About
the ORIEL
Project and its
Partners
The
ORIEL Project
...is
developing tools and procedures to promote access to and integration
of a wide range of information resources in the life sciences.
The
tools developed through ORIEL will:
-
enable
effective linking of different types of biological information
(literature, factual and multimedia databases)
-
make
navigation easy, thereby encouraging the creative exploration
of the information landscape
-
facilitate
communication by making data presentation and information
visualisation user-friendly.
- The ORIEL
Project (IST-2001-32688), funded by the EU and coordinated by
the European Molecular Biology Organisation (EMBO) aims to provide
research communities with tools to manage large, complex,
multimedia datasets and to navigate through an increasingly intricate
and potentially confusing information landscape.
Methodologies
- ORIEL's
methodologies will be tested and applied in a critical user
environment represented by the EU-funded E-BioSci platform
(QLRI-CT-2001-30266).
Developments
- Methods
-
- leading
to the creation of new concepts of the scientific literature,
based on machine-understandable documents.
- Technologies
-
- permitting
effective linking of a wide range of biological digital
information sources, including molecular, genomic and multi-dimensional
image databases,
- promoting
ease of cross-database navigation, leading to creative
exploration of the information landscape.
- Protocols
-
- facilitating
effective data representation and information visualisation
through the construction of adaptive interfaces that meet
the needs of individual users.
Background
- The emerging
fields of genomics and bio-informatics are having far-reaching
effects on all aspects of the Life Sciences. Additionally, biotechnology
and biomedicine, that will benefit enormously from new genome-based
technologies, have become important growth areas in the European
life sciences industry.
- Genomics
research is characterized by the production of vast amounts
of raw and derived data. The integration of the exponentially
growing amounts of these and associated biological information
in digital form (publications, sequence and sequence-related
information, digital image data) is presenting one of the
most demanding current challenges to information technology.
- There is
an urgent need to better exploit the potential of the Internet
and other communication networks to develop novel technology and
intelligent middleware for the integration of large, complex and
disparate information resources.
Objectives
- The ORIEL
project will explore and further develop methods, technologies
and protocols aimed at the integration, dissemination and
exploitation of large, complex and disparate digital information
resources. With a view to making such technologies widely available,
it will focus on the Life Sciences as a data-intensive and highly
demanding testbed that will
- permit
effective linking of different types of biological information
displaying complex inter-relationships (literature, factual
and multi-media image databases)
- promote
ease of navigation leading to creative exploration of
the information landscape and
- facilitate
user-friendly data presentation and information visualisation.
Milestones
- The development
of new concepts that will enhance the efficiency of integration
of different types of biological data currently maintained in
a wide spectrum of digital collections and resources across Europe.
- The development
and optimization of interactive and adaptive user interfaces
to promote intelligent access to, retrieval and analysis of data
stored in digital form.
E-BioSci
and ORIEL
- E-BioSci
is EMBO's initiative to provide a federated network of European
platforms for a wide range of high quality electronic services
relating to information access and retrieval in the life sciences.
- The ORIEL
Project will promote access to and integration of E-BioSci
services. In return, E-BioSci will provide a staging area
in which ORIEL components can be pre-released prior to rigourous
testing by sub-sets of research community users. This staging
facility will serve both as development area for testing and integrating
ORIEL prototypes within E-BioSci, as well as evaluating their
effectiveness with core users of the live service.
- Both projects
build on the complementary expertises and strengths of partner
institutions in different locations in Europe. They aim to foster
optimal pooling and use of European biological archives and
data collections, and will involve the development of common
protocols for efficient searching and retrieval of different types
of information (including images, sequence data and full text
published literature) held in different locations and in different
formats. Some of these goals are long term and will require significant
research and prototyping to achieve them.
Graphic
representation of the relationships between ORIEL and E-BioSci projects
ORIEL
Partners
CINES
| CNR-IBC | CNR-ITB
| CSIC | EBI
| EMBO | EUR
|
CINES
(Centre Informatique National de l'Enseignement Supérieur)
(Workpackages
WP5, WP6, WP7)
- Created in 1980
in Montpellier (France), CINES is supervised by the French Ministry
of Research and provides the French research community with computing
resources and services. CINES' three core competencies are:
- High performance
computing: Numerous scientific disciplines use equipment of the
Centre for resolving problems which require extreme powers of calculation
and large memory capacities. CINES also offers users the possibility
to visualise the results of calculations by animated sequences and
to produce supports of broadcasting.
- Large databases
and documentation systems: CINES is the privileged partner of
the Higher Education Bibliographical Agency (ABES) as well as the
official server of the libraries network SIBIL-FRANCE. CINES is also
involved in several multimedia projects.
- Wide Area
Network expertise: CINES is connected to the French National Research
Network (RENATER) and also participates in the national network committee
CRU and its different workgroups. A RENATER local office will soon
be located in the CINES building. Many collaborations are in progress
between RENATER and CINES, including security and performance.
 
CNR-IBC
(Consiglio Nazionale delle Ricerche) (National Research Centre)
(Workpackage
WP3, WP6, WP7)
- Hosts the CNR-EMMA
facility of the European Mouse Mutant Archive. In collaboration
with European partners and the Mouse Genome DataBase at the Jackson
Laboratory, it has defined informatics policies aimed at the implementation
of the EMMA-Resource DataBase (EMMA-RDB).
- For more information,
please vist http://www.cnr.it.
