Biodiversity Informatics 2004 Taxonomic Databases Working Group Annual Meeting, 11-17 October 2004 University of Christchurch, New Zealand (hosted by Landcare Research)

Papers

Abstracts (in alphabetical order by senior/presenting author surname)

Specimen Image Databases for Taxonomic Research: Experiences on File and Metadata Handling
Downloadable presentation
Arturo H. Ariño (Presenting), David Galicia. Department of Zoology and Ecology, University of Navarra, Pamplona, Spain.

Digital image technology has provided a reliable, convenient way to store images of natural history collections’ specimens. Current web technology, and in particular shared taxonomic database schemas already developed or under development, can now ensure easy distribution and almost universal access to high-quality images formerly available only through hard copies.

In many respects, the caveats and shortcomings of these digital images are very similar to those on the traditional chemical photography. However, metadata from digital images are much easier to document and maintain, i.e. as EXIF data. Additional metadata and imaging procedures can be used to store information that dramatically increases the validity of these images for taxonomic studies, i.e. by facilitating biometrics or image analysis.

We will discuss some experiences on this taxonomically-oriented use of scientific imaging, including considerations on imaging, precision, morphometrics, colour reproducibility, metadata, formats, databasing, and storage efficiency.

SDD support tools
Jacob Asiedu, and Robert A. Morris, University of Massachusetts at Boston Department of Computer Science, U.S.A.

We discuss experience developing two SDD tools: a prototype lightweight SDD description editor implemented in C# under .NET, and an SDD debugging aide in Java. The first assumes that an SDD Terminology has been built by some community. It supports the scoring of descriptions in ways that insure only those states of a character are offered which are defined for the character in the given Terminology. (This cannot be enforced by XML Schema validation against the SDD Schema, which knows nothing about any particular Terminology.) The second tool primarily supports programmers developing SDD applications, though it might also find use by people attempting to write SDD instance document with generic editors like XML Spy or XML Notepad. It addresses the heavy dependence of SDD on Schema keys and key references. Typically these are randomly chosen integers, and it is difficult, for example in a Description, for a human to understand what is the referent in the Terminology of a given key reference. The SDD DebugRef tool chases all references in the SDD document and annotates them with a heuristically chosen indication of what the target is, and, optionally, of the full XPath from the document root to the target.

Problems and solutions to modelling species distributions at a global scale: the importance of taxonomic and specimen databases
Peter Brewer and Frank Bisby, Centre for Plant Diversity and Systematics, The University of Reading, Reading. RG6 6AS. United Kingdom

Various methods for modelling the potential distribution of plants and animals have been developed over the last decade or more. However, the spatial resolutions at which these studies have been completed have been limited to local, regional and continental scales. During this research, attempts to model the global distribution of a number of plant species have successfully identified a number of key problems with scaling existing modelling approaches to a global perspective. Whilst the modelling algorithms themselves have no inherent problem modelling distributions at a global scale, there are difficulties associated with the specimen and climate data required to perform these predictions. Although there are an increasing number of specimen databases online they are almost exclusively limited in geographic extent. Specimen data must therefore be collated from multiple sources creating further problems associated with taxonomy. A firm grasp of a species taxonomic status is required to ensure all specimens of a particular species concept are retrieved. Additional problems are posed by the climatic datasets required by the bioclimatic modelling algorithms. Whilst monthly climate data can be used in regional modelling studies, climate data must be pre-processed in global studies to ensure seasonal offsets between hemispheres are accounted for. Methods for overcoming all these hurdles are proposed and the importance of Global Species Databases (GSDs) in global distribution modelling is discussed.

BDWorld: A grid-based workflow manager for high-throughput distributed computing in biodiversity research
Neil Caithness ¹ , Shonil Bhagwat ³ , Peter Brewer ¹ , Oliver Bromley ⁴ , Frank A. Bisby ¹ , Alastair Culham ¹ , Nick J. Fiddian ² , W. Alex Gray ² , Andrew C. Jones ² , Malcolm Scoble ³ , Tim Sutton ¹ , Richard J. White ² , Paul Williams ³ , Xuebiao Xu ² , and Chris Yesson ^1
1 Centre for Plant Diversity & Systematics, School of Plant Sciences, The University of Reading , Reading RG6 6AS , UK . {P.W.Brewer|F.A.Bisby|N.Caithness|A.Culham|T.Sutton|C.Yesson}@reading.ac.uk
² Cardiff University, School of Computer Science , Queen’s Buildings, 5 The Parade, Cardiff CF24 3AA , UK . {N.J.Fiddian|W.A.Gray||Andrew.C.Jones|R.J.White|X.Xu}@cs.cardiff.ac.uk
³ Department of Entomology, The Natural History Museum , London SW7 5BD , UK . {S.Bhagwat|M.Scoble|P.Williams}@nhm.ac.uk
⁴ School of Biological Sciences, University of Southampton , Southampton SO16 7PX , UK . O.Bromley@soton.ac.uk

The goals of the BDWorld project are to create an extensible framework for supporting distributed computing in biodiversity research, and to use this framework in three real exemplar study areas. From the researcher’s perspective the system consists of a graphical work-flow manager that provides access to a suite of remote data resources and analytical tools. From the system’s perspective there is a layered architecture that protects us from the ever changing grid communications technology, a workflow designer, a workflow enactment engine, a metadata repository, a resource locator, a resource matcher, and a suite of wrappers or proxies for the actual resources. We present an overview of the system, and show examples of its use in high-throughput computing in the field of bioclimatic modelling.

Progress in, and plans for, the development of the Ocean Biogeographic Information System, including the need for standards to enable mapping marine species over the internet
Mark J. Costello ¹, Phoebe Zhang ², Karen Stocks ³, Fred Grassle ^2
1 Leigh Marine Laboratory, University of Auckland, PO Box 349, Warkworth, New Zealand.  m.costello@auckland.ac.nz
² Institute of Marine Sciences, Rutgers State University, 71 Dudley Road, New Brunswick, NJ 08901-8521, USA
³ San Diego Supercomputing Centre, University of California at San Diego, 9500 Gilman Drive, L Jolla, CA 92093, USA

The Ocean Biogeographic Information System has tripled the amount of data it serves in the past 12 months to 5 million records of about 30,000 species, and remains one of the largest data providers to the Global Biodiversity Information Facility.  Users can select from different ocean environmental data layers to map species distributions on, and use two alternative range predicting models.  It uses the name service of the Catalogue of Life from Species 2000, and is actively working with CoL and the marine science community to have a Catalogue of Marine Life available as the species authority files for OBIS and GBIF.  We estimate there are 230,000 marine species described of which most will have few locations.  A special effort is required to capture the distribution of these rare species.  Links to the source databases provide additional information on the marine species and environment.    

OBIS is largely a distributed system.  Interoperability was initially achieved using a defined html call and XML return based on a small set of fields (genus, species, latitude, longitude); providers implemented this individually.  Now OBIS uses DiGIR based on the OBIS Schema.  The OBIS schema is an extension of the Darwin Core Version 2, and is backward-compatible (i.e. OBIS implementations of DiGIR can respond to calls from systems using the Darwin Core).  Fields such as citation, start and end latitude/longitude (to allow transect data), and number collected (vs. number preserved) were added to meet OBIS user needs.  The standard OBIS portal interface allows querying on genus, species, common name, latitude and longitude.  The advance interface allows querying on combinations of these fields plus date, depth, and date source.  This will need to expand in the future to allow searches on habitat type and higher classification, and to hold abundance data and polygon spatial data (versus just lines and points).  OBIS supports, adopts and will help develop international standards, so as to have a technically efficient and reliable open-access service to the public and scientific communities.

Geospatial Interoperability Standards and Emerging TDWG Specifications
Phillip C. Dibner, Ecosystem Associates.

The discussion starts with a backgrounder on the structure, philosophy, and several standards created by the Open Geospatial Consortium. It then provides some views on how (and whether) to integrate OGC standards with TDWG's current work.

The integration of DiGIR and BioCASe
Döring, M., Giovanni, R., Hobern, D., Vieglais, D., Güntsch, A., Blum, S., Wieczorek, J., de la Torre, J.

DiGIR and BioCASe are XML-based protocols for search and retrieval of data stored in distributed and heterogeneous sources. They are being used by most part of the existing biodiversity networks. Together, these networks are currently serving approximately 40 million records from biological collections databases and observation databases.

During the GBIF's Data Access and Database Interoperability subcommittee meeting held in Oaxaca 2004, the importance of integrating both protocols into a single common standard has been fully recognized and considered a priority. Since then, GBIF promoted a study involving representatives from both protocols. The results of that work include considerations taken from other existing standards such as XQuery, OpenGIS specifications and SOAP, and also a proposal for a new integrated protocol.

CHRONOS : A federation of databases to support taxonomic data preservation for the paleobiological community
Doug Fils¹, Cinzia Cervato¹ Vladimir Davydov² Pat Diver³, Brian Huber⁴, and Mark Leckie⁵

¹Iowa State University , Dept. Geological and Atmospheric Sciences, 253 Science I, Ames , Iowa , 50011 , USA (fils@chronos.org)
² Boise State University, Boise , Idaho , USA
³ DivDat Consulting, Houston , Texas , USA
⁴ National Museum of Natural History, Smithsonian Institution, Washington DC , USA
⁵ University of Massachusetts , Amherst , USA

Earth system history research depends increasingly upon the analysis of voluminous, multidisciplinary, time-calibrated data. CHRONOS is a community resource dedicated to making available Earth history data and information, together with a toolkit to analyze and visualize them. This international, interactive network of paleobiology, biostratigraphy, radioisotope geochronology, and sedimentary geochemistry data is made accessible through a common site (www.chronos.org) and has been funded by the U.S. National Science Foundation since August 2003. The paleobiological community associated with CHRONOS is organized in working groups that cover so far ten taxonomic groups. Having adopted and implemented existing standards (DarwinCore and DiGIR) for taxonomic data, CHRONOS is striving to partner with biological database projects to adapt resources developed for the bioscience community, and to promote initiatives in the paleobiological community to make available in digital format taxonomic data for the study of Phanerozoic biodiversity.

