Tools for Identifying Biodiversity: Progress and Problems

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TABLE OF CONTENTS

 

Devising the EDIT Platform for Cybertaxonomy

Walter G. Berendsohn

 

 Descriptive Data in the EDIT Platform for Cybertaxonomy

Maxime Venin, Agnes Kirchhoff, Hélène Fradin, Anton Güntsch, Niels Hoffmann,
Andreas Kohlbecker, Elise Kuntzelmann,Ôna Maiocco, Andreas Müller,
Régine Vignes Lebbe, Walter G. Berendsohn

 

An online authoring and publishing platform for field guides and identification tools

Gregor Hagedorn, Gisela Weber, Andreas Plank, Mircea Giurgiu, Andrei Homodi, Cornelia Veja, Gerd Schmidt,
Pencho Mihnev, Manol Roujinov, Dagmar Triebel, Robert A. Morris, Bernhard Zelazny, Edwin van Spronsen,
Peter Schalk, Christian Kittl, Robert Brandner, Stefano Martellos, Pier Luigi Nimis

 

A search tool for the digital biodiversity resources of KeyToNature

Mircea Giurgiu, Andrei Homodi, Cornelia Veja, Gregor Hagedorn, Pier Luigi Nimis

 

Developing Web-based Search Portals on Birds for Different Target Groups

Renate Steinmann, Andreas Strasser, Andrea Mulrenin, Amy Trayler, Sander Pieterse, Ivan Teage,
Michael De Giovanni, John J. Borg, Noel Zammit

 

Simple Identification Tools in FishBase

Nicolas Bailly, Rodolfo Reyes Jr., Rachel Atanacio, Rainer Froese

 

The Catalogue of Life: towards an integrative taxonomic backbone for biodiversity

Frank A. Bisby, Yuri R. Roskov

 

BHL-EUROPE: Biodiversity Heritage Library for Europe

Jana Hoffmann, Henning Scholz

 

A Pan-European Species-directories Infrastructure (PESI)

Yde de Jong 

 

ViBRANT–Virtual Biodiversity Research and Access Network for Taxonomy

Dave Roberts, Vince Smith

 

Identifications in BioPortals™

Wouter Addink, Edwin van Spronsen, Peter H. Schalk

 

Types of identification keys

Gregor Hagedorn, Gerhard Rambold, Stefano Martellos

 

Learning, Identifying, Sharing

Philippe A. Martin, Noël Conruyt, David Grosser

 

Identification with iterative nearest neighbors using domain knowledge

David Grosser, Noël Conruyt, Henri Ralambondrainy

 

A MediaWiki implementation of single-access keys

Gregor Hagedorn, Bob Press, Sonia Hetzner, Andreas Plank, Gisela Weber, Sabine von Mering,
Stefano Martellos, Pier Luigi Nimis

 

Simple matrix keys from Excel spreadsheets

Gregor Hagedorn, Mircea Giurgiu, Andrei Homodi

 

Wiki keys on mobile devices

Gisela Weber, Gregor Hagedorn



 A Wiki-based Key to Garden and Village Birds

Tomi Trilar



Wiki-keys for the ferns of the Flora of Equatorial Guinea

Francisco Cabezas, Carlos Aedo, Patricia Barberá, Manuel De la Estrella, Maximiliano Fero,
Mauricio Velayos

 

MyKey: a server-side software to create customized decision trees

David Gérard, Régine Vignes Lebbe

 

Xper²: managing descriptive data from their collection to e-monographs

Visotheary Ung, Florian Causse, Régine Vignes Lebbe

 

FRIDA 3.0 Multi-authored digital identification keys in the Web

Stefano Martellos

 

Flora Bellissima, an expert software to discover botany and identify plants

Thierry Pernot, Daniel Mathieu

 

Modifiable digital identification keys

Edwin van Spronsen, Stefano Martellos, Dennis Seijts, Peter Schalk, Pier Luigi Nimis

 

The Open Key Player: A new approach for online interaction and user-tracking in identification keys

Mircea Giurgiu, Andrei Homodi, Edwin van Spronsen, Stefano Martellos, Pier Luigi Nimis

 

mprovement of identification keys by user-tracking

Gerd Schmidt, Mircea Giurgiu, Sónia Hetzner, Fred Neumann

 

