sónia Dias
Integrating the monitoring of agricultural pests into biodiversity assessments Abstract
Gail E Kampmeier
Can Biodiversity Informatics (help to) save the AQUATIC genetic resources? Abstract
Nicolas Bailly, Roger S. V. Pullin
A global information portal to facilitate access and use of information on genebank accessions Abstract
Michael C. Mackay
Accessing information on domestic animal diversity Abstract
Beate Scherf, Dafydd Pilling
The Crop Wild Relatives Portal: Conservation and utilization of crop wild relatives through better use of information – a global project with Armenia, Bolivia, Madagascar, Sri Lanka and Uzbekistan Abstract
Imke Thormann, Dany Hunter, Armen Danielyan, Beatriz Zapata Ferrufino, Jeannot Ramelison, Anura Wijesekara, Sativaldi Djataev

Agriculture Information for development

ARCAD- Agropolis Resource Center for Crop Conservation, Adaptation and Diversity : a new open multi-function platform devoted to agrobiodiversity. Objectives and challenges Abstract
Jean-Louis Pham, Jean-Pierre Labouisse
BIODIVERSITY NETWORKS IN AFRICA: FROM KNOWLEDGE MANAGEMENT TO TECHNICAL AND INSTITUTIONAL IMPLEMENTATION Abstract
Charles Kahindo, Franck Theeten, Patricia Mergen, Garin Cael, Michel Louette, Olivier Bakasanda, Motonobu Kasajima, Patricia Kelbert, Jorg Holetscheck, Elizabeth Arnaud, Dheda Djailo
Digitization and richness of type specimen collections at the Paris herbarium - spotlight on the Global Plants Initiative Abstract
Pascale Chesselet, Jean-Noël Labat
Plant Resources of Tropical Africa (PROTA): a tool for sustainable development Abstract
Michel Chauvet
Sud-Expert-Plantes Abstract
Eric Chenin

Wild Ideas!

Convergence of Ontology, Hypothesis, Workflow, and Query Abstract
Mark D Wilkinson
Have Standards Enhanced Biodiversity Data? Global correction and acquisition patterns Abstract
Javier Otegui, Arturo H. Ariño
Moving biodiversity to the cloud Abstract
Javier de la Torre

Taking Data Integration Forward

Using Distributed Annotations for Continuous Quality Control of Biodiversity Data Abstract
Paul J Morris, James Macklin, Maureen Kelly, Robert A Morris, Zhimin Wang

Computer Demonstration

TaxoBrowser: a visual mashup for taxonomic browsing Abstract
Stéphane Azard, Julie Chabalier, Amandine Sahl, Olivier Rovellotti
The Moorea Biocode Project: Tracking Barcoded Specimens From Collecting Event to Sequence Abstract
John Deck
A graphical system for computer-assisted plant identification Abstract
Pierre Grard, Pierre Bonnet, Juliana Prosperi, Le Bourgeois Le bourgeois, Claude Edelin, Frédéric Theveny, Alain Carrara
eFlore: An Electronic Flora Abstract
GREGOIRE DUCHE
The Biofinity Project: An Extensible Semantic Bridge between Biodiversity and Genomics Abstract
Stephen D. Scott, Leen-Kiat Soh, Etsuko Moriyama, Federico Ocampo, Mary Liz Jameson, Steve Harris, Ian Cottingham, Shawn Baden, Adam Eck, Derrick Lam, Catherine Anderson, Yuji Mo, Dan Clark, Matt Moore
Maximising the potential of digitised literature-INOTAXA prototype and TDWG standards Abstract
Chris Lyal, Anna Weitzman
GCP Crop Ontology Browser Abstract
Martin Senger, Rosemary Shrestha, Elizabeth Arnaud
Using Citizen Science to Process Digital Herbarium Labels Abstract
Michael Giddens
EURISCO - The European Plant Genetic Resources Search Catalogue Abstract
Milko A. Škofič, Sónia Dias
The Atrium Biodiversity Information System: sharing, managing, analyzing, and disseminating biodiversity data Abstract
Mathias W Tobler, John P Janovec, Jason H Best, Amanda K Neill, Anton Webber
Become an e-Taxonomist with Xper² Abstract
Visotheary Ung, Régine Vignes-Lebbe
Plazi: Building Communities and Software for Increasing the Utility of Digitized Biodiversity Publications Abstract
Guido Sautter, Donat Agosti, Terry Catapano, Robert A. Morris
CleanTax: An Integrated Framework for Mapping Biological Taxonomies and Merging Taxonomically Organized Presence/Absence Data Sets Abstract
David Thau, Shawn Bowers, Bertram Ludäscher
A biodiversity cartography portal for nature conservationists, scientists, and naturalists Abstract
Tania Walisch, Guy Colling, John van Breda
A Framework and Workflow for Extraction and Parsing of Herbarium Specimen Data Abstract
Jason H Best, William E Moen, Amanda K Neill
The Encyclopedia of Life: Pathways to contribution Abstract
Cynthia Parr, Patrick Leary