CHRONOS is currently hosting a taxonomic dictionary for Mesozoic planktonic foraminifera that is being used as a prototype for database and metadata testing. We are also working with the Treatise of Invertebrate Paleontology to develop, host, and network their digital Paleobank database.

Towards a language for indicating relationships among taxonomic concepts
Franz, Nico M.¹ (presenter) & Peet, Robert K.^2
1National Center for Ecological Analysis and Synthesis, 735 State Street, Suite 300, Santa Barbara, CA 93101, U.S.A., franz@nceas.uscb.edu
²Department of Biology, CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, U.S.A., peet@unc.edu

Based upon previous efforts by taxonomists and database developers, a new language is proposed to express the relationships among taxonomic concepts. The system employs a limited set of symbols adopted from set theory. Accordingly, the referential extensions of two concepts may be congruent (= =), more or less inclusive of each other (> or <), overlapping (><), exclusive (!), or ambiguous (?). The system offers experts the choice to specify the meaning of a concept only in reference to its constituents (ostensively, abbreviated with "ost.") or its properties (intensionally, "int."), to combine the two ways of defining ("int./ost."), or to ignore the distinction (i.e. to "somehow" conceive its extension, "ext."). One may also indicate whether there is any continuity ("con.") in the evidential support provided for succeeding concepts. We discuss how adopting this language would affect the future of a largely internet-based taxonomy.

Development of web-based interactive system for taxonomy of the plants of Indian Subcontinent
Ganeshaiah, K. N.¹, Rajanikanth, G.², Mohan, G.S.^{2, 3}, Nanditha Mahadev¹, Uma Shaanker, R.^1
1University of Agricultural Sciences, GKVK, Bangalore - 560065, India
²Ashoka Trust for Research in Ecology and the Environment (ATREE), Hebbal, Bangalore - 560024, India.
³For correspondence: mohan@atree.org

This paper offers the details on the efforts at our center in developing a computer aided taxonomic networking system for Indian subcontinent. Taxonomists in India have difficulties in accessing the relevant specimens and literature because a significant proportion of both are distributed in different parts of the world. Further, owing to the logistic hurdles in keeping up with the developments in plant systematics elsewhere in the globe, Indian taxonomists have been facing difficulty in updating their own work. However, it is possible to overcome these hurdles through creation of a digital database on the relevant specimens and literature and an interactive cyber networking system through which taxonomists can objectively and continuously interact.

In this direction, we have been developing a regional “Cyber Taxonomy” platform for the Indian subcontinent. As first step, we have developed; a) taxonomic database from over 300 flora books b) website on taxonomy, images, distribution of Indian plants and, c) software system to track linkages among different nomenclatures. We plan to convert this platform into an interactive “Cyber Taxonomy” system for the region. We hope this model would serve as a viable and workable alternative for the conventional taxonomy in developing countries.

THE TRANSMISSION ENGINE: accessing biological content linked to names representing different taxonomic concepts
Marc Geoffroy & Anton Güntsch, Department of Biodiversity Informatics, Botanic Garden and Botanical Museum Berlin-Dahlem, Koenigin-Luise-Str. 6-8, 14191 Berlin, Germany

Biological content (e.g. protection status, uses, description, sequences) is linked to taxonomic concepts (represented by a taxon name with a circumscription). If relationships are defined between concepts (e.g. congruence, inclusion), then content linked to one concept can be accessed through another one. We call this a transmission of content. However, calculating the influence of the transmission on the reliability of the content data in the new context is a complex task. Abstracting, concepts are nodes and relations are edges in a graph. Content is an “attribute” of nodes and relationships are an “attribute” of edges. With this approach transmission of content amounts to “carrying” a node attribute through the graph. Rules to compute resulting relationships between nodes connected through paths must be established. Set criteria to evaluate the relevance of such paths (e. g. its maximal length) and relationships (e. g. “exclude” relationship) must be accounted for and the applicability of transmitted information has to be modified accordingly. The Transmission Engine is a tool to accomplish this task. We present a protype Java implementation of the Engine and its caching mechanism (computation within graphs is very time consuming) and sketch the computation and the representation of taxonomic concept graphs used.

Research Challenges in Using Distributed GIS Services to Support Biodiversity Visualization and Analysis
Robert Guralnick ¹, David Neufeld ². ¹Asst. Professor and Curator Dept. of EEB and CU Museum University of Colorado Boulder Boulder CO 80309-0265. ²CU Museum University of Colorado Boulder Boulder CO 80309-0265.

During development of an NSF supported online mapping application for visualizing and analyzing biodiversity information, we confronted two major research challenges.   The first challenge was determining how to best access distributed point-based information about species occurrences across the landscape given network bandwidth limitations.  The second challenge was building an application that could access heterogeneous distributed datasets of collections information and spatial environmental reference layers.  In order to determine the most effective means to transport potentially large datasets of geospatial point data, we calculated file sizes returned from remote servers for 100, 1000 and 10,000 records using three different methods:  XML, ArcSDE, and PNG images.  The best solution in all cases was to develop a remote image mapping service to generate PNG images.  This solution scales particularly well as the number of records returned increases.  Using image fusion had the added advantage of allowing access to heterogeneous data sources as long as the returned data is a spatially referenced image.  Our architecture is built on a Java Server Pages Model-View-Controller2 (MVC2) design pattern that allows for access, in our case, to remote ArcIMS servers and Web Map Services (WMS) servers.   The solutions presented here are not specific to biodiversity information and should be of general use for all developers of web-based mapping services that access distributed data sources. 

Proxy data objects provide optional linking to external objects and small modular data interfaces from which DarwinCore and LinneanCore- like protocol interfaces can be constructed Gregor Hagedorn (Federal Biological Research Center, Institute for Plant Virology, Microbiology, and Biological Safety, Königin-Luise-Str. 19, 14195 Berlin, Germany)

Ideally, biodiversity data are expressed using well-defined object types (with generally accepted and intuitive property and object composition concepts) and all objects required in relations are available in digital form, identifiable through resolvable globally unique identifiers. Reality is different. a) the complex models like ABCD, SDD, TCS etc. are under debate and not necessarily fully stable. A consequence is that simplified "Cores" like DarwinCore or LinneanCore are proposed. b) Most required data are not digitized at all. Wherever data should naturally refer to other biodiversity domains alternative models are required to either linking something external or provide a sufficient internal object definition. Such a definition also involves a simplified set of core elements.

I therefore propose to combine the two problems and define relatively simple data interfaces, that can serve both for protocol/query purposes and for the definition of local proxy objects (= either link to external entities, or provide a local definition). Data interfaces shield the complexity of a fuller model (i.e. the full model can be treated as a black box). They should be rough enough to fit to several models, but also detailed enough to allow the definition of proxy data (i. e. make a substantial semantic definition). Data interface are often implicitly used in current practice. 'Specify' uses a simplified literature and nomenclature interface, DarwinCore contains name, identification and geographical location interfaces, Taxon Concept Schema contains interfaces for literature and specimen, and Linnean Core has a literature interface. Agreeing on a common set of such interface concepts would allow to build Darwin and LinneanCore as well as much of SDD, TCS, etc. from a the same building blocks, drastically reducing the investment needed for a full global biodiversity information system.

Use case scenarios for TaxonConceptSchema (TCS, Napier)
Gregor Hagedorn (Federal Biological Research Center, Institute for Plant Virology, Microbiology, and Biological Safety, Königin-Luise-Str. 19, 14195 Berlin, Germany)

Some use case scenarios of supplying data nomenclatural and concept data in the Taxonomic Concept Schema (TCS) format and of linking ecological or descriptive data to TCS data are discussed. How well are these use cases supported by TCS? Furthermore, the NameAtomizedType is studied, to see whether it is possible to have a larger common bio-name type, with extensions for different taxonomic codes, rather than having completely different name types for each code. Also, no provision seems to be made to support the concept parts of a name in the atomized format.

Introduction to UBIF (Unified Biosciences Information Framework)
Gregor Hagedorn (Federal Biological Research Center, Institute for Plant Virology, Microbiology, and Biological Safety, Königin-Luise-Str. 19, 14195 Berlin, Germany)

The currently proposed TDWG standards have significantly overlapping type definitions. The goal of UBIF (http://efgblade.cs.umb.edu/twiki/bin/view/UBIF) is providing a unifying framework from which multiple TDWG standards can derive common structures, type definitions and enumerations. It may (but does not have to provide the framework for commonly accepted simplified data interface concepts and linking mechanisms. UBIF is intended to be co-authored widely by authors of all contributing schemata. The draft submitted to TDWG is currently ca. 80% SDD-based and 20% ABCD-based - this needs a lot of change, we need a much wider framework! It is hoped that the meeting in Christchurch will provide fruitful discussions, add new common types and remove others considered of no truly general use.