ARIES: an expert system supporting legislative tasks. Identifying animal materials using the Linnaeus II software

Leo W.D. van Raamsdonk

 

An integrated system for producing user-specific keys on demand: an application to Italian lichens

Juri Nascimbene, Stefano Martellos, Pier Luigi Nimis

 

“Flora Italiana Digitale”: an interactive identification tool for the Flora of Italy

Riccardo Guarino, Sabina Addamiano, Marco La Rosa,

Sandro Pignatti

 

eFlora and DialGraph, tools for enhancing identification processes in plants

Fernando Sánchez Laulhé, Cecilio Cano Calonge, Antonio Jiménez Montaño

 

A catalogue of bird bones: an exercise in semantic web practice

Gudmundur Gudmundsson, Seth D. Brewington, Thomas H. McGovern, Aevar Petersen

 

Anthos.es: 10 years showing Spanish plant diversity information in the Internet

Leopoldo Medina, Carlos Aedo

 

An interactive tool for the identification of airborne and food fungi

Giovanna Cristina Varese, Antonella Anastasi, Samuele Voyron, Valeria Filipello Marchisio

 

The Estonian eFlora

Tiina Randlane, Malle Leht, Andres Saag

 

Keys to plants and lichens on smartphones: Estonian examples

Andres Saag, Tiina Randlane, Malle Leht

 

IIKC: An Interactive Identification Key for female Culicoides (Diptera: Ceratopogonidae) from the West Palearctic region

Bruno Mathieu, Catherine Cêtre-Sossah, Claire Garros, David Chavernac, Thomas Balenghien, Régine Vignes Lebbe,
Visotheary Ung, Ermanno Candolfi, Jean-Claude Delécolle

 

Indochinese bamboos: biodiversity informatics to assist the identification

of “vernacular taxa”

My Hanh Diep Thi, Régine Vignes Lebbe, Ha Phuong Nguyen, Bich Loan Nguyen Thi

 

Identification tools as part of Feedsafety research: the case of ragwort

Leo W.D. van Raamsdonk, Patrick Mulder, Michel Uiterwijk

 

Two identification tools applied on Mascarene’s corals genera (Xper2) and species (IKBS)

Yannick Geynet, Noël Conruyt, David Grosser, Gérard Faure, David Caron

 

Interactive, illustrated, plant identification keys: an example for the Portuguese flora

Maria Helena Abreu Silva, Rosa Maria Ferreira Pinho, Lísia Graciete, Martins Pereira Lopes, Paulo Cardoso da Silveira

 

The ORCHIS software used to identify 100 orchids species of Lao PDR

Pierre Bonnet, André Schuiteman, Boukhaykhone Svengsuksa, Daniel Barthélémy, Vichith Lamxay,

Soulivanh Lanorsavanh, Khamfa Chanthavongsa, Pierre Grard

 

A collaborative and distributed identification tool for plants

Philippe Laroche

 

Alternative 2D and 3D Form Characterization Approaches to the Automated Identification of Biological Species

Norman MacLeod

 

VeSTIS: A Versatile Semi-Automatic Taxon Identification System from Digital Images

Nikos Nikolaou, Pantelis Sampaziotis, Marilena Aplikioti, Andreas Drakos, Ioannis Kirmitzoglou,
Marina Argyrou, Nikos Papamarkos, Vasilis J. Promponas

 

Iterative Search with Local Visual Features for Computer Assisted Plant Identification

Wajih Ouertani, Pierre Bonnet, Michel Crucianu, Nozha Boujemaa, Daniel Barthélémy

 

Image data banks and geometric morphometrics

Anna Loy, Dennis E. Slice

 

Outline analysis for identifying Limodorum species from seeds

Sara Magrini, Sergio Buono, Emanuele Gransinigh, Massimiliano Rempicci, Silvano Onofri, Anna Scoppola

 

Geometric morphometrics as a tool to resolve taxonomic problems: the case of Ophioglossum species (ferns)

Sara Magrini, Anna Scoppola

 

Geometric morphometric analysis as a tool to explore covariation between shape and other quantitative leaf traits in European white oaks

Vincenzo Viscosi, Anna Loy, Paola Fortini

 