CNR-ITB
(Consiglio Nazionale delle Ricerche) (National Research Centre)
(Workpackage
WP3,
WP6, WP7)
- Bio-informatics
division of CNR, which was established in 1989 to work on the framework
of the Human Genome Project. Originally focused on developing
tools for the genome sequence analysis and prediction of gene structure
in different organisms, attention has more recently been shifted towards
study of genefunction, promoter prediction, gene expression analysis
and the development of databases integrated with sequence analysis
tools.
- For more information,
please vist http://www.cnr.it.
CSIC
(Consejo Superior de Investigaciones Científicas)
(Workpackage
WP4, WP7)
- The Spanish
Council for Scientific Research (CSIC), established in 1939, is
the largest multidisciplinary public research organisation in Spain.
It is an autonomous body within the Ministry of Science and Technology
and its main objective is to promote and carry out research contributing
to scientific and technological progress in Spain. The CSIC can
be considered as the backbone for development of science and technology
in Spain. The research activities of CSCI cover virtually every field
of knowledge: Agricultural Sciences, Biology & Biomedicine, Chemistry,
Science & Technology, Food Science & Technology, Humanities
& Social Sciences, Materials Science & Technology, Natural
Resources, Physics: Science & Technology
- As a part of
its commitment to the Spanish scientific community, the CSIC makes
available a part of its infrastructure and a variety of services,
among which mention may be made of its information, documentation
and library networks.
- For more information,
please visit: http://www.csic.es
 
EMBL-EBI
(European Bioinformatics Institute)
(Workpackage
WP4, WP7)
- The European
Bioinformatics Institute (EBI) is the central European node for managing
factual databases in the Life Sciences. The following databases
are managed at the EBI:
- The International
DNA data library, the Swissprot and SPTREMBL protein database,
the EMBL Interpro database of protein families, the European
Macromolecular Structure Database (MSD), the Array Express
database of microarray data and the ENSEMBL databases of
annotated large scale genomic sequence.
- In addition to
providing these databases and services built on top of these, EBI
has a vigorous research role in bioinformatics. Both data sources
and new algorithms are investigated and developed at the EBI, along
with research into technical developments to enable new technologies
to be deployed for life sciences.
- EBI is at the
Hinxton Wellcome Trust Genome Campus, which is the world's premier
campus for public domain large scale life science data research.
- For more information,
please visit: http://www.ebi.ac.uk.
EMBO
(European
Molecular Biology Organization)
(Workpackages
WP0, WP7, WP8)
- Active
development and support of trans-national approaches to molecular
biology through fellowships, courses and workshops. Leads in European
molecular biology publishing (EMBO Journal, EMBOreports).
- For more information,
please visit: http://www.embo.org.
BioSemantics
Group, Department of Medical Informatics, Erasmus University
The Biosemantics
Group Rotterdam is an initiative of the Department
of Medical Informatics of the Erasmus MC - University Medical Center
Rotterdam, the Netherlands. Through innovative fundamental and applied
research it aims at developing and validating advanced techniques for
the processing and analysis of large, complex, and heterogeneous medical
and biological data sets. In addition to research the group is involved
in the training of under- and postgraduate medical students and radiologists.
ICGEB
(International Centre for Genetic Engineering and Biotechnology)
(Workpackage
WP3, WP7)
- International
research organization focussing on advanced research and teaching
in molecular biology and biotechnology. Maintains the ICGEBnet
Bioinformatics Service with over 1100 users throughout the world.
Bioinformatics research at ICGEB is carried out in two main areas:
a) Maintenance and development of SBASE protein sequence domain library
and b) physico-chemical properties of DNA.
- For further information,
please visit: http://www.icgeb.trieste.it.
IGH
(Institut de Génétique Humaine)
(Workpackage
WP5, WP6, WP7)
ingenta
(Workpackages
WP1, WP6)
- Ingenta was formed
through a public/private partnership with the University of Bath to
provide electronic distribution and marketing for the publishers of
scholarly content and to develop the industry's primary portal site
for the knowledge worker. Ingenta operates the renowned BIDS services
for the UK higher education community. Ingenta bases its North American
operation in Cambridge, MA and its European operations in Oxford and
Bath, UK.
- In March 2000
Ingenta merged with the UnCover Company and in May 2000 it became
listed on the AIM market of the London Stock Exchange. In June 2000
Ingenta acquired the Publishers Communication Group (PCG), based in
Cambridge, MA. In October 2000, Ingenta acquired Dynamic Diagrams.
In February 2001, Ingenta merged with CatchWord. In March 2002, Ingenta
acquired HERON, formerly a government-funded initiative providing
online course packs to Higher Education Institutions in the UK.
- The combined
company currently works for almost 200 publisher clients, and hosts
or links to 5,400+ academic journals. The Group’s customer base
includes 7 of the world’s top 8 journal publishers – Blackwell
Publishing, Elsevier Science (including Academic Press), John Wiley
& Sons, Kluwer Academic Publishers, Oxford University Press, Taylor
& Francis and the Sage Group.
- For more information,
please visit: http://www.ingenta.com
INRIA
(Institut National de Recherche en Informatique et Automatique)
(Workpackage
WP2, WP7)
LIRMM
(Laboratoire d'Informatique, de Robotique et de Microéelectronique
de Montpellier)
(Workpackage
WP5, WP6, WP7)
UOXFAT
- University
of Oxford
(Workpackage
WP1, WP7)
- Founding partner
of the 4th Framework BioImage
Database Project, with responsibility for digital video data.
Experience in digital video encoding and compression artefacts,
automated content analysis and query by content of biological videos.
Developer of VIDOS, a patent-pending Web-based video editing and customization
tool.
- For more information,
please visit: http://www.ox.ac.uk.
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