Poster

Development of open source software for the management of observational data Abstract
Michel Deshayes, Beatrice Carpy, Marie Demarchi, Sophie Gras, Isabelle Moins, Elise Mouysset, Aurelien Peironnet
Lifemapper: Finding the Good Life Abstract
Aimee M. Stewart, James H. Beach, C.J. Grady, David A. Vieglais
EBONE, a project to design and test a European biodiversity observing system, integrated in time and space Abstract
Rob H. G. Jongman, France F.O. Gerard, Philip Roche, Michel Deshayes
AfriBes-Towards a social network of scientific and technical information for Africa Abstract
Maxime Thibon
TermForm : an online Web application to define and share concepts for the development of a trait-based ontology Abstract
Marie-Angelique LAPORTE, Isabelle MOUGENOT, Eric GARNIER
Domestic Animal Diversity Information System - A clearing house mechanism Abstract
Beate Scherf
Semantic data integration for the analysis of the genetic diversity of plants Abstract
Wollbrett Julien
EURISCO – The European Plant Genetic Resources Search Catalogue Abstract
Sonia Dias
Orylink: a personalized integrated system for functional genomic analysis Abstract
Pierre Larmande
eRelevé: a suite of solutions for biodiversity data management Abstract
Amandine Sahl, Olivier Coullet, Jean-Francois Leger, Yves Hingrat, Julie Chabalier, Olivier Rovellotti, Eric Lenuz
STERNA Semantic Web-based integration of digital resources on birds Abstract
Stijn Cooleman, Guntram Geser, Michel Louette, Maarten Heerlien, Danny Meirte, Patricia Mergen, Andrea Mulrenin
The Diversity Workbench Framework: Data retrieval with DiversityMobile and Dataflow from DiversityMobile to GBIF Abstract
Markus Weiss, Stefan Jablonski, Gerhard Rambold, Dagmar Triebel, Bernhard Volz, Tobias Schneider
The Diversity Workbench framework as data repository for biological data Abstract
Markus Weiss, Dagmar Triebel, Gregor Hagedorn, Stefan Jablonski, Gerhard Rambold, Tobias Schneider, Bernhard Volz
Ca-SIF: A SHARED AND STANDARDIZED CATALOGUE TO PROVIDE INFORMATION ON FOREST ECOSYSTEMS Abstract
Wilfried Heintz, Guy Landmann, Damien Maurice
Metadata – a Core Component of the GBIF Network Abstract
Éamonn Ó Tuama, Tim Robertson
Enhancing the Access and Publication of Biodiversity Data in Central Africa: The CABIN Technical Infrastructure Abstract
Franck Theeten, Patricia Mergen, Olivier Bakasanda, Jörg Holetschek, Patricia Kelbert, Montonobu Kasajima, Garin Cael, Charles Kahindo
Canadensys : unlocking Canada's biological collection information Abstract
Desmet Peter, Anne Bruneau, Luc Brouillet
The importance of a good balance between physical collection management and digitisation. How SYNTHESYS aims for a benchmark standard throughout Europe. Abstract
Garin Cael, Patricia Mergen, Robert Huxley, Simon Owens
The Musa Germplasm Information System Enhances Knowledge of Banana Diversity Abstract
Max Ruas, Stéphanie Channelière, Guilhem Sempere, Manuel Ruiz, Elizabeth Arnaud, Ines Van den Houwe, Jean-Pierre Horry, Nicolas Roux
Biodiversity Heritage Library for Europe – Interoperability of European biodiversity digital libraries Abstract
Adrian Smales, Kai Stalmann, Henning Scholz
Pl@ntWood: A computer-assisted identification tool for 110 species of Amazon trees based on wood anatomy Abstract
Carolina Sarmiento, Christine Heinz, Pierre Détienne, Pierre Bonnet
EDIT Community Single Sign-On Abstract
Lutz Suhrbier, Andreas Kohlbecker, Andreas Müller
Capabilities and interfaces of a prototype Filtered Push network Abstract
Zhimin Wang, Maureen A Kelly, David B Lowery, James A Macklin, Paul J Morris, Robert A Morris, Donna Tremonte
Crop Ontology: a controlled vocabulary for trait descriptions for maize, wheat, chickpea, sorghum, banana and plantain, potato and rice Abstract
Rosemary Shrestha, Ramil Mauleon, Reinhard Simon, Jayashree Balaji, Stephanie Channelière, Martin Senger, Kevin Manansala, Thomas Metz, Guy Davenport, Richard Bruskiewich, Elizabeth Arnaud
Using the Electronic Field Guide Project’s software to make digital guides Abstract
Robert Stevenson, Robert Morris, Robert Sheldon