Landmark based morphometric variation in Common dolphin (Delphinus delphis L.,1758)

Paola Nicolosi, Anna Loy

 

DNA barcoding: theoretical aspects and practical applications

Maurizio Casiraghi, Massimo Labra, Emanuele Ferri, Andrea Galimberti, Fabrizio De Mattia

 

Strength and Limitations of DNA Barcode under the Multidimensional Species Perspective

Valerio Sbordoni

 

DNA Barcoding and Phylogeny of Patellids from Asturias (Northern Spain)

Yaisel Juan Borrell, Fernando Romano, Emilia Vázquez, Gloria Blanco, Jose Antonio Sánchez Prado

 

Molecular Identification of Italian Mouse-eared Bats (genus Myotis)

Andrea Galimberti, Adriano Martinoli, Danilo Russo, Mauro Mucedda, Maurizio Casiraghi

 

Identifying algal symbionts in lichen symbioses

Martin Grube, Lucia Muggia

 

Identification of polymorphic species within groups of morphologically conservative taxa: combining morphological and molecular techniques

Kim Larsen, Elsa Froufe

 

Coffee species and varietal identification

Patrizia Tornincasa, Michela Furlan, Alberto Pallavicini, Giorgio Graziosi

 

Mislabelling in megrims: implications for conservation

Victor Crego-Prieto, Daniel Campo, Juliana Perez, Eva Garcia-Vazquez

 

Seeds in subtribe Orchidinae (Orchidaceae): the best morphological tool to support molecular analyses

Roberto Gamarra, Emma Ortúñez, Ernesto Sanz, Iris Esparza, Pablo Galán

 

Lentils biodiversity: the characterization of two local landraces

Vincenzo Viscosi, Manuela Ialicicco, Mariapina Rocco, Dalila Trupiano, Simona Arena,
Donato Chiatante, Andrea Scaloni, Gabriella Stefania Scippa

 

A model study for tardigrade identification

Roberto Bertolani, Lorena Rebecchi, Michele Cesari

 

DNA Barcoding of Philippine plants

Esperanza Maribel G. Agoo

 

Molecular and ecophysiological characterisation of the Tunisian bee: Apis mellifera intermissa

Mohamed Chouchene, Naima Barbouche, Lionel Garnery, Michel Baylac

 

Biological identifications through mitochondrial and nuclear molecular markers: the case of commercially important crabs from Indian EEZ

Sherine Sonia Cubelio, K. K. Bineesh, K. Raj, Suraj Tewari, Achamveettil Gopalakrishnan,

Valaparambil Saidumohammad Basheer, Wazir Singh Lakra

 

Barcoding Fauna Bavarica – Capturing Central European Animal Diversity

Lars Hendrich, Michael Balke, Gerhard Haszprunar, Axel Hausmann, Paul Hebert,

Stefan Schmidt

 

Molecular techniques for identifying North Sea fauna

Thomas Knebelsberger, Sandra Ditzler, Silke Laakmann, Inga Mohrbeck,

Michael J. Raupach

 

DNA Bank Network – connecting biological collections and sequence databases by long-term DNA storage with online accession

Matthias Geiger, Nicolas Straube

 

Mitochondrial DNA sequences for forensic identification of the endangered whale shark, Rhincodon typus (Smith, 1828): A Case study

Kavungal Abdulkhadar Sajeela, Chandran Rakhee, Janardanan Nair Rekha, Achamveettil Gopalakrishnan,
Valaparambil Saidumohammad Basheer, Joe Kizhakkudan Shoba, Kizhakkudan Joe, Wazir Singh Lakra

 

An assignment-based elearning course on the use of KeyToNature e-keys

Pencho Mihnev, Nadezhda Raycheva

 

User needs for interactive identification tools to organisms employed in the EU-Project KeyToNature

Astrid Tarkus, Emanuel Maxl, Christian Kittl

 

Teaching biodiversity with online identification tools from KeyToNature: a comparative study

Felicia Boar, Adelhaida Kerekes

 

Digital Tools in the Botanical Garden of Madrid

Marina Ferrer, Esther García

 

Use of KeyToNature Identification Tools in the Schools of Slovenia

Irena Kodele Krašna

 

