CORDIS Archive

Area 8 - Infrastructures

In line with the conclusions of groups of Commission's advisers on biological research infrastructures, projects should support the development of a consolidated system of biotechnology information management, the typing and distribution of highly demanded biological materials and the streamlining of these operations in conformity with the highest quality standards. The provision of the following services will be carried out by consortia involving the core facilities and networks of research organizations connected throughout Europe with front-line biotechnological research. For this reason, tasks under this area will be preferably linked to major research projects mobilizing large communities for the specific objectives retained under this programme.

The services offered by the activities listed below are meant to have a beneficial impact on all the other research areas as described in this programme. This impact will be amplified beyond the resources set aside by this area 8 by encouraging the use of such services and their support for tailor-made applications under projects linked to other areas of the present workprogramme. Therefore, projects from other areas of the workprogramme for which such services would appear to play a necessary role in achieving their specific research objectives will be highly welcome. This statement applies to all areas, specially to Areas 2 (Genome Analysis) and 6 (Structural biology).

8.1 Information infrastructures

Objectives

Coordinated development of existing biotechnology information infrastructures and integration of new, emerging databases and other information sources within a common, coherent framework. Information services will serve the various user profiles in the Community at large (industrial, academic, policy makers) providing user-friendly interfaces and, as much as possible, unique access points to sets of related information sources with functional or thematic links. Special attention shall be paid to ensuring that these services match the research needs, including those of industry and particularly SMEs. To this effect, regular reports providing information on the use and acceptance of the services provided will be requested to consortia. Necessary actions shall be taken to ensure proper publicity and wide spread distribution of information contained in databases. Developments in this area will specially underpin objectives of Areas 2 (Genome analysis), 6 (Structural biology) and 7 (Prenormative Research, Biodiversity and Social Acceptance).

Research tasks

8.1.1 Information resources on molecular sequences and structures

For all tasks described below, research activities on novel bioinformatics techniques will be developed so as to improve the service aspect by investigating new algorithms for analyzing sequences and structures taking advantage of new computational techniques and computer architectures and by providing flexibility and dynamic evolution of databases. The following tasks will be provided by consortia of organisations constituted as networks including the centre (or centres) for common information sources surrounded by producers or users. Coordination and synergy with European bioinformatics networks will be assured.

• Collection, annotation, maintenance and distribution at a European scale of nucleotide and protein sequences. Proponents should ensure full access to and distribution of already existing electronically available data collections of nucleotide and protein sequences. International agreements with major nucleotide and protein sequence data providers should be assured. Projects will have a user-oriented approach allowing European researchers to easily submit and access data. For this purpose, telematic links and advanced electronic distribution media will be provided and maintained on a regular basis.
  
  
• Coordinated provision of specialised databases (tRNA, rRNA, ALU sequences, promoters, restriction enzymes libraries, taxonomic sequence databases, genetic maps, etc.) ensuring cross reference with main sequence databases (nucleotide and protein) and common access methods.
  
  
• Provision of macromolecular structural databases (proteins, carbohydrates, etc.). Selected networks will provide full access to validated 3D structures (atomic coordinates, volumes). Cross reference to main sequence databases will be assured. Networks of research centres will investigate new tools for validation of submitted 3D coordinates in order to ensure consistence of central databases.

Priority will also be given to research projects underpinning scientific objectives under Area 6 (Structural Biology).

8.1.2 Taxonomic information and storage databases

Provision of information at the European level on biological resources and collections established in Europe giving access for large sectors of the European research community to catalogues of biological repositories relevant to the objectives of the present programme. The services will be carried out by consortia involving storage centres and information system providers. Projects will be as comprehensive as possible facilitating users to access other sources of information (cross references to sequence or structural databases, for example).

8.1.3 A European network of bioinformatics nodes

Coordination will be made of European national and specialized nodes of bio-computing so as to ensure the establishment and maintenance of a bioinformatics network. The proponents should be able to harmonize and share scientific and technical resources and services provided by each agreed node. The network should have a user-oriented approach providing European biotechnology users with at least, the following services:

• Regular distribution of and access to relevant biotechnology databases among agreed nodes.
• Training activities
• User's support.

The implementation of these services should be underpinned by:

• Sharing of technological and scientific resources of local nodes.
• Development of protocol and interface standards facilitating data interchange.
• Enhancing bioinformatics awareness.

Close cooperation should be established with organisations providing biotechnology relevant databases so as to ensure a broad distribution. The European dimension of the network should be promoted by fostering the participation of nodes in all the EC Member States.