Introduction to SDD (Structured Descriptive Data)
Gregor Hagedorn¹, Bob Morris², Kevin Thiele³, P. Bryan Heidorn^{4 1}Federal Biological Research Center, Institute for Plant Virology, Microbiology, and Biological Safety, Königin-Luise-Str. 19, 14195 Berlin, Germany, ²University of Massachusetts at Boston, Department of Computer Science, U.S.A., ³Centre for Biological Information Technology, Australia, ⁴Graduate School of Library and Information Science, University of Illinois at Urbana-Champaign.

This outlines some fundamentals of the SDD proposal (which are based on the UBIF proposal) and then concentrates on the proposed 1.0 schema for coded descriptions and the terminology supporting these descriptions. Of special importance are the changes introduced in the quantitative measurements, in the sample data, and in the (principally type polymorphic) approach to characters and modifiers. To improve the focus of the discussion, Identification keys and Natural language descriptions as proposed in SDD will
*not* be discussed, unless requested by email in advance!

Building a Global Network using TDWG Standards
Donald Hobern, Global Biodiversity Information Facility Secretariat, Universitetsparken 15, 2100 København Ø , Denmark

The GBIF Network has been developed using TDWG standards to integrate specimen/observation data (DiGIR, including BioCASe modification; Darwin Core, including various extensions; ABCD Schema). GBIF also plans to integrate data using the Taxonomic Concept Transfer and Structured Descriptive Data Schemas.

The GBIF Data Portal (www.gbif.net) shows a simple prototype overview of the accessible data. The portal will soon be enhanced to offer XML web services for users to access data from throughout the network. These services will use the same data standards being used by the individual data providers.

These development activities have demonstrated the strengths of the existing TDWG standards and have also helped to highlight the value of some of the proposed updates to these standards, (particularly to the DiGIR-BioCASe protocol) and of the common access models included in the UBIF proposal.

Global Infrastructure for Biodiversity Informatics
Donald Hobern , Global Biodiversity Information Facility Secretariat, Universitetsparken 15, 2100 København Ø , Denmark

As increasing numbers of portals and application tools make use of biodiversity data, there is a need for a several shared resources to be made available as common infrastructure. In 2003 and 2004 GBIF has been focussing on the development of a registry of biodiversity data resources and on an index of biodiversity data records. These will be made available as publicly accessible resources for use by the whole community. The code for the Data Portal will be redeveloped to allow it to be deployed for national or thematic portals.

Other key resources will also be required in order to support biodiversity informatics as a flexible discipline. GBIF wishes to start work on a Schema Repository to provide easy access to biodiversity-related schemas and associated documentation, including mappings between related concepts in different schemas. This service should make it easy for software tools to connect to data services using different schemas and to transform their outputs into preferred formats. It should also allow software interfaces to present users with meaningful descriptions of the significance of different data elements.

GBIF is also investigating mechanisms to associate specimens, observations, taxon concepts, etc. with persistent and reusable globally unique identifiers. Such identifiers would not only make it simpler to refer to a specific item, but would also assist tools with detection of duplicate records retrieved via different routes.

Central services will also be developed to perform a range of validation checks for XML-based biodiversity data.

Using informal names within taxonomic datasets; a practical perspective
Charles Hussey, The Natural History Museum, Cromwell Road, London SW7 5BD, UK, e-mail c.hussey@nhm.ac.uk (presenter)
Dr Steve Wilkinson, Joint Nature Conservation Committee, Monkstone House, City Road, Peterborough PE1 1JY, UK, e-mail steve.wilkinson@jncc.gov.uk

Drawing upon experience with the National Biodiversity Network Gateway (www.searchnbn.net) and Nature Navigator (www.nhm.ac.uk/naturenavigator) projects, we shall explore issues with using vernacular names and informal higher group names. The latter have proved useful for providing a browsing interface and for filtering and sorting results returned by a search. Informal group names are also useful for clarifying unfamiliar scientific names, and their use can improve accessibility.

Initial dissemination of MBARI’s unique deep-sea biodiversity data
Nancy Jacobsen Stout, Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road , Moss Landing , California 95039 USA.

The Monterey Bay Aquarium Research Institute (MBARI) has developed a software and hardware system, Video Annotation and Reference System (VARS), to facilitate the creation, storage, and retrieval of video annotations based on remotely operated vehicle (ROV) deep-sea dive video . This video library contains footage of the biological, chemical, geological, and physical aspects of the Monterey Bay submarine canyon, other regions of the Pacific and the Gulf of California . The VARS software components reference a knowledge database of over 3,500 known biological, geological and technical concepts. This hierarchical information allows for consistent and rapid classification, description, and complex querying of objects observed on video. Recently, MBARI released a prototype of the query tool on its website ( www.mbari.org\vars). U sers can request observation times, locations, and conditions, as well as still images, when available. In addition, plans are underway for modifying the database schema to be more readily shared among global databases. This includes discussions with OBIS on becoming a data contributor specializing in the deep-sea. MBARI is eager to receive feedback and to continue improving worldwide access to this annotation data.

Fauna Europaea; all European animal species on the web
Yde de Jong¹, Melina Verbeek¹, Verner Michelsen², Fedor Steeman², Nicolas Bailly³, Claire Basire³. ¹Zoological Museum Amsterdam, P.O. Box 94766, NL-1090 GT Amsterdam, The Netherlands. ²Zoological Museum, Department of Entomology, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. ³Muséum National d'Histoire Naturelle (MNHN), Institut de Systématique (CNRS FR 1541), Laboratoire d'Ichtyologie, 43 rue Cuvier, 75231 Paris cedex 05, France

For the first time in history all names of the European land and fresh water species are integrally available on the Web. This public service is presented as Fauna Europaea. Fauna Europaea covers about 130.000 species, which is much more than the originally projected number of 100.000 species when starting Fauna Europaea. This is a huge success for all the more than 400 contributing specialists throughout Europe , and an unparalleled effort in the world so far. A first release of the Fauna Europaea index via the web portal (for public access) has been presented at 27 th of September 2004.

Fauna Europaea was a European Commission (EU) funded project for a period of 4 1/2 years (starting March 2000) and provides a web based information infrastructure with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to Ural, excluding Caucasus region), and some additional optional information. Fauna Europaea is a unique (standard) reference for many users in science, government, industry, nature conservation, and education. Considering the current concepts established in the Zoological Code of nomenclature a new database structure has been designed. To ensure the collation of high quality data, more then 400 specialists, including 65 Group Coordinators, have been contracted. Advanced on-line and off-line tools for data import and data management were developed, and innovative procedures for data validating applied, including regional and thematic validation meetings, and advanced digital tools to check for technical and logical correctness. Expansion of the current geographic coverage of Fauna Europaea, to also include the non-European parts of Northern Asia, and the inclusion of additional data types (including vernacular names), is in preparation.

Fauna Europaea established a formal relationship with its sister projects Euro+Med PlantBase and the European Register of Marine Species (ERMS), which are developing comparable, services for terrestrial plant and marine species respectively. The advanced integration of the results (databases) of these projects is now being realized through a so-called Euro-Hub, which is an effort of the EU-funded Species-2000 Europe project.

Overview of nomenclatural practices in Zoology and Botany with respect to the consequences of integrating zoological and botanical checklists data into a single virtual environment
Yde de Jong, Zoological Museum Amsterdam, P.O. Box 94766, NL-1090 GT Amsterdam, The Netherlands

Within the context of the EU project EuroCat, on the integration of the three main European taxonomic indices on animal, plants and marine species (Fauna Europaea, Euro+Med PlanstBase and ERMS respectively) to provide combined access into a single so called 'EuroHub', it was recognized that different nomenclatural concepts are applied in all three databases. As the underlying SPICE technical infrastructure was initially developed from a botanical perspective, the applicability on the zoological situation, especially its uninominal synonymy, is problematic. The main issue is that nomenclatural history, as kept within botanical nomenclature through binominal synonymy, including authorship citing and gender shifts, is considered insignificant according to the International Code of Zoological Nomenclature (ICZN). As a consequence past nomenclatural 'acts' are not preserved and no exact transition of accepted and synonym names into a single historically appropriate (full) binominal index is possible. In addition complication occur with merging heterogonous data sets into a single data presentation and when cross-mapping data sets (e.g. using LITCHI).

The Taxonomic Concept Schema (TCS) Overview and Rationale
Jessie Kennedy, School of Computing, Napier University, Merchiston Campus, 10 Colinton Road, Edinburgh EH10 5DT, Scotland.

This presentation will give an overview of the proposed TDWG Taxonomic Concept Schema for exchanging information about names and concepts, highlighting the in aims of the design of the schema and how these have been achieved in the model. In particular it will discuss the relationship between names and concepts and how both can be encompassed using the same model. It will also discuss how the different notions of taxonomic concept adopted by different taxonomic database groups can be represented for transfer using this same model. The TCS is not a "new" model of taxonomy but rather an inclusive model which captures the range of various interpretations of concept uncovered during our analysis. The TCS can allow transfer of concepts fit for particular purposes; although not all representations of concepts possible in the TCS will necessarily be suitable for all purposes.

Genebanks as GBIF data providers – first experiences
Helmut Knüpffer¹, Nobert Biermann¹, Dag Terje Endresen², Pawel Kolasinski³, Wieslaw Podyma^{3, 4}, Javier de la Torre^5
1Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany (knupffer@ipk-gatersleben.de)
²Nordic Gene Bank, POB 41, SE-230 53 Alnarp, Sweden
³Plant Breeding and Acclimatization Institute (IHAR), PL-05870 Blonie, Radzików near Warsaw, Poland
⁴Present address:
⁵Botanic Garden & Botanical Museum Berlin-Dahlem, Königin-Luise-Str.6-8, D-14191 Berlin, Germany

Genebanks are living collections of plant genetic resources (PGR), comprising wild and cultivated plants from all over the world, representing thousands of plant species. Their primary aim is to make germplasm of crop plants and their wild relatives available to plant breeders and researchers. They also play an important role in preserving plant biodiversity.