New key-tools for pollen identification in research and education

Jade Dupont, Nathalie Combourieu Nebout, Jean-Pierre Cazet, Florian Causse, Régine Vignes Lebbe

 

The UK urban tree survey

Bob Press

 

Tree School – A new Innovation for Science and Education

Della Hopkins, Karen James

 

Engaging Schools in Cutting Edge Science: From the Educator’s Perspective

Adrian Richardson, Della Hopkins

 

Educational or emotional languages? An interactive experiment with the Lucanian flora (S-Italy)

Riccardo Guarino, Patrizia Menegoni, Sandro Pignatti

 

Online sharing educational content on biodiversity topics: a case study from organic agriculture and agroecology

Nikos Palavitsinis, Nikos Manouselis, Kostas Kastrantas, John Stoitsis, Xenofon Tsilibaris

 

JSTOR Plant Science

Michael Sean Gallagher

 

ecoBalade: Towards a workflow for Citizen Science Nature Trails

Julie Chabalier, Khaled Talbi, Patrick Peters, Amandine Sahl, Olivier Coullet, Olivier Assunçao, Olivier Rovellotti

 

Electronic data recording tools and identifying species in the field

Alexander Kroupa, Anke Hoffmann, Juan Carlos Monje, Christoph L. Häuser

 

Cost Assessment of the Field Measurement of Biodiversity: a Farm-scale Case Study

Stefano Targetti, Davide Viaggi, David Cuming

 

Markets for biodiversity information products: real or imaginary?

Bill Hominick, Peter Schalk

 

A Basic Business Model for Commercial Application of Identification Tools

Christian Kittl, Peter Schalk, Nicola Dorigo Salamon, Stefano Martellos

 

Keys to Nature: A test on the iPhone market

Rodolfo Riccamboni, Alessio Mereu, Chiara Boscarol

 