8.1.4 Horizontal information resources: literature, directories databases

Provision of common environments for a simplified access to a number of databases with functional or thematic links. Indexing and cross-reference systems will facilitate users to navigate between various sources of data. It is important to be noted that this action aims to integrate diverse sources of information rather than the creation of the databases themselves. Examples of typical projects could be

• Common access to bibliographic databases connecting various literature sources with proper links to factual data (sequences, structures, etc.)
• Common access to databases of directories of biotechnology projects, active centres and laboratories, investigators and catalogues of bioinformation sources.
• Common access to databases of molecular resources: clones, probes, reagents.

Projects will be addressed via the establishment of consortia of database producers (primary databases, publishers, data producers, hosts). The Community support will aim to help in the initiation of these initiatives. As an integral part of the work, consortia will investigate alternative financial sources in order to ensure the continuation of the project once the Commission's support is finished.

8.2 Genetic archives and stock centres

Objectives

The development of bioresource centres will be coordinated and their biological collections will be made accessible to the scientific community at large.

Proposals to organize the bioresource supply in Europe should be presented by consortia involving stock centres and networks of laboratories engaged in active research.

The objectives of this programme will be:

• To make collections more efficient by improving conservation techniques and logistic aspects (classification, storage, retrieval, delivery).
• To achieve a more extensive and efficient use of genetic resources in plants, animals and microorganisms, particularly where new genetic techniques (gene tagging, gene replacement, eg. knock-out mice) form the basis of an unprecedent variability of mutant phenotypes.

Coupling of biological stocks and related Information Systems will be fostered (cf. 8.1.2).

Research tasks

8.2.1 Genetic archives

Integrated provision of and access to genetic information as isolated chromosomes, genomic DNA and cDNA libraries, isolated genes, etc. Consortia of various genetic information centres providing coordinated access to different sources of genetic materials will be fostered.

8.2.2 Stock centres

Collection, conservation and provision of diverse organism strains and mutants (cryogenic storage of semen, oocytes, embryos, stem cells and cell lines).

Special attention will be paid to the development of a mouse (and rat) stock centre. Specially for mouse, novel techniques have recently been developed allowing the creation of mutants exhibiting any desired trait or combination of traits of high biotechnological and biomedical interest. Therefore, it is essential to provide the means to characterize and store this ever increasing amount of new mutants and to grant access to this repository to the European research community at large.

Drosophila and plant (Arabidopsis) stock centres could be considered as well.

Expected benefits of this action will be, among others i) the availability of mutants created for specific research objectives and ii) the possibility of creation of new organisms combining various mutations via the interbreeding of existing stored strains.

8.3 Assessment of infrastructures

Objectives

Provision of a European Biotechnology Infrastructures Observatory service producing, on a periodical basis, information on the quality, degree of coverage and user's satisfaction of biotechnology infrastructures.

Research tasks

• Provision of qualitative and quantitative assessment on current functioning of infrastructures (information and biological resources), degree of user's satisfaction and utilisation as well as perceived gaps and problems by users.
• Identification of new services needed in a quickly changing research environment in order to best serve the research requirements.
• Provision of an up-to-date catalogue of existing infrastructures, access methods and contact points.
• Continuing analysis of standards and procedures operated by consortia under contract, their comparability to, and compatibility with other information services established at the international scale.

Synergies with other specific programmes

• Cooperation and synergy with initiatives developed in the information technology and telecommunication programmes of both Directorate General III (Industry) and Directorate General XIII (Telecommunications, Information Market and Exploitation of Research) will be essential. In particular, projects will take into account technical findings and achievements of these programmes (networking, logic support and advanced treatment of information, database design, access and communication, health telematics, IT and telecommunication standards).
  
  
• Developments on inventories of biotechnology projects will take into account DGVI (Agriculture) initiatives, specially in relation with the AGREP database. Proper coordination mechanisms will be contractually requested to consortia in order to foster complementarity and avoid overlaps.
  
  
• The actions falling under the Council Regulation n°1467/94 of 20 June 1994 on the conservation, characterization, collection and utilization of genetic resources in agriculture will be excluded from the research tasks considered under 8.1.2 and 8.2.2, while ensuring at the same time the desired synergies between them.
  
  
• Projects aiming at providing access to large installations should normally be addressed to the Human Capital and Mobility programme. Nevertheless, whenever the access to large installations constitutes a necessary step for a project to achieve research objectives covered by this workprogramme, funds from the Biotechnology programme could be afforded within the relevant scientific area.