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II.
Symposium on Data, Information and Knowledge: Biodiversity and
the Life and Medical Sciences
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Lois Blaine
Bioinformatics Dept.
American Type Culture Collection
10801 University Boulevard
Manassas, VA 20110-2209 US
Phone: +1 703 365 2749
Fax: +1 703 365 2740
Email: lblaine@atcc.org
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Prof.
Ashok Kolaskar
Bioinformatics Dept.
American Type Culture Collection
10801 University Boulevard
Manassas, VA 20110-2209 US
Phone: +1 703 365 2796
Fax: +1 703 365 2740
Email: akolaskar@atcc.org |
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Dr. Micah Krichevsky
Bionomics International
12231 Parklawn Drive
Bethesda, MD 20852 US
Phone: +1 301 881 2804
Fax: +1 301 881 1625
Email: micahk@eudoramail.com
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Dr.
John Rumble
National Institute of Standards and Technology
Standard Reference Data
100 Bureau Drive, Stop 2310
Gaithersburg, MD 20899-2310
Phone: +1 301 975 220
Fax: +1 301 926 0416
Telex: 898493 GARG
Email: john.rumble@nist.gov
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Professor Akira
Tsugita Proteomics Research Laboratory
Amakubo 1-16-1
Tsukubu 305-0005, Japan
Phone: 81 298 51 1601
Email: tsugita@proteo.gr.jp
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Theme
II-1: Behavioral Science Databases: Cultural Revolution,
Scientific Necessity – D. Johnson (US), M. Sabourin (Canada)
Behavioral Science
Databases: Cultural Revolution, Scientific Necessity
D. Johnson (US), M. Sabourin (Canada)
Theme
II-2: Biodiversity Information Systems – L. Blaine
If population counts
are a prognostic indicator of long term survival, biodiversity
information systems are among the least endangered species on
the planet. Since the United Nations Conference on the Environment
and Development (UNCED) held in Rio de Janiero in 1992, and the
subsequent formation of the Convention on Biological Diversity
(CBD), there has been an enormous international focus on cataloging,
exploring phylogenetic relationships, and characterizing the world's
biota. We have witnessed a proliferation of software tools and
databases at the local, regional, and international levels that
include species inventories and checklists, taxonomic treatments,
species descriptions, and rules of nomenclature.
The challenges for
the future in biodiversity will be to find better methods of establishing
and displaying taxonomic relationships among organisms, capacity
building to sustain information resources in the biodiversity-rich
regions of the world, and providing seamless interconnections
among the disparate data sources. This symposium will focus on
solutions to these challenges from the dual perspectives of database
content and software development for improved data management
and dissemination.
Submitted abstracts
include:
The Global Biodiversity
Information Facility (GBIF): What it is, what it will do and how
it will be established
Ebbe Nielson, CSIRO, Canberra, Australia
The Impact of the
Internet on Biodiversity: Good or Evil
Leonard (Kris) Kristalka, Natural History Museum, University of
Kansas
Fish Biodiversity:
Preliminary Insights and Suggestions for a Research Agenda
Rainer Froese, ICLARM, CGIAR, Philippines
European Register of
Marine Organisms (ERMS) Database
Richard White, U. of Southampton, U.K.
The Role of BIOSIS
in Biodiversity Information
Maureen Kelly/Judith Howcroft, BIOSIS, USA/U.K.
Unlocking the Bioinformatics
Treasure Trove of Knowledge
Alex Gray, U. of Cardiff, U.K.
Biodiversity Information
Networks in Brazil: The Experience with BINbr and Biota/Fapesp
Dora Canhos, Brazilian Tropical Database, Campinas, Brazil
Which is more useful
for the interoperability of Biological Databases, CORBA or XML?
Hideaki SUGAWARA and Satoru MIYZAKI
WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)
Design and Implementation
of the Cybershell Museum on the Web, using an Animation Technology
Sung-Soo Hong, Bu-Young Ahn, Hyung-Seon Park and Sang-Rak Lee
Department of Computer Engineering, Hoseo University, Chungnam
336-795 Republic of Korea
Theme
II-3: Recent Trends in Bioinformatics – Dr. Sylvia
Spengler (US)
The rapidly increasing
availability of whole genome sequences is spawning a new generation
of bioinformatics approaches to data mining and data analysis.