Making the TDWG Ontology understandable for experts of other scientific and scholarly domains Abstract
Karl-Heinz Lampe, Mark Fichtner
Siregal: the INRA Plant Genetic Resources Information System Abstract
Sophie Durand, Erik Kimmel, Cyril Pommier, Jean-Marie Prosperi, Delphine Steinbach, Hadi Quesneville
LSIDs for managing biological names in data integration Abstract
Nina Laurenne, Mikko Koho, Arto Mertaniemi, Hannu Saarenmaa
4D4Life Integrated Development and Documentation Infrastructure for Sustainable Software Production Abstract
Núria Torrescasana Aloy, Dennis Seijts, Gideon Gijswijt, Wouter Addink, Peter Schalk
The GBIF Data Portal Abstract
José Cuadra, Samy Gaiji, Andrea Hahn, Tim Robertson
The GBIF Harvesting and Indexing Toolkit (HIT) Abstract
Kyle Braak, Andrea Hahn, Samy Gaiji, Tim Robertson, Markus Döring
Global Biodiversity Resources Discovery System Abstract
Vishwas Chavan, Eamonn O'Tuama, Tim Robertson, Jose Cuadra, Samy Gaiji
SINGER, THE SYSTEM WIDE INFORMATION NETWORK ON GENETIC RESOURCES OF CGIAR Abstract
Rajesh Sood, Kiran Viparthi, Gautier Sarah, Milko Skofic, Elizabeth Arnaud
Ephesis : Environment and Phenotypes Information System, a GnpIS module Abstract
Cyril Pommier, Erik Kimmel, Pierre Roumet, Delphine Steinbach, Hadi Quesneville
An Application Profile Using Darwin Core Rendered in the New Dublin Core Application Profile Framework Abstract
William E. Moen, Amanda K. Neill, Jason Best
Scanning and Passport Data Extraction from Bioversity - Collecting Mission Reports and Related Documents Abstract
Hannes Gaisberger, Imke Thormann, Milko Skofic, Lorenzo Stabile, Tom Hazekamp, Aixa del Greco, Elizabeth Arnaud
TaxoBrowser: a visual mashup for taxonomic browsing Abstract
Stéphane Azard, Julie Chabalier, Amandine Sahl, Olivier Rovellotti
Composition Assistance for Multiple Existing Scientific Workflow Systems Abstract
Russell McIver, Andrew Clifford Jones, Richard White
Automatic Biodiversity Literature Enhancement Abstract
David King, Alistair Willis, Anton Dil, David Morse, Chris Lyal, Dave Roberts
Exchanging specimen interaction data using Darwin Core Abstract
Antonio Mauro Saraiva, Etienne Américo Cartolano Júnior, Renato De Giovanni, Tereza Cristina Giannini, Pedro Luiz Pizzigatti Correa
The Biodiversity Data Digitizer (BDD) tool Abstract
Etienne Americo Cartolano Junior, Antonio Mauro Saraiva, Jorge Augusto Teles, Diogo Borges Krobath, Pedro Luiz Pizzigatti Correa
The GBIF Integrated Publishing Toolkit Abstract
Markus Döring, Tim Robertson
4D4Life Work Package 7: Serving user needs with a new system architecture for the Catalogue of Life Abstract
Richard J White, Andrew C Jones, Alex R Hardisty
The Future of EOL: Phase II Implementation Abstract
Cynthia Parr
Building a scalable, open source storage solution for biodiversity data Abstract
Phil Cryer, Anthony Goddard
The Global Names Architecture: an integrated and federated approach to enabling discovery and access to biodiversity information. Abstract
David Remsen
Computer Tools for Descriptive Data Management for the Taxonomist Abstract
Ôna Maiocco, Régine Vignes-Lebbe
PESI: A European web portal for all species in Europe Abstract
Ward Appeltans, Bart Vanhoorne, Marie-Line Villers, Leen Vandepitte, Wim Decock, Francisco Hernandez, Marc Geoffroy, Anton Guentsch, Walter Berendsohn, Mark Costello, Yde de Jong
The Biofinity Project: Transforming Biodiversity Research Abstract
Mary Liz Jameson, Federico Ocampo, Daniel R. Clark, Matthew R. Moore
Crop science and breeding: contributions in the field of bioinformatics by the Generation Challenge Programme, an international crop breeding research programme Abstract
E van Strien
Specify Collections Software: Cross-Platform, Open-Source, Collaborative, Robust, Localizable, Multidisciplinary, Mature, Portable, and Free. Abstract
Jim Beach
At the frontline of publishing in systematic zoology: ZooKeys Abstract
Lyubomir Dimitrov Penev, Terry Erwin, Jeremy Miller
Repatriating the Botany of Tropical Africa Abstract
Henry R. Engledow, Quentin J. Groom, Piet Stoffelen, Alain Empain, Sofie De Smedt, Steven Dessein, Petra De Block, Elmar Robbrecht

