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Development of an integrated information management system for human genome data (IGD)

Objective



We aim to develop an open software system to handle human genome data. The system, called IGD, will integrate information from many genomic databases and experimental resources into a comprehensive target-end database (IGD TED). Users will use front-end client systems (IGD FRED)to download data of interest to their computers and merge them with their own local data. FREDS will provide persistent storage of and instant access to retrieved data, friendly graphical user interface, tools to query, browse, analyse and edit local data, interface to external analysis, and tools to communicate with the outside world. The TED will be implemented using both relational and object-oriented technologies in parallel; it will be accessible over the network (online and offline) as a read-only resource for multiple clients. Tools will be developed for automated updating of the TED from its resource databases and data setsy which include major databases for nucleotide and protein sequences and structures, genome maps, experimental reagents, phenotypes, and bibliography, and sets of raw data produced at genome centres and laboratories. Beside character-based access via Gopher, WAIS, FTP, and several query language interface to the TED, we will develop a specialized front-end client, IGD FRED, with its own database manager, based on the ACEDB program. The FRED will support graphical display methods for sequence feature maps, chromosomal genetic and physical maps, and for experimental objects like clone grids, etc. FRED data will be coupled with rules and knowledge via PROLOG interface. FRED will also provide interface to important analysis software packages, and tools to submit data to external databases in their own format. The IGD schema will model objects and processes in considerable detail