As the volume of sequence data grows, the potential for understanding
the function of genes and their role in health and disease becomes
a reality. New methods of drug discovery that utilize bioinformatics
tools and methodology will dramatically increase our ability to
control and cure diseases. However, a major challenge for the
21st century will be to harness the enormous volume of biological
data to enhance the ability of the research community to convert
data to knowledge. Access channels to specific types of information
and improved pathways for connecting the various building blocks
that yield discovery are mandatory if we are to take full advantage
of the data influx. This session will focus on computerized approaches
to knowledge building in the biological sciences.
Submitted abstracts
include:
Current Challenges
in Bioinformatics
S. Spengler, LBL, Berkeley
Biological Sequence
Databases, Knowledge Representation and Molecular Similarity
Sandor Pongor, ICGEB, Trieste.
The Human Brain Project:
Neuroinformatics
Stephen Koslow, NIH, USA
The State of the Art
of Proteome Study and Interaction with a Protein Sequence Database
Akira Tsugita (Proteomics Research Laboratory, Tsukuba, Japan)
Functional Role of
Bacteriophage Transfer RNA's
Takashi Kunisawa
Application of Proteome
Analysis in Cyanobacteria Taxonomy
Junko Shimura, Naoaki Tezuka Makoto M. Watanabe, and Akira Tsugita,
Japan
Parasite Genome Databases:
Sequence to Function in an Efficient Manner
Al Ivens and Bart Barrell
Untangling Proteomics,
Gene Expression and Genetic Networks
D. Galas
Theme
II-4: Quality Issues in Bioinformatics – T.N. Bhat,
J. Rumble, G. Gilliland
The biotechnology sector
has generated vast amounts of data and will continue to do so
in the future. Consistent schema, uniform validation tools and
standard database interfaces are needed to allow efficient queries
and exchange of data. Quality and uniformity are two major issues
for dependable and reliable results. However, data diversity is
an important consideration from the point of view of accommodating
a wide range of applications. By diversity we mean inclusion of
the diverse nomenclature and description systems in place in biology.
The need for uniformity
amid diversity may come in several contexts. Some examples are,
molecule names, validation parameters, and definition of homology,
definition of a domain, data formats and database query interfaces.
A right balance between "order" and "disorder"
among these terminologies is crucial for successful data exchange
and user query interfaces. Another issue of great importance is
the distinction between user deposited data and the value added
information introduced by the organizers of the database. Most
of the present efforts on data validation are in place only at
the time of deposition of the data and they operate through the
regular channels of refereeing. Often, for the purpose of improving
quality and data uniformity, databases introduce new information.
The topic of this session is to define and discuss these quality
issues in bioinformatics and to propose improvements and ‘preferred
validation procedures and guide lines’. The session is expected
to focus on both archival databases (e.g., GenBank, SWISS-PROT,
PDB ) and derived databases (e.g., SCOP, ModBase). Often, databases
provide a citation for the database. However, due to practical
and evolutionary reason, the citation may or may not adequately
document the scope of the database. It is hoped that this session
attempts to address these issues as well.
Quality Issues in Biomacromolecular
Structure Databases
T.N. Bhat and G. Gilliland, NIST, USA
Validation of Protein
Name Assignments in Databases
W.C. Barker, F. Pfeiffer, National Biomedical Research Foundation,
USA
Organisation
and Standardisation of Information in SWISS-PROT and TrEMBL
Michele Magrane EMBL Outstation, Wellcome Trust Genome Campus
DANTE: A Workbench
for Sequence Analysis
Javier Tamames* and Anna Tramontano
Problems with the denominator
in epidemiological studies
Dirk J. van Schalkwyk , Faculty of Business Informatics, Cape
Technikon, South Africa
Quality Issues in Data
Banks for Molecular Biology
A. M. Lesk, University of Cambridge Clinical School, Wellcome
Trust Institute for Molecular Mechanisms of Disease, Wellcome/MRC
Building, Hills Road, Cambridge CB2 2XY, U.K
Round Table Discussion
II-A: Standards in Biological Information Systems
A.M. Lesk, M. Krichevsky, W.C. Barker, M. Magrane.
Theme
II-5: Biological collections and information systems: Mobilizing
natural history knowledge – J. Beach and W. Berendsohn
The acquisition, cultivation,
preservation, and storage of objects in biological collections
is an integral part of biological research in many sub-disciplines.