Contributed Abstracts and Papers

Herbarium Digitisation at Royal Botanic Gardens, Kew Abstract
Kathryn Beck, Sarah Phillips
A data standard to integrate Farmers Knowledge and Science Abstract
Adriana Alercia, Frederick van Oudenhoven, Pablo Eyzaguirre
DarwinCore Germplasm Extension and deployment in the GBIF infrastructure Abstract
Dag Endresen, Samy Gaiji, Tim Robertson
INSPIREing Europe Abstract
Kathi Schleidt

Working Sessions

The jKey wiki key player and builder Abstract
Stephan Opitz, Gregor Hagedorn
GBIF LSID-GUID Task Group report and discussion on persistent identifiers Abstract
Greg Riccardi, Richard J White, Eamonn O Tuama
Crop Ontology: a Reference Controlled Vocabulary on Crop Trait Information Abstract
Elizabeth Arnaud, Rosemary Shrestha, Martin Senger, Mauleon Ramil, Milko Skofic
Fine-Grained Semantic Markup of Descriptive Data for Knowledge Applications in Biodiversity Domains Abstract
Hong Cui, James Macklin, Chunshui Yu, Partha Pratim Sanyal
Harnessing the long tail: Small biodiversity data publishers Abstract
Vishwas Chavan, Eamonn O'Tuama, David Remsen
Taxonomic Name Processing Abstract
David Remsen, Markus Döring
The role of persistent identifiers in tracking taxon changes Abstract
Andrew C Jones, Richard J White, Ewen R Orme
An Open Source Annotation Service for the Atlas of Living Australia Abstract
Ron Chernich, Stephen Crawley, Donald Hobern, Jane Hunter
A Species Conservation Information System for the State of Louisiana Abstract
Nelson Rios, Henry Bart
WebBiodiverse - a tool for visualising biodiversity distribution and the taxonomic, phylogenetic and spatial relationships between taxa. Abstract
Ajay Ranipeta, Paul Flemons, Shawn Laffan, Dan Rosauer
Wiki publishing workshop Abstract
Gregor Hagedorn, Stephan Opitz
Recording and sharing annotations during two stages of museum specimen digitization: Apiary and Atrium Abstract
Amanda K Neill, Jason H Best, John P Janovec, Mathias A Tobler, William E Moen, Tiana F. Franklin, M. Brooke Byerley
Key construction with polymorphic characters Abstract
Zhimin Wang, Robert A. Morris
TDWG Collaboration and Fund Raising in the Year of Biodiversity Abstract
Lee Belbin
A graphical tool for computer-assisted plant identification Abstract
Pierre Grard, Pierre Bonnet, Juliana Prosperi, Thomas Le Bourgeois, Claude Edelin, Frédéric Théveny, Alain Carrara
Pl@ntNote: a flexible software for the management and share of data on plants Abstract
Philippe Birnbaum, Jean-François Molino, Jérôme Perez, Frédéric Théveny
Interoperability of databases on useful plants Abstract
Helmut Knuepffer, Michel Chauvet
EDIT Advanced Scratchpads tutorial Abstract
Simon Rycroft, Kehan Harman, Dave Roberts, Vince Smith
Multimedia Resources Metadata Schema Abstract
Vishwas Chavan, Robert A Morris
Bringing advanced statistical data analysis to the web: the integration of R with the Atrium Biodiversity Information System Abstract
Mathias W Tobler, John P Janovec, Jason H Best, Amanda K Neill, Anton Webber
Linked Literature and the Biodiversity Heritage Library Abstract
Chris Freeland
Experiences Building a Species Profile Model Web Service Abstract
Terry H. Catapano, Robert A. Morris
EDIT tutorial for programmers - CDM Library Abstract
Andreas Kohlbecker, Ben Clark, Pepe Ciardelli, Niels Hoffmann
A matrix based character editor for Scratchpads Abstract
Kehan Tristam Harman, Simon David Rycroft, Ben Scott, David McL. Roberts, Vincent Simon Smith
IBIS-ID, an Adobe FLEX based identification tool for SDD-encoded multi-access keys Abstract
Mircea Giurgiu, Andrei Homodi, Gregor Hagedorn
The Environment Ontology – Linking Environmental Data Abstract
Norman Morrison
TERMINIZER - ASSISTING MARK-UP OF TEXT USING ONTOLOGICAL TERMS Abstract
David Hancock