The number of germplasm accessions is estimated by FAO at 6 million worldwide, preserved in hundreds of genebanks, many of them well documented. For three decades, genebanks have exchanged their data and built up joint „Central Crop Databases“, especially in Europe, using PGR-specific data exchange standards.

Data exchange standards for PGR and biodiversity collections are compared, and the experiences of the first genebanks that became GBIF data providers are reported. The Nordic Genebank (NGB, Alnarp, Sweden) and The Polish Genebank (IHAR, Radzików) with 29,878 and 40,459 accessions, respectively, are using the Darwin Core. The German Genebank (IPK, Gatersleben) with 109,711 accessions is linked via the ABCD (Access to Biological Collections Data) standard.

To facilitate the full integration of PGR collections into GBIF, ABCD was extended. It is suggested to use GBIF mechanisms and facilities (e.g., data provider and protocol building tools) also within the PGR community.

Repatriation of Specimen Data to Reinforce National Systems of Biodiversity Information
Patricia Koleff, Jorge Soberón, Cecilia Fernández and Juan Manuel Martínez.
National Commission for the Knowledge and Use of Biodiversity (Conabio), Liga Periférico- Insurgentes Sur 4903 Col. Parques del Pedregal. Tlalpan 14010. Mexico D.F. Mexico (pkoleff@xolo.conabio.gob.mx)

Biodiversity management requires knowledge of the distribution of species. Scientific collections can contribute substantially to document species occurrence but unfortunately most specimens in museums and herbaria are not computerized. Moreover, most of the specimens that were collected in developing, biodiversity rich nations are deposited in institutions in the developed countries. In this work we present some of the methods that Conabio (The National Commission for the Knowledge and Use of Biodiversity of Mexico) has used to access the data in the labels of nearly a million specimens in collections abroad. Often the specimens come with digital images. Conabio has obtained about 76,500 digital images of specimens from foreign collections. Voucher specimens information has been compiled in databases, accordingly to standards. Geo-reference of specimen records lacking of geographical coordinates data adds remarkable value to specimen data. Some of these data are already web available through the collection nodes of the World Biodiversity Information Network (REMIB). We also discuss issues related to data quality control and complementary data needed for different kinds of analysis.

Use and Functions of GBIF UDDI Registry
Giorgos Ksouris¹, Hannu Saarenmaa², GBIF Secretariat Universitetsparken 15, DK-2100 Copenhagen.

GBIF UDDI registry is the central global directory where data providers advertise their services so that users, search engines, and portals can discover them. This paper describes GBIF Secretariat’s implementation of the UDDI Registry. UDDI fundamentals, including its core data types are presented and its use and functions in the GBIF metadata infrastructure discussed. The features of UDDI are compared to other solutions and details of how the registry has been deployed in order to meet the needs of GBIF goals are described. In particular, use of taxonomies to group data providers by country and thematic network is important from the standpoint of GBIF participants and the networks GBIF works with. The paper concludes with an analysis of new features that can solve some limitations in the currently used UDDI version, how UDDI can help to achieve a distributed architecture for GBIF, and contributes to the discussion on using UDDI for a unified biodiversity information framework.

TCS explained - schema elements/attributes and their use in different scenarios
Robert Kukla, Napier University, Merchiston Campus, 10 Colinton Road, Edinburgh EH10 5DT, Scotland.

After introducing and justifying some general guidelines that helped shape the TCS, the general structure of the schema is presented and explained. The talk then focuses on the individual elements and attributes, what they mean and how they should be used. Dependencies between items are explained and possible alternative interpretations given (if appropriate). In cases where a particular feature is the direct result of feedback from the community it is pointed out and the solution is given and explained.

Interpreting Taxonomic Databases and mapping their structure to the TCS
Robert Kukla, Napier University, Merchiston Campus, 10 Colinton Road, Edinburgh EH10 5DT, Scotland.

Following on from the previous talk this presentation will summarise the experiences gained from transforming taxonomic data from different data sources to XML files compliant with the TCS. Some approaches used to represent taxonomic information in databases allow for different interpretations of (taxonomic name) data as taxonomic concepts. Advantages and disadvantages of alternative mappings are explained for different contexts. The talk concludes with a discussion on how taxonomic data might be queried and transferred over the network using the TCS.

Digitized Insect Specimen Access: new digitization tools
Karl-H. Lampe, Zoologisches Forschungsinstitut & Museum A. Koenig (ZFMK), Adenauerallee 160, 53113 Bonn, Germany

In practise the overall efficiency of data-basing the inventory of traditional entomological collections depends on two factors: suitable software and management measures to ensure the highest possible data quality already in the input process. Lessons learned from the development of the specimen-based database BIODAT, from the DORSA- (Digitized Orthoptera Specimen Access) project and preliminary results of the DIG-(Digitization of key Insect Groups at ZFMK) project, which is especially designed to develop a ‘good practise’, recommend: (1) a lockstep programme for data-basing, (2) split record function, (3) visualisation of geo-referenced gathering sites during data entry, (4) semi-automatic/automatic data transformation from original format into additional alternative ones, (5) semiautomatic data transfer of taxo- and geo-referenced information units. Current activities deal with the introduction of semantic feedback mechanisms into the practise of data-basing entomological collections.

MorphBank: Web Image Database Technology for Biology
Fredrik Ronquist¹, David Gaitros², Austin Mast³ (Presenting)
¹ School of Computational Science and Information Technology, Florida State University, USA.
² Department of Computer Science, Florida State University, USA
³ Department of Biological Science, Florida State University, USA

The development of fast Internet connections and the availability of low cost, high quality digital imaging techniques is revolutionizing research and teaching in disciplines that rely on the interpretation of macroscopic and microscopic observations.  This is manifest in the recent, rapid proliferation of 2D- and 3D-image databases on the web.  MorphBank is a searchable web repository of biological images with features suited to biodiversity studies.  Work is underway to add sophisticated community annotation technology to MorphBank, which will allow users to link their observations to particular pixels in images, without compromising the original image file, and search and annotate each other's observations.  The history and objectives of MorphBank, applications of the new annotation technology, the design of a new image-handling client, and the outcomes of the September 2004 Biological Image Database Workshop at Florida State University will be discussed.

Mapping of OECD-MDS (culture collections standard) to ABCD
Mergen, P., Guissart, F., Swings, J., Berendsohn, W., Hobern, D., Dawyndt, P., Wautelet, F.

On 27-28 October 2003 an expert workshop “Towards a global infrastructure for microbial information” took place in Brussels. It was co-organised and co-funded by the Global Biodiversity Information Facility (GBIF), the World Federation of Culture Collections (WFCC) and Belgium (the Belgian Coordinated Collections of Microorganisms (BCCM), the Belgian Biodiversity Information Facility (BeBIF) and the Belgian Biodiversity Platform (BBPF). It gathered 58 experts in biodiversity and microbial information from 13 countries.

In this international context the main objectives of this workshop were to define standards and protocols for sharing microbial information i.e. to determine: which microbial data Microbial Resources Centres (MRCs) want to share with GBIF and within the future Global Biological Resource Centres Network (GBRCN), how to share it, and which data MRCs want to access from GBIF Microbial Resources Centres.

The participants agreed to test the use of GBIF network and data exchange standards to make an index of MRCs core data available for searching.. The Access to Biological Collection Data (ABCD, http://www.bgbm.org/tdwg/CODATA/Schema/default.htm) XML schema, that offers many possibilities and concepts, has been reviewed by experts in microbial data in order to make it match to the requirements of MRCs. This recommendations have been transmitted to the ABCD Task group to be implemented to the ABCD version 2 developments. Trials of mapping the microbial data, including additional information on sequences and literature against the DarwinCore and ABCD schemas have been performed. BeBIF initiated a testing phase that is open to any culture collection worldwide. DarwinCore tests can be followed at http://digir.bebif.be , ABCD tests at http://biocase.bebif.be/querytool and both are available at http://www.gbif.net

The recommended standard mapping for microbial information against ABCD will be presented to a wide range of microbial experts at the 10 th International Congress for Culture Collections (ICCC-10, 10-15 October 2004, Tsukuba , Japan ).

Tropicos: The Next Generation - Lessons Learned on the Biodiversity Information Highway
Chuck Miller & John Sheppard, Missouri Botanical Garden, St. Louis, Missouri, USA. Email: chuck.miller@mobot.org; john.sheppard@mobot.org

This presentation will provide an overview of the design, lessons learned, new techniques and future plans for Tropicos: The Next Generation.

During development of Tropicos:TNG many lessons have been learned including new approaches to enabling rapid response times with massive relational data content, new data structures and functions for partial dates and geo-political ambiguities, taxonomic visualization techniques, UTF encoding, DIGIR/ XML interfaces, and systematic botanist requirements versus general reference users.

Tropicos:TNG implements feature-rich graphical user interfaces, web services and a more robust and responsive data model built on relational database technology, n-tier component model, and real-world performance testing. In future Tropicos:TNG will link to as many other systems as possible via web services or out-links using eventual TDWG/GBIF standards.

Since 1982 Tropicos has been the primary tool of 50 MBG botanists and associated support staff to prepare published taxonomic works as well as MBG collectors for field collection, curators for herbarium management, and analysts for biodiversity projects. It includes over 1 million plant names/concepts with relations/references/types and almost 2 million name-linked specimens, a taxonomic web of facts that is a prime on-line reference for systematic botanists globally. Over 40,000 name, specimen, and reference queries are received daily at www.tropicos.org.