Biological collections include microbial and tissue culture collections,
plant genetic resources, natural history museums, botanical and
zoological gardens, natural substance collections, as well as
observation data (surveys, mapping projects) and multimedia data
such as animal sounds and pictures of organisms. They are maintained
principally by natural history museums, but also by private or
public research laboratories or institutes in fields like biotechnology,
environmental science, agronomy, and pharmacology, to name but
a few.
It has been estimated
that biological collections world-wide hold more than 2.5 billion
specimens - and each of them represents a data record of the occurrence
of a specific organism at a specific time and place. The object
presents a falsifiable source of information, i.e. it can be re-observed
to verify a scientific hypothesis based on it. In addition to
physical specimens, there exists an immense quantity of observation
records (e.g. presence/absence data for plants in quadrants taken
for floristic mapping, observations of migratory animals, etc.).
Taken together, this represents an immense knowledge base on global
biodiversity. Field and research notes often contain further detailed
data, and the object itself can be a physical resource for research
and industry.
Currently, this knowledge
base is largely under-utilised, because its highly distributed,
heterogeneous, and complex scientific nature obstructs efficient
retrieval. Over the past decade, the underlying information structures
have been investigated and fairly comprehensive reference models
exist. Databasing collection inventories also rapidly progresses,
although the total number of available records still looks small
compared to the total. The current challenge lies in the networking
of collections, be it on the level of the individual specimen
or observation record (where available), or by means of meta-information
on the collection or sub-collection level.
Submitted abstracts
include:
The Species Analyst-A
Distributed Network of Biodiversity Information
D. Vieglas, University of Kansas
Maximise Common Denominators:
Towards and International Data Access Profile for Biological Collection
Information
A. Guntsch and W. G Berendsohn, Botanic Garden and Botanical Museum
Berlin-Dahlem, Königin-Luise-Str. 6-8, 14191 Berlin, Germany
Biological Collections
as a Tool for the Construction of Predictive Distributional Maps-An
Example of Italian Lichens
NIMIS Pier Luigi & Martellos Stefano, Università di Trieste, Via
Giorgieri 10, I 34127 Trieste, Italia.
Using Natural History
Museums to Create National Biological Surveys : A Mexican Case
Study
Adolfo G. Navarro, Museo de Zoología, Facultad de Ciencias, Mexico
Putting Natural History
Museum Collections Data to Work in Solving Problems: Invasive
Species, Global Climate Change and Agricultural Planning
Dr. A. Townsend. Peterson Natural History Museum
Building the Encyclopedia
of Life From Biological Collections Databases
Dr. James Beach, Biodiversity Research Centre, University of Kansas
Theme
II-6: Biosafety and Risk Assessment: Ethical Systems and
Use of Data – M. Krichevsky
The introduction of
genetically modified organisms in the food chain and the environment
gave rise to strident debate, political activity, and civil disobedience.
Scientists and commercial institutions interpret data as "proving"
safety. Other scientists and social activists interpret data as
"proving" risk. Wherein lies the "truth"?
This symposium considers the nature of the data used in the process
of assessing risk, how the data are used, ethical perspectives
leading to disparate views of safety, and public perception of
data and the derived conclusions.
Topics include:
Introductory
Remarks on Biosafety and Risk Assessment
Micah I. Krichevsky, Bionomics International, US
Data
Needs to Support Risk Assessment Decisions
Morris A. Levin, University of Maryland, Baltimore, MD, USA
Mark Segal, U.S. EPA, Washington, DC, USA
Use
and Misuse of Data in Biosafety Debates: Antibiotic Resistance,
Butterflies, Mustard
Micah I. Krichevsky, Bionomics International, US
The
"Precautionary Principle" - When Data Are Inconclusive
Julian Kinderlerer,
University of Sheffield, Sheffield, UK
Giovanni Ferraiolo, International Centre for Genetic Engineering
and Biotechnology, Trieste, Italy
Round
Table on Conflicting Ethical Systems for Evaluating Biosafety
Data
Giovanni Ferraiolo,
International Centre for Genetic Engineering and Biotechnology,Trieste,
Italy
Micah I. Krichevsky, Bionomics International, USA
Morris A. Levin, University of Maryland, Baltimore, MD, USA
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