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Biotechnology Information and Knowledge Grid

Objective

Purpose of the biogrid project is to conduct a trial for the introduction of a grid approach in the biotechnology industry.

This trial consists of two major steps:
(i)the integration of three existing technologies and
(ii) the production of a working prototype.

The existing technologies to be integrated are:
(i) PSIMAP agent technology
(ii) classification server: Automatic model classification
(iii) space explorer: knowledge visualisation technology.Bio Grid will change the perspective of biologists from a partial view of biological data towards a holistic view of documented data seamlessly integrated with expression and interaction data. This constitutes the basis of a next generation research infrastructure for large proteomics and genomics databases.

Objectives:
The project is focused at the development of an information and knowledge grid allowing knowledge discovery and access to multiple types of unstructured data.

Scientific objectives:
Effective concept recognition, pattern matching, intelligent data sourcing agents and tagging technology;
Automated categorisation in a metadata hierarchy of the specified biotechnology research domain;
Detailed functional knowledge management interoperability methodology design;
Domain knowledge mapping, implementing a logical domain ontology;
Effective integration of agent, classification logic and visualisation technology. Business objectives: Information grid supporting a next generation classification research infrastructure for large proteomics and genomics databases; Efficient transnational enterprise collaboration;
Faster time to market biotech innovation.

Work description:
This section describes the project work plan towards realisation of the objective: to conduct a trial for the introduction of a grid approach in the biotechnology industry.This trial consist of two major steps: (i) the integration of three existing technologies and (ii) the production of a working prototype.

The project is focused at the development of an information and knowledge Grid allowing knowledge discovery and access to multiple types of unstructured data, effectively visualised and accessible in a structured data model. In the initial phase of the project, the required biotechnology domain is analysed and existing structures and standards are identified in WP1.WP2 uses the results of WP1 to create a logical structure (hierarchy) of the information structure (ontology) of the scientific area. Also the algorithms by which the data from the identified data source in WP1 can be positioned in the hierarchy is being developed in WP2. In the second phase of the project the three existing technologies (Classification Server, PSIMAP and SpaceExplorer) are integrated consecutively to the common data structure defined in WP2 This involves implementing the logic developed in WP2 in the existing agent technology used to source relevant data and position it in the developed taxonomy. WP4 is concluding with a working prototype of the agent technology. Wp5 implements existing visualisation technology to present the data structure to the users in an easy accessible manner. The second phase is concluding with a fully functional second prototype to conclude the project. In the third phase, WP6, validates the project. In this work packages metrics are introduced for technical, organisational and business parameters together with the activities for collection and evaluation of resulting data. Finally, dissemination and exploitation of the project results are addressed in wp7.

Milestones:
The end result of the project will consist of a working prototype of a next generation classification research infrastructure for biotech knowledge interoperability. This consists of (i) automatic classification in a hierarchy metadata repository (ii) intelligent agent sourcing system (iii) accessible visualisation user interfaces.

Major deliverables are: month 6 integration requirements report; month 16 Evaluation of 1st prototype; month 20 Final functional prototype.

Funding Scheme

ACM - Preparatory, accompanying and support measures

Coordinator

RIJKSUNIVERSITEIT GRONINGEN
Address
Broerstraat 5
9712 CP Groningen
Netherlands

Participants (5)

CITY UNIVERSITY LONDON
United Kingdom
Address
Northampton Square
EC1V 0HB London
MEDICAL RESEARCH COUNCIL
United Kingdom
Address
Park Crescent 20
W1B 1AL London
TECHNISCHE UNIVERSITAT DRESDEN
Germany
Address
Helmholtzstrasse 10
01062 Dresden
UNIVERSITY OF CYPRUS
Cyprus
Address
Kallipoleos Street 75
1678 Nicosia
ZOOROBOTICS B.V.
Netherlands
Address
Wassenaarseweg 72
2333 AL Leiden