Taxonomic Names Meet Formal Parsers: Building Better Biodiversity Databases
Brook Milligan, Department of Biology, New Mexico State University, Las Cruces, New Mexico 88003 USA

One common characteristic of many relational databases is the use of multiple fields to represent a single concept. One example from the Darwin Core schema is the representation of taxonomic names, where three fields are used to represent the full name of a species. One consequence of this practice is that the integrity of information split among these fields must be guarranteed independently by every data entry mechanism. Unless all are in strict agreement, no statements can be made about the integrity. Furthermore, every client using the data must include complex logic for handling all cases (including erroneous or meaningless ones) involving presence and absence of information in each of the several fields. To solve this problem I present an approach that unifies taxonomic name information into a single field, embeds the relevant logic within the database, and relies on the formal nomenclature of relevant taxonomic groups to ensure integrity of the information. This guarrantees that information entered into the database follows established nomenclatural conventions regardless of the data entry mechanism. Clients are greatly simplified because they need not check the integrity of the information; rather, they need only to retrieve it. Integration of such techniques into taxonomic and biodiversity databases will greatly simplify the curation of information.

Network access to XML data embedded in JPEG2000 images
Matthew Calder, Jacob Asiedu, and Robert A. Morris, University of Massachusetts at Boston Department of Computer Science, U.S.A.

We will give a brief overview of the structure of JPEG2000 files and the unusual mechanism they provide by which internet connections can be made /into/ such files, extracting not only Regions of Interest (ROIs) in the image(s) in the file, but also remote extraction of XML data embedded in them. We will sketch future development, by which remote invocation of XPath or XQuery requests into embedded XML We will illustrate with a system in which ROIs can be semi-automatically added as so-called Media Resources to an SDD file that is itself embedded in the JPEG2000 file. This collaboration between an ROI editor and an SDD editor suggests that interface standards should be developed by which JPEG2000-aware applications can cooperate locally or across the network.

iPlants -Procedures for Collaborative Data Gathering
Alan Paton¹, Chuck Miller² & Melissa Tulig^3
1 Royal Botanic Gardens , Kew , UK . A.Paton@kew.org, ² Missouri Botanical Garden , St Louis . Chuck.Miller@mobot.org. ³ New York Botanical Garden, Mtulig@nybg.org

iPlants aims to produce an online index of all the world’s plant species together with, where possible, an image and a preliminary conservation assessment. Achieving such a goal requires a collaborative effort among major botanical institutions and the broader botanical community, at the centre of which will be a large-scale compilation and digitisation effort. Currently, Missouri Botanical Garden, New York Botanical Garden and RBG Kew are collaborating to develop the iPlants concept by means of a pilot project.

The pilot is defining and testing procedures necessary for a collaborative approach to constructing such an index. In particular it is exploring: how to accelerate work towards an accessible working list of accepted plant species; how to combine specimen data from different institutions and use them to produce preliminary conservation assessments; how best to present information produced and link it to other science and conservation data sources online.

This talk will concentrate on the procedures trialed and standards used in checklist production and specimen based conservation assessment. Checklist production involves standardising, deduplicating and compiling substantial amounts of data from sources such as IPNI and TROPICOS, and recording references to the taxon concept applied. Merging specimen records involves use of a modified Darwin Core schema while rapid conservation assessments are being derived by GIS.

Protonyms, References, and Assertions: An introduction to the Taxonomer data model
Pyle, Richard L. Database Coordinator for Natural Sciences, Bishop Museum, 1525 Bernice St., Honolulu, HI 96817, USA.

I will describe portions of the data model called “Taxonomer,” that I developed to manage both taxonomic names and taxonomic concepts. The core entities of this model are Agents,References, and Assertions (along with their associated Protonyms). Agents (people and organizations) in this context refer primarily to taxonomic authorities. References are broadly defined as date-stamped and documented information (usually in the form of a publication), according to the Agents who serve as the Reference authors. Assertions consist of basic elemental information about the treatment of taxonomic names by taxonomic authorities as documented in a particular place and time, via References. Protonyms are a special subset (subtype) of Assertions, which constitute original descriptions of taxonomic names. All Assertions are anchored to a Protonym, such that Protonyms represent the taxonomic “name”, and Assertions represent the abstract taxonomic concept implied by the specific treatment of a name by authors of the corresponding Reference. The primary data content used to populate and test the data model derives from various sources, including museum specimen databases, research projects, published checklists, and comprehensive taxonomic listings and authorities. A detailed description of the taxonomic components of this model are available at: www.phyloinformatics.org/pdf/1.pdf

A New Computing Tool for Automated Georeferencing of Natural History Collection Data
Rios, Nelson & Bart, Henry L. Jr., Tulane University Museum of Natural History, Building A-3 Wild Boar Rd., Belle Chasse, LA 70037, U.S.A. nelson@museum.tulane.edu

It is estimated that the number of biological specimens in museums and herbaria worldwide exceeds 2.5 billion. Revived interest in these collections and biodiversity informatics has brought about many efforts to digitize museum records. Sadly, geographic coordinates are not available for the vast majority of these records. Thus, our ability to utilize this vast information resource in large-scale spatial studies is limited. Traditional methods for georeferencing collection data from text descriptions are tedious and time consuming, typically involving finding the locality on either a hardcopy or digital maps, plotting the locality, and determining the coordinates. This process can be very time consuming, even with digital maps.

In 2002, with funding from the U.S. National Science Foundation, we began work on a computing solution to this task. The end result is GEOLocate, a software tool that interprets textual descriptions of locality information into geographic coordinates for North America, projects these coordinates onto digital maps, provides an efficient mechanism to correct the displayed locality information, supports external data input and batch processing, and provides built-in auto updating capabilities over the web.

www.DNA-surveillance: Web-based Genetic and Phylogenetic Identification of Taxa -- tools, methods and future developments
Author: C. Scott Baker, Merel Dalebout, Greg Ewing, Matt Goode, Shane Lavery, Allen Rodrigo, and Howard Ross, School of Biological Sciences and the Bioinformatics Institute, University of Auckland, Auckland New Zealand.

We have developed a web-based platform for the identification of unknown samples, based on the phylogenetic placement of query mitochondrial sequences, using a validated and curated database of reference sequences.  This is presently available for the identification of unknown cetacean tissue at www.dna-surveillance.auckland.ac.nz.  In this talk, I will describe the underlying philosophy of our approach, and the tools and algorithms we use.  I will also discuss our plans for future developments and enhancements.

Implementing OpenGIS standards for the GBIF-Austria web portal
Paul Schreilechner¹, Michael Hadrobolec², Kerstin Placer², Robert Venier¹. ¹BIOGIS Consulting GmbH, Dr.-Hans-Lechner-Strasse 6, 5071 Wals-Siezenheim. ²Umweltbundesamt GmbH, Spittelauer Lánde 5 , 1090 Wien/Österreich.

The development of the GBIF-Austria web portal was started early this year with a pilot project supported by the Austrian Federal Ministry of Agriculture, Forestry, Environment and Water Management (Bundesministerium für Land- und Forstwirtschaft, Umwelt und Wasserwirtschaft - BMLFUW) . Seven partners are implementing special software components based on BioCASE-protocol and ABCD schema. One of the modules of the project deals with spatial data and production of dynamic maps. According to the philosophy of using open source software based on public standards we are using the webmapping server “degree” which is the official reference implementation of the Open Geospatial Consortium standard “Web Map Service 1.1.1 (WMS)”.

Whenever a user starts a query, the portal software requests the distributed individual data nodes and stores the query results in a temporary cache which is used for subsequent queries. On demand a distribution map is generated by the portal software by requesting a map from the degree webmapping server. The distribution sites are mapped as a dynamic layer via a OGC compliant web feature service by querying data cached individually for each session.

Thus the open software architecture of the project enables integration of additional webmapping services and functional extensions for spatial analysis.

A call for TDWG support in the creation of invasive alien species standards
Annie Simpson¹, Elizabeth Sellers¹, Hannu Saarenmaa² and Robert A. Morris³. ¹National Biological Information Infrastructure, USGS, Reston, Virginia, USA, ²GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen, Denmark. ³University of Massachusetts at Boston Department of Computer Science, U.S.A. asimpson@usgs.gov, esellers@usgs.gov

The need for a global invasive species information network (GISIN) has been discussed in different fora since the year 2000 (1,2). Invasive alien species (IAS) are estimated to cause USD$1.4 trillion in damage per year to world economies, societies, biodiversity, and human health (3). Providing unified access to the world's IAS information systems will dramatically assist decision-makers in our fight to control the effects of IAS, but to achieve this goal, taxonomic and other data standards are needed for the GISIN. At the international meeting to implement a GISIN, held in Baltimore on 4-6 April 2004, its interim Steering Committee was directed to approach TDWG for assistance in creating these needed standards (4). The meeting was attended by 76 experts from 26 countries. A brief overview will be given of the types of GISIN standards needed and of the support offered by members of the GISIN and the Convention for Biological Diversity Secretariat.

1-[CBD/COP] Conference of the Parties to the Convention on Biological Diversity. 2002. Scientific and Technical Cooperation and the Clearing-House Mechanism: Report of the Joint Convention on Biological Diversity/ Global Invasive Species Programme Informal Meeting on Formats, Protocols and Standards for Improved Exchange of Biodiversity-Related Information. (25 April 2004; www.biodiv.org/doc/meetings/cop/cop-06/information/cop-06-inf-18-en.pdf)

2-Edwards JL. 2004. Research and societal benefits of the Global Biodiversity Information Facility. BioScience 54: 485-486.

