The Protein Function and Metabolic Pathways (PFMP) Database Project
On April 1 ,1998 a research group at the EBI (Group Leader, Shoshana Wodak) has undertaken a project on the development of an integrated resource on protein function and metabolic pathways. The project is a joint venture between the EBI-EMBL and 3 pharmaceutical-agrochemical companies, Hoechst-Marion-Roussel, Monsanto, and Zeneca.
The EBI interest in this area stemmed from the realisation that while significant efforts are being devoted world-wide to the development of databases for genomic and protein sequences, and to databases of macromolecular 3D structures, relatively little has been done so far concerning information on protein function, and comparatively little is available for relating genome and protein sequence data to what is known about protein function, metabolic and other biologically important pathways.
The main goal of the project is to develop an object-oriented database for representing information on protein function and biochemical pathways. This database will make it possible to query this information in a much more flexible and sophisticated way than hitherto possible. It should also offer programmatic access to the data, which should be particularly useful in the interpretation of gene expression and proteome analysis data.
The database will recast and extend an existing rich collection of data on enzyme function (BRENDA) developed by Prof. D. Schomburg at the University of Cologne. This information will be integrated with representations of metabolic pathways, obtained from a number of publicly available sources and by curation done at the EBI. The whole will be underpinned by a consistent data structure.
The project also includes a one year pilot study whose remit is to explore the extension of the data model to include information on other types of key biochemical pathways, such as regulation of gene expression and signal transduction. This particular aspect of the project benefits from a close collaboration with Prof. George Cohen of the Inst. Pasteur in Paris.
As part of the project, biochemical pathway editor and visualisation tools are being developed. In particular, a Java-based graphical tool has been designed which allows the user to interact with a diagrammatic representation of a pathway. The underlying data structure for the pathway will form part of the database object model. In ongoing work, the pathway editor will be integrated fully with the object database and will allow for creation of new pathway diagrams to be stored in the database as well as viewing and modification of existing pathways.
The project has already had important practical benefits for the scientific community. With mounting interest at the EBI for data on protein function, gene regulation and metabolism, resources pertaining to these data were recently made accessible via the SRS system (Thure Etzold). This includes BRENDA (D.Schomburg), EMP, the Enzyme and Metabolic Pathway resource (E.Selkov), KEGG, the Kyoto Encyclopaedia of Genes and Genomes (Goto & Kanehisa), TRANSFAC, the Transcription Factor Database (E. Wingender), and Regulon-DB, the database on transcriptional regulation in E-coli (J. Collado). This will continue to happen in the future, for new data curated by the PFMP project.
Article by: Shoshana Wodak
Resources and further information
European Bioinformatics Institute (EMBL-EBI)Institute of Biochemistry
BRENDA - enzyme function database at the EBI
University of Koeln
Institute Pasteur, Paris (France)
- BRENDA - enzyme function database
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