Author Index

Browse

Recent Submissions

Now showing 1 - 5 of 89
  • Publication
    Tools for identifying biodiversity: progress and problems
    (EUT Edizioni Università di Trieste, 2010)
    Nimis, Pier Luigi
    ;
    Vignes Lebbe, Régine
    The correct identification of organisms is fundamental not only for the assessment and the conservation of biodiversity, but also in agriculture, forestry, the food and pharmaceutical industries, forensic biology, and in the broad field of formal and informal education at all levels. In this book, the reader will find short presentations of current and upcoming projects (EDIT, KeyToNature, STERNA, Species 2000, Fishbase, BHL, ViBRANT, etc.), plus a large panel of short articles on software, taxonomic applications, use of e-keys in the educational field, and practical applications. Single-access keys are now available on most recent electronic devices; the collaborative and semantic web opens new ways to develop and to share applications; the automatic processing of molecular data and images is now based on validated systems; identification tools appear as an efficient support for environmental education and training; the monitoring of invasive and protected species and the study of climate change require intensive identifications of specimens, which opens new markets for identification research.
      1465  9153
  • Publication
    Indochinese bamboos: biodiversity informatics to assist the identification of “vernacular taxa”
    (EUT Edizioni Università di Trieste, 2010)
    Vignes Lebbe, Régine
    ;
    Diep Thi, My Hanh
    ;
    Nguyen, Ha Puong
    ;
    Bich Loan Nguyen, Thi
    Bamboo (Bambusoides – Gramineae) is one of the most important natural resource in Southeast Asia. However, bamboo identification has many difficulties. In the area of SEP programme «Indochina Bamboos» (2008-2010), the final objective is to update the bamboo flora of Indochine (Vietnam, Laos, Cambodege) and to publish an e-flora including free access keys, digital images and information about the traditional and economic use of bamboos. During field trips in Vietnam, Laos and Cambodgia, samples, pictures and morphological description sheets were collected in various locations and previously assigned to the local vernacular names. We use an informatic program, Xper2, to assist the comparison and identification of “vernacular bamboo taxa” based on morphological characteristics.
      1181  2205
  • Publication
    Mitochondrial DNA sequences for forensic identification of the endangered whale shark, Rhincodon typus (Smith, 1828): A Case study
    (EUT Edizioni Università di Trieste, 2010)
    Kavungal Abdulkhadar, Sajeela
    ;
    Rakhee, Chandran
    ;
    Janardanan Nair, Rekha
    ;
    Gopalakrishnan, Achamveettil
    ;
    Valaparambil, Saidumohammad Basheer
    ;
    Kizhakkudan, Joe Shoba
    ;
    Kizhakkudan, Joe
    ;
    Lakra, Wazir Singh
    The whale shark (Rhincodon typus), the largest fish in the ocean, has become susceptible to over-exploitation and has a global conservation status of ‘vulnerable to extinction’ as listed by World Conservation Union in the Red list of threatened species. The increase in demand for its meat, skin and fins in international trade is a severe threat to the animal and its indiscriminate capture will have to be taken seriously as they may have a major impact in the marine ecosystem. Rhincodon typus was nominated in Appendix II of Convention on International Trade in Endangered Species (CITES) in April 2000, to enable adequate regulation of trade of whale shark products. Whale shark (Rhincodon typus) is enlisted as one of the protected species in India and its fishing prohibited under Schedule Ι of the Indian Wildlife Protection Act, 1972, according to the Order No.1-2/2001 WL1 Dated 28.05.2001, Govt. of India, so as to conserve the species in Indian waters. still illegal fishing prevails in Indian waters and the catch is processed in the vessel itself and sold in markets as meat chunks. To curb the illegal trade and marketing of fishery products from whale shark, for devising good management practices and for the strict law enforcement, accurate and reliable species identification methods using molecular tools are of paramount importance. In an effort to establish a comprehensive identification data set, we have generated a species-specific partial sequence data of the mitochondrial genome of properly identified stranded whale shark samples, covering the 16S rRNA (546 bp),Cyt b (541bp), COI (600bp) genes as the reference genetic profile helping in accurate identification of any body parts of the species. In the year 2008, flesh suspected as that of the Wildlife protected whale shark (Rhincodon typus) was seized from fishermen by the Forest Range Officer (Govt. of Kerala), Kannur, Kerala, India and was brought before the Judicial First Class Magistrate, Thalassery, Kannur, Kerala, India. The detailed sample analysis and confirmation of species was carried out at NBFGR Cochin Unit (R.P.330/08, dt 29. 09. 2008). Based on DNA sequencing of 16S rRNA(525bp) and COI (600bp) Cyt b(541bp) genes and comparing with the sequences earlier generated by NBFGR (FJ375724, FJ375725, FJ375726, FJ456921, FJ456922, and FJ456923), the suspected sample was identified as that of endangered Whale Shark (Rhincodon typus) and the result was communicated to the court. This is the first criminal case in India in which scientific evidence was sought in forensic identification of the meat of an aquatic organism enlisted in the Wildlife Protection Act of India and the DNA markers reiterated their ability to reliably identify product/meat sample of a species, thus helping in curtailing illegal trade of the endangered organisms.
      1625  1002
  • Publication
    Keys to Nature: A test on the iPhone market
    (EUT Edizioni Università di Trieste, 2010)
    Riccamboni, Rodolfo
    ;
    Mereu, Alessio
    ;
    Boscarol, Chiara
    Several keys running on mobile devices were developed by the KeyToNature project. Most of them are freely downoadable online. The rapid spread of smartphones has opened up new opportunities in the production and distribution of multimedia applications for the educational sector, including interactive keys to identify organisms. This market is new, still partly unexplored and changing fast. The Department of Life Sciences of the University of Trieste and Divulgando Srl, have tested its potential by uploading in the iTunes Store different types of keys for the iPhone, some of them for free, others for sale. This paper introduces the issue of global market applications, summarizes the experience gained in our case-studies, and suggests ways to make these applications economically viable.
      1421  2180
  • Publication
    A Basic Business Model for Commercial Application of Identification Tools
    (EUT Edizioni Università di Trieste, 2010)
    Kittl, Christian
    ;
    Schalk, Peter
    ;
    Dorigo Salamon, Nicola
    ;
    Martellos, Stefano
    Within the three-year EU project KeyToNature various identification tools and applications in formal education for teaching biodiversity have been researched and developed. Building on the competencies of the involved partner organisations and the expertise gained in this domain, the paper outlines a business model which aims at commercially exploiting the project results on a broader scale by describing the value proposition, products & services, value architecture, revenue model and the intended market.
      1471  1088