3-Pimentel, D., editor. 2002. Biological invasions: economic and environmental costs of alien plant, animal, and microbe species. Boca Raton/London/New York/Washington DC; CRC Press, 369 pp.

4-Saarenmaa, H. The Global Biodiversity Information Facility and GISIN. pp 66-71. In: Sellers, E., Simpson, A., Fisher, J.P., S. Curd-Hetrick, editors. 2004. Experts Meeting on Implementation of a Global Invasive Species Information Network (GISIN), Proceedings of a Workshop. 6-8 April, 2004. Baltimore, Maryland, USA. Full proceedings online at http://www.gisinetwork.org; Article online at http://invasivespecies.nbii.gov/as/GISINProc2004HTML/GISINProc200466.html

Integrating Observational Data into Biodiversity Information Networks
Bruce A. Stein and Lynn S. Kutner. NatureServe, 1101 Wilson Boulevard, 15^th Floor, Arlington, Virginia, 22209 USA

Much of the biodiversity data currently available in web-accessible, interoperable formats derive from specimen-oriented databases.  Large amounts of observational data exist that complement the collections-record, helping document the distribution and condition of organisms, and revealing changes over time. Because of the heterogeneity of observational techniques and data sets, the development of observational data standards has lagged, complicating efforts to fully integrate such data into global information networks. NatureServe has long been involved in developing and supporting protocols for the development and quality control of observational data, focusing especially on documenting the occurrence and viability of species populations and ecological communities. There is, however, a need for more broadly applicable observation data standards to help mobilize the vast amount of existing observational data. With the support of the Gordon and Betty Moore Foundation, NatureServe is initiating a collaborative process designed to facilitate development of such broadly applicable observational data standards. We will describe the need for such standards, lay out the tentative process for surveying current observational data standards and for harmonizing these approaches, and seek input and involvement from the TDWG community in this effort.

SEEK Project Taxonomic Object Service: Making Sense of Names and Concepts
Stewart, Aimee M., Gales, Robert, Software Developers, Biodiversity Research Center, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS 66045, USA. Email: astewart@ku.edu; rgales@ku.edu.

The NSF-funded, Science Environment for Ecological Knowledge Project (SEEK, seek.ecoinformatics.org), is addressing the modeling and management of taxonomic names and concepts in a database context and network architecture that will support Internet search and retrieval of concepts, names, and the taxonomic and nomenclatural relationships among them.  The SEEK Taxon Working Group has sought to enumerate the use cases and the questions that will likely be asked of a concept resolution and name service by systematists, ecologists and other users, and then to implement a production web service that address those needs.  The public SEEK Taxonomic Object Service (TOS) will provide information about the relationships among taxa via SOAP and web interfaces.  The TOS has been written in an extensible object-oriented architecture that will allow users to plug in their own algorithms for matching concepts and determining the relevance of taxonomic relationships. We will demonstrate the SEEK TOS during the presentation.

Towards indexing the biodiversity of the Carpathian region (Europe)
Eduard Stloukal, Department of Zoology, Comenius University, Bratislava, Slovakia.

The Carpathian Mountains are of the largest mountain ranges of Europe , with wide range of habitats and areas of untouched nature.

While the total expected number of animal species known from Europe reach about 100,000, there are up to 50,000 species of animal species recently known from the Carpathian Mountains .

The Carpathian Mountains , as a barrier between Balkan – Eastern European areas and Central and Western Europe , play significant role in evolution of European nature and they are recently (altogether with surrounding lowlands) considered as one of the areas with the highest species and habitat diversity in the whole Europe .

The Carpathian Mountains afford refuge for many species dislodged from areas intensively used by human population and by naturally changing environment. High number of endemic species and primary type species (e.g. species with type localities bounded to the Carpathian Mountains ) do occur in vast forested uplands, alpine mountains, and carstic or marshland areas. Determinative role of Carpathians is obvious in distribution of animal species in Central and Easter Europe as well as for seasonal migration of animals.

In spite of the importance of the Carpathian Mountains for Pan-European nature, knowledge of the biodiversity as a headstone for its protection is still incomplete and no informational and/or indexing system operates in this area.

Partial faunal dataset on taxonomic or regional level are maintained by some academic or governmental institutions or by individual persons, however no facility have been operating towards indexing of the biodiversity of the whole Carpathian area or covering all animal taxa.

Project built on the experience and tools of the Databank of Slovak fauna and the Fauna Europaea should develop biodiversity information system on taxonomy and distribution of all species of the Carpathian fauna.

openModeller - An open, collaborative environmental niche modelling toolkit
Tim Sutton (BDWorld), Mauro Muñoz (Cria), Ricardo Pereira Scachetti (University of Kansas), Peter Brewer (BDWorld), Renato De Giovanni (Cria),  Neil Caithness (BDWorld)

A number of software tools and algorithms exist for modelling species' environmental niche preferences. A collaborative project between Cria (Brazil), the University of Kansas (USA) and BDWorld (UK) aims to provide an extensible, open environment for environmental niche modelling. Available under the GNU Public License (GPL), this cross-platform software aims to institute a paradigm shift in the way that niche modelling software is made available to a distributed user base. Using the plugin architecture, a number of algorithms have been implemented including Genetic Algorithm Ruleset Production (GARP), Climate Space Model (CSM), bioclimatic envelope model and others. Deployment options for openModeller include user friendly standalone desktop GUI's, invocation via a scripting environment such as python or java; web services; and as a Grid resource. openModeller is being used within the BiodiversityWorld and SEEK projects.

In this talk the design principles and motivation behind the openModeller project will be discussed. We include examples of openModeller usage within the BDWorld virtual laboratory, and as a standalone user friendly GUI application.

The Application of Globally Unique Identifiers in Taxonomic Databases
Dave Thau, SEEK Project Group, University of Kansas and www.learningsite.com

Over the past decade or two, numerous databases containing information about biological taxa have come on line. Sharing information between these databases is complicated by a number of factors, not the least of which is the lack of a universal mechanism for identifying a resource in a database. Globally unique identifiers (GUIDs) are a mechanism by which information resources can be uniquely identified across the Internet. A leading GUID system is Life Science Identifiers (LSIDs). This talk will introduce the notion of GUIDs, discuss their usefulness in the context of taxonomic databases, and demonstrate the application and utility of the LSID system in databases containing taxonomic information. If time permits, questions such as “Who provides the GUIDs?” “What happens if a database goes offline?” and “What sorts of things should be identified by GUIDs?” will be addressed.

A world of conceptual schemas: mapping of standards to databases and other standards
J. Torre, W. Lipp, M.Döring, A. Hahn & W. Berendsohn. Freie Universität Berlin , Botanic Garden and Botanical Museum Berlin -Dahlem, Department of Biodiversity Informatics and Laboratories, Königin-Luise-Str. 6–8, D–14191 Berlin, Germany
{a.hahn, j.torre, m.doering, w.berendsohn, w.lipp}@bgbm.org

Conceptual schemas are increasingly used to integrate data in distributed networks. ABCD defines over 700 elements describing specimen data. It acts as a simple ontology: the result of mapping databases to ABCD is a unified description of these databases. Collection databases may contain hundreds of attributes, resulting in thousands of possible mappings. A configuration tool is needed, which provides (1) lexical analysis of the terms in the schema (the ‘Google approach’); (2) a structured catalog of terms in the schema (the ‘Yahoo approach’); (3) the incorporation of experts’ assessments of the importance of terms for certain domains; (4) formats and tools to identify terms of the schema with terms of other schemas or standards. The first three requirements have been implemented in a BioCASe configuration tool. The forth requirement is extending this practical approach. We have started creating a prototype for a general repository of concepts. At the core, a database holds an extensive set of concepts, which can be mapped to (versions of) standards. Functions for mapping and comparing elements or subtrees are needed, incorporating those realised in the configuration tool. The repository can be used for data transformation services, automatic update of wrapper configurations, documentation of standard mappings, and general documentation of data used in specific networks.

Taxon names and concepts: building a strong foundation for biodiversity information
Weitzman, A. L. ¹ & Lyal, C. H. C.^2
1The National Museum of Natural History, Smithsonian Institution, Washington DC, USA, weitzman@si.edu
²The Natural History Museum, Department of Entomology, London SW7 5BD, UK, c.lyal@nhm.ac.uk

What is needed for the taxonomic community and for GBIF is a standard for Name data. This is first a standard for the elements required to define a name and its valid publication (Bot.) or availability (Zoo.). Standards for taxonomic concepts are a separate need, which, though important, also require a standard for the name elements themselves. There are currently a number of different projects using a variety of elements for names, including: ITIS, Species 2000, ABCD (and therefore Names), Darwin Core (including various versions) SDD, Linnaean core, Taxonomer, UBio and taXMLit.

The elements needed to define a name are relatively straightforward and fall into the category that we have defined in another talk as primary or unambiguous. The elements needed to define a concept are, on the other hand, in the category of attributed or interpretative. The former includes genus, species epithet, holotype (or its equivalent, if defined), author(s), and citation (protologue, Bot.; original publication Zoo.) while the latter includes relationship to higher taxa and other taxa, specimens included (except for the holotype or its equivalent, e.g., lectotype or neotype). We will present a comparison of the elements currently in use in the above projects and suggestions for what is needed to develop a primary core name standard.

