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Participants | sling-fp7.org

Participants

SLING has five contracted partners (EMBL-EBI, SIB, TUBS, EPO and Enzymeta GmbH) who have agreed to cooperate pursuant to the terms of a Consortium Agreement which specifies the organisation of the Project work and management, and defines the respective rights and obligations of the Beneficiaries.

Organisation Short Name Short description (fields of excellence) and specific roles in the consortium
EMBL Outstation - The European Bioinformatics Institute EMBL-EBI

The European Bioinformatics Institute (EBI) has a long-standing mission to collect, organise and make available databases for biomolecular science. It makes available a collection of databases along with tools to search, download and analyse their content. These databases include DNA and protein sequences and structures, genome annotation, gene expression information, molecular interactions and pathways. Connected to these are linking and descriptive data resources such as protein motifs, ontologies and many others. In many of these efforts, the EBI is a European node in global data-sharing agreements involving, for example, the USA and Japan.

The utility of the EBI to the scientific community today is evidenced by massive use of its services. Typically its web portal sees well over three million hits per day from a user community of several hundred thousand individual scientists. The community served ranges from basic academic researchers through to applied research in diverse areas including pharmaceuticals, agriculture and nutrition. Alongside the core service activities, the EBI is a basic research institute, with bioinformaticians regularly publishing the biological findings of computational investigations of biomolecular information.

The constituency of the EBI most emphatically includes the commercial sector as well as academic research. It has a flourishing "Industry Club" and "SME support programme" for European companies involved in bioinformatics.

Swiss Institute of Bioinformatics SIB

The Swiss Institute of Bioinformatics (SIB) has the mission to promote research, the development of databanks and computer technologies, and teaching and service activities within the field of bioinformatics in Switzerland, with international collaborations. The Swiss-Prot group of the SIB, headed by Prof. Amos Bairoch, is responsible, in collaboration with EBI and the Protein Information Resource (PIR), for the UniProtKB/Swiss-Prot protein knowledgebase (http://www.uniprot.org/ and http://www.uniprot.org/), a curated protein sequence database which strives for high annotation standards and a high level of integration with other databases. The Swiss-Prot group also maintains and distributes related databases including PROSITE (http://www.expasy.org/prosite/), a database of protein families and domains, ENZYME (http://www.expasy.org/enzyme/), a repository of information relative to the nomenclature of enzymes and NEWT (http://www.ebi.ac.uk/newt/index.html), a database of taxonomy. The Swiss-Prot group is also involved in the diffusion of bioinformatic resources to the international community through the ExPASy (Expert Protein Analysis System) proteomics server, which is maintained by the SIB (http://www.expasy.org/).

The Technical University of Braunschweig TUBS

The Department of Bioinformatics & Biochemistry at the Technical University Braunschweig (TUBS) headed by Prof. Dr. Dietmar Schomburg is doing experimental and theoretical research, software and database development on metabolome analysis, metabolic networks, enzyme classification, and systems biology including virtual cell simulation. The database BRENDA (http://www.brenda-enzymes.info), Pathway hunter tool for metabolic network analysis (http://pht.tu-bs.de), CUPSAT (http://cupsat.tu-bs.de) and other software tools and databases are developed and made available to the scientific community. The department integrates theoretical and experimental research for the analysis of complex biological phenomena and genotype/phenotype analysis. The department has close links to a large number of national and international research groups and centres within the scope of Networks of Excellence and strategic cooperation plans.

European Patent Office EPO

The European Patent Organisation (Epo) is an intergovernmental organisation that was set up on 7 October 1977 on the basis of the European Patent Convention (EPC) signed in Munich in 1973. It has two bodies - the European Patent Office, located in Munich with a branch in The Hague and sub-offices in Berlin and Vienna. The European Patent Organisation has legal personality; it is represented by the President of the European Patent Office.

The EPO provides a uniform application procedure for individual inventors and companies seeking patent protection in up to 38 European countries. - the Administrative Council, which supervises the Office's activities. It is made up of representatives of the contracting states, exercises legislative powers on behalf of the Organisation, is responsible for policy issues relating to the Organisation and supervises the Office’s activities. The EPO collects patent data and patent related data worldwide, and continuously improves its automatic processes of acquiring, validating and loading data into various databases. The high quality of the EPO databases is maintained by unique extensive data-correction activity. With regard to the production and dissemination of patent information, the aim of the EPO is to provide access to patent information in Europe for the general public and for industry and non profit entities in order to stimulate innovative activity - an aim that is of paramount importance.

The EPO has a long-standing collaboration with the EBI focussed on the electronic acquisition of biomolecular information in patent applications. Historically, such information (e.g. DNA sequence data) was submitted only in printed documents. Working with the EBI, the EPO has established procedures to get this information in parseable form at the time of patent application. This streamlines the application procedure, simplifies the patent examination process, and enables the information to be included in public domain databases such as those at the EBI and made available under SLING. Intercontinental data-sharing agreements with comparable organisations throughout the globe help to improve completeness of the collections. However, we are confident that Europe leads the world in this particular mode of operation.

Enzymeta GmbH Enzymeta GmbH

ENZYMETA GmbH was founded in 2001 with the principal intention for enzyme database development. Since then, this small company has been in constant collaboration with the Institute of Biochemistry of Prof. Dietmar Schomburg, from 2001 to 2006 at the University of Cologne and since 2007 at the Technische Universität Braunschweig. Major contents of the BRENDA enzyme database have been developed and curated by ENZYMETA. The staff has a long-standing experience in the acquisition and supervision of external experts which are necessary for covering all aspects of enzymology. ENZYMETA works in close cooperation with the IUBMB (International Union of Biochemistry and Molecular Biology) on enzyme classification and enzyme nomenclature.