The Species 2000 standard data set, common data model and transfer protocols
Richard White ¹, Frank Bisby ², Andrew Jones ¹, Xuebiao Xu ¹, Ed Donovan ¹, Yuri Roskov ², Alex Gray ¹ & Rainer Froese ^3
1 School of Computer Science, Cardiff University, Cardiff CF24 3XF, U.K.
² School of Plant Sciences, The University of Reading, Reading RG6 6AS, U.K.
³ Institute of Marine Research, D-24105 Kiel, Germany

The Species 2000 Project has created a prototype Catalogue of Life. Species data from a distributed array of Global Species Databases (GSDs) is accessed through a Web portal, Web Service and an Annual Checklist CD-ROM.

Each species entry in the Catalogue derives from a GSD and contains basic information known as the Standard Data Set: scientific name, synonyms, common names, taxonomic placement, a comment, geographical localities, bibliographic references, date of last editing and a hyperlink to further information.

Because the GSDs are independently implemented and managed, they do not share the same database schema. Instead, the Species 2000 Common Data Model (CDM) defines six operations, known as Requests, which the GSD or its wrapper can support to transfer defined data elements reliably to a client. The CDM does not provide a database implementation schema and should not be used as a model for setting up new GSDs. For this purpose we propose a schema developed to support a new version of the Annual Checklist.

The CDM forms the basis for several communications protocols previously and currently used by Species 2000, including CGI/HTML, Corba, CGI/XML and SOAP, and will be compared with the draft TDWG Taxonomic Concept Schema (TCS).

Formal Taxon Concept and Rough Set Approximation
Nozomi Ytow¹, Akira Sato², David R. Morse³, David McL Roberts^4
1 Gene Reserch Center, University of Tsukuba, Tsukuba, Ibaraki, 305-8572 Japan. ² Academic Computing and Communication Center, University of Tsukuba,
Tsukuba, Ibaraki, 305-8571 Japan. ³ Faculty of Mathematics and Computing, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom. ⁴ Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom

Taxon concepts can be implicit (undefined) or defined as sets either of individuals or character states.  Multiple taxonomy databases and taxonomic data from multiple data sources require an appropriate method to manage these alternative representations.  Formal concept analysis, FCA, (Ganter and Wille, 1996, 1999) allows the handling of
taxon concepts as a pair of sets called extension (character states, a circumscription) and intension (specimens, ostensive definition). Although FCA has an affinity with taxonomy, it inherits a restriction from set theory, that a set is a definite list of elements.  In reality, a taxon consists of an indefinite collection of individuals, specimens and character states as knowledge about the taxa and its relatives increases.  Rough set approximation separates the including and excluding boundaries, defining a zone of uncertainty, which mathematically  relaxes the problem of indefinite sets and facilitates the detection of incompatible concepts.

Name Usage as Pricipal Data Vehicle for Name/Taxon Data Exchange
Nozomi Ytow¹, Akira Sato², David R. Morse³, David McL Roberts^4
1 Gene Reserch Center, University of Tsukuba, Tsukuba, Ibaraki, 305-8572 Japan. ² Academic Computing and Communication Center, University of Tsukuba,
Tsukuba, Ibaraki, 305-8571 Japan. ³ Faculty of Mathematics and Computing, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom. ⁴ Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom

Taxon concepts are always context dependant and must change to accommodate new knowledge.  They are consequently inherently unstable.  Taxomic data models either use taxon concept or name-usage as their principal vehicle.  Although both are developments of the potential taxon (Berensohn, 1995), they differ in their definition of the terms 'taxon concept' and 'name'.

'Name' is sometimes mistakenly considered to be no more than a literal, i.e. a string of letters, rather like a luggage label.  But consider: if the label were detached from its concept, what would it represent?  We should properly regard the name as the relationship between the intension (membership list) and extension (character states) sets.

In using a name (a name-usage), an author must always employ a taxon concept and it could not be otherwise.  The benefit of using name-usage as the principal data vehicles that it records simply the fact that a name was used and does not necessitate taxonomic scrutiny, although the data structure can be designed to maintain a flag indicating such scrutiny if it is required.  Name-usage based schema consequently have wider coverage of data sources than schema based on taxon concept, make fewer demands on the data-creator and require less maintenance.

taXMLit: a vital piece of the puzzle for digitally interoperable taxonomy
Weitzman, A. L. ¹ & Lyal, C. H. C.^2
1The National Museum of Natural History, Smithsonian Institution, Washington DC, USA, weitzman@si.edu
²The Natural History Museum, Department of Entomology, London SW7 5BD, UK, c.lyal@nhm.ac.uk

A major problem for access to biodiversity information is the multiplicity of forms and places where it is stored. While data standards for storage and exchange of taxonomic names and specimen data are being developed, literature is still generally not accessible electronically or, if it is, the format is not one that enables interoperability with other data types. For taxonomic descriptions, identification aids, and other data, this is a particular problem, and in many parts of the world taxonomic work is hindered through lack of access to the literature. We offer a potential standard appropriate for all taxonomic literature, taXMLit that will enable interoperability with specimen databases, taxonomic authority files, and other datasets. In addition to integrating literature and other data sources, the schema opens possibilities of generating new tailored web products including relevant taxonomic information taken from different publications and other sources, and a way of speeding taxonomic publication. The first testbed for taXMLit is the Biologia Centrali-America Centennial (BCAC) project, which will make available all 58 biological volumes of that work as well as modern treatments of selected taxa included in the original, and linking them all to other appropriate electronic data.

Data standards: objective data, subjective data, and data interchange
Weitzman, A. L.¹ & Lyal, C. H. C.^2
1The National Museum of Natural History, Smithsonian Institution, Washington DC, USA, weitzman@si.edu
²The Natural History Museum, Department of Entomology, London SW7 5BD, UK, c.lyal@nhm.ac.uk

Biodiversity data comprise both primary and interpreted elements. The latter should be attributed and presented with appropriate metadata. Examples of objective and subjective elements will be presented in each of the above contexts and arguments for including them within a standard vs. putting them in extensions to standards will be discussed. In designing taXMLit for taxonomic literature, we chose to design it to hold only elements from the literature source as originally presented and not to include interpretations of that text. An 'interpretation layer' or extension is being designed to function as both a simple layer around the publication that will allow contributors to add information and as a complex proxy layer between the digitized publication and other digitized information sources, including a variety of kinds of authority files. This facility will enable data to be entered independently after the digitization, in the same manner that any piece of text or data requires and receives interpretation in the normal course of use. The TIL will also allow both interpretations and linkages to be attributed and dated, and allow for multiple interpretations of the same information by the same or different people or publications. This may also be needed to address the issues related to taxonomic concepts that the Names designers are grappling with. We also expect that, because the various data sources effectively will use one another as authority files, the TIL will also facilitate linkages between different taxonomic treatments, and between the treatments and other data sources. While the taXMLit uses elements that cover the same concepts as those used in other schemas (e.g. ABCD, designed for specimen data), the individual elements are not exactly the same, for a number of reasons. The TIL will facilitate mapping and linkage between schemas.

Posters

Abstracts (in alphabetical order by senior/presenting author surname)

Biodiversity World: Towards an Extensible Virtual Laboratory for Biodiversity Research
Author: Richard White, Andrew Jones, Alex Gray, Xuebiao Xu, Nick Pittas, Nick Fiddian, Frank Bisby, Alastair Culham, Neil Caithness, Tim Sutton, Peter Brewer, Chris Yesson, Oliver Bromley, Malcolm Scoble, Paul Williams, Shonil Bhagwat.

The Biodiversity World project is designing and developing a Grid-based Problem-Solving Environment, to allow scientists to access heterogeneous data and analysis resources that were originally designed for use in isolation, and to compose these resources into complex workflows for carrying out biodiversity research studies.

Biodiversity World: Towards an Extensible Virtual Laboratory for Biodiversity Research
Author: Richard White1, Andrew Jones, Nick Pittas, Alex Gray, Tim Sutton, Xuebiao Xu, Oliver Bromley, Neil Caithness, Frank Bisby, Nick Fiddian, Malcolm Scoble, Alistair Culham, Paul Williams, Paul Valdes

In Biodiversity World we are exploring how a problem-solving environment (the BDWorld PSE) can be designed and developed to make heterogeneous data sources and analytic tools for biodiversity informatics available in a GRID environment.  Our aim is to provide scientists with tools with which they can readily access resources that were originally designed for use in isolation, composing these resources into complex workflows, and to make it as straightforward as we can for new resources to be created and introduced to the system. 

Taxonomic authority files for the Mexican biodiversity information system
Patricia Koleff, Susana Ocegueda, Diana Hernández & Jorge Soberón.
National Commission for the Knowledge and Use of Biodiversity (Conabio), Liga Periférico- Insurgentes Sur 4903 Col. Parques del Pedregal. Tlalpan 14010. Mexico D.F. Mexico (pkoleff@xolo.conabio.gob.mx)

Scientific names are the key to organize and retrieve biological information. As an effort to manage, analyse and divulgate our biodiversity information, Conabio established the National Biodiversity Information System of Mexico (SNIB, for it spanish acronym) that is based on specimen data from national and foreign collections. In order to guarantee interoperability and integrity among databases that supply information to the SNIB, Conabio uses the Taxonomic authority filesas standards of quality control. These files consist in hierarchical databases reviewed by expert taxonomists, based on recognized classification systems, that integrate valid/accepted names and their synonymies with the respective references. Common names and distribution information are integrated when available. About 50,000 valid names of different taxons, that include around 15 000 valid species names, have been integrated and are available through the Conabio’s website, and recently begun to integrate them to ITIS-North America, a regional initiative to retrieve taxonomic information on plants, animals, fungi, and microbes of North America and the world.

Conabio has ~10% of the estimated national biodiversity, therefore it’s necessary support the elaboration of authority files. Such information is essential for the decision-making regard the use and conservation of biodiversity, supported by a scientific knowledge.

Automatized knowledge extraction from paper documents
Guillaume Rousse and Eric de la Clergerie, INRIA

A large amount of knowledge in systematics is still available from non-numerical documents only, such as books and photos, whereas most computer projects are hampered by data input problems. The ongoing Biotim project explores the means to reduce this gap, by providing automatized acquisition of structured data directly from raw paper documents, for text and image simultaneously. This poster presents global project objectives, and focuses on current state of the text analysis process.

Integrating Biodiversity Information Systems - Landcare Research NZ
Jerry Cooper, Aaron Wilton, Nick Spencer, Mike Wilson, Mark Fuglestad, Kevin Richards, Mike Cochrane. Landcare Research, PO Box 69 , Lincoln 8152, New Zealand.

Landcare Research has a wide range of biodiversity datasets associated with ecological and systematic research programmes. These datasets include those considered to be nationally significiant such as National Vegetation Survey Databank and the national collections (e.g., Allan Herbarium, New Zealand Fungal Herbarium, New Zealand Arthropod Collection), and smaller research datasets in a variety of formats (e.g., spreadsheets, personal databases, Nexus files). Until recently these data were in legacy systems and could not be easily discovered, accessed or integrated. A project was undertaken to address these limitations. In addition, scientific names were identified as a key linkage between these datasets and the management of names was also considered. As part of our requirements to integrate these datasets a taxonomic information system was constructed based on XML, Web Services and the .Net framework. Implemenation of this infrastructure and the capture of over 80,000 names relevant to the NZ biota is allowing interoperability of datasets within Landcare Research. As a result, the delivery of integrated biodiversity information from a variety of resources, and for a variety of end users has been facilitated.

XML Delivery of Digitised New Zealand Floras and Faunas
Nick Spencer, Jerry Cooper and Aaron Wilton. Landcare Research, PO Box 39-141, Christchurch, New Zealand

[abstract to be added]

Data Repository and Metadata Integration: A case study
Nick Spencer, Susan Wiser, Larry Burrows. Landcare Research, PO BOX 69, Lincoln 8152, New Zealand.

Metadata has become increasingly critical in the management and integration of datasets held in the National Vegetation Survey databank (NVS). NVS is New Zealand ’s largest archive for plot-based vegetation observational data. It has a large number of datasets concentrating on indigenous plant communities but there is some variation in content and data standards. There is an ever increasing need to integrate these datasets internally as well as with remote datasets to facilitate re-synthesis for both global-scale and national-scale biodiversity questions. A comprehensive metadata schema (XML) and system architecture has been developed to address these needs. The system provides for the ability to search and identify data resources, determine suitability of use , and secures both personal and institutional knowledge of datasets overtime. B eyond these traditional functions, we can extend the value and usefulness of these datasets through integration with additional information resources, such as taxonomic authority databases, specimen collection databases and spatial services.

Replication framework for regional and thematic portals in GBIF network
Donald Hobern, Giorgos Ksouris, Ciprian Vizitiu & Hannu Saarenmaa. GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen, hostmaster@gbif.org

GBIF information system reached operational phase in early 2004 and is scaling up rapidly.  Tens of millions of data records are already being served by nearly one hundred data providers.  The data providers announce their availability in GBIF's global registry http://registry.gbif.net/.  GBIF Data Portal http://www.gbif.net/ indexes the records on the providers and offers a user interface for searching, browsing, displaying and downloading the data.  Operating this service has high availability requirements which calls for a mirroring solution.  There also is a need to implement a distributed architecture with regional and thematic portals that use the relevant parts of shared indexed data.  Data for one region or theme can originate from any data provider in the world, so it is not sufficient for a regional or thematic portal to index its known "partnering" providers.  The poster describes the requirements and status of implementation for replication of the GBIF Data Portal components in this context.  The strategy includes support for  distributed execution of Data Portal administrative functions to maintain the Data Index,  distributed execution of the Data Portal interface and services for data access, and    implementation of local shadows of Data Portal components deployed as regional or thematic portals.

Integrating Descriptive Data from Floras
Wood, M. M.¹, Lydon, S. J.², Wang, S.¹, Huxley, R.³ & Sutton, D. A.^{3 1} Department of Computer Science, University of Manchester. ² Earth Science Education Unit, Keele University.³ Department of Botany, Natural History Museum

"Interoperability" usually refers to the format of databases: we address the compatibility of legacy data. The MultiFlora system automatically extracts information from the texts of multiple Floras describing the same plant taxa, and integrates it into a single, formally structured data resource.

In earlier work, we showed that the distribution of information across Floras is highly "sparse": different authors describe different characters for the same
taxon. Here we analyse the range of ways in which the same information can be differently presented. These include:

Units of measure: 80cm / .8m
Number ranges: 4 / 3-5 / 3-(4)-5
Exact synonyms: two-parted / bi-partite
Near-synonyms: e.g. words for leaf shape and for hairiness
Degrees of specicity: yellow / rich golden yellow
Temporal reference: after flowering / in fruit. This is a particularly challenging
problem for automatic analysis, as it requires active reasoning, not just
arithmetical calculation or look-up in a synonym list.

We aim to identify automatically which descriptive elements are directly equivalent, and which are genuine disagreements between authors, or species
diagnostics. We aim also to enable automated translation between legacy standards, and integration of existing descriptive data with any newly agreed standard to emerge from the Systematics community.

Computer Demonstrations

Abstracts (in alphabetical order by senior/presenting author surname)

Demonstrations of SDD systems
Matthew Calder and Jacob Asiedu, University of Massachusetts at Boston Department of Computer Science, U.S.A.

Demonstrations of a lightweight SDD Description editor, of an SDD debugging aide, and of collaboration between embedded SDD and a simple Region of Interest editor for JPEG2000 images. Requires a WinXP system with .NET framework (not necessarily full SDK) and Java (not necessarily full JDK) installed. Ideally there would be two such systems networked and in close proximity, or ability to put one of our laptops on the same network, but neither of these is entirely necessary. If resources permit, there could be two separate demonstrations, one for the SDD Description editor and debugging aide, and another for the JPEG2K demos. However, if the demo session is long enough, we could just cycle through these at a single demo desk.

The PyWrapper serving BioCASe, ENBI and Species2000
Döring, M. & de la Torre, J. Department of Biodiversity Informatics, Botanic Garden and Botanical Museum Berlin-Dahlem, Koenigin-Luise-Str. 6-8, 14191 Berlin, Germany

The PyWrapper developed by BioCASE is serving as a generic database wrapper which is successfully being operated for the BioCASe network (including access by GBIF data portals) and for Species2000 Global Species Databases. A project within the European Network of Biodiversity Information (ENBI) provides a helpdesk and active assistance for data providers wishing to participate in the network. Flexibility in serving different data standards as well as leaving existing database structures in place as much as possible is the major software design goal for the PyWrapper.

This software demonstration provides a look behind the curtain for the PyWrapper and shows the variety of current and potential usages. It will briefly show some of the software developed around it, present the latest development efforts and show some elaborate configuration aspects.

A TAXONOMIC WEB-EDITOR: carrying out taxonomic revisions online
Marc Geoffroy , Anton Güntsch, Jinling Li , Javier de la Torre & Walter G. Berendsohn Department of Biodiversity Informatics, Botanic Garden and Botanical Museum Berlin-Dahlem, Koenigin-Luise-Str. 6-8, 14191 Berlin, Germany

We have implemented a web editor on the basis of the concept-based Berlin Model, which is or will be used in several projects such as FloraWeb, Euro+Med, Med-Checklist, IOPI Species Plantarum and the Dendroflora of El Salvador. The system is based on a centralized database management server. This approach minimizes the need for reintegration of shared data such as scientific names, authors or references. The software has been implemented on an application server using Macromedia ColdFusion , i.e. there is no particular client software that has to be installed by users. Instead, standard World Wide Web browser software will suffice to carry out taxonomic work. The editor supports data entry and editing of all data contained in the Berlin Model core database: Scientific names and nomenclatural details as well as taxonomic trees and synonym relationships can be built and modified. Furthermore, the editor supports displaying, adding, and editing of factual information associated with taxa (e.g. geographic distributions). Finally the editor enables taxonomists to establish relationships between “foreign” taxonomic concepts and their own, and therefore to build bridges to parallel taxonomies.

We acknowledge support by the European Union (Euro+Med project) and the Federal Agency for Nature Conservation (MoReTax project), among others, for the development of the editor.

Initial dissemination of MBARI’s unique deep-sea biodiversity data (See presented paper list for abstract)
Author: Nancy Jacobsen Stout, Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road , Moss Landing , California 95039 USA.

Demonstration of the BeBIF portal
Author: Patricia Mergen

Protonyms, References, and Assertions: An introduction to the Taxonomer data model (See presented paper list for abstract)
Author: Rich Pyle, Database Coordinator for Natural Sciences, Bishop Museum, 1525 Bernice St., Honolulu, HI 96817, USA.

Demonstration of BioGIS software
Author: Paul Schreilechner, Robert Venier. BIOGIS Consulting GmbH, Dr.-Hans-Lechner-Strasse 6, 5071 Wals-Siezenheim

Fauna Europaea; all European animal species on the web
Author: Yde de Jong, Zoological Museum Amsterdam, P.O. Box 94766, NL-1090 GT Amsterdam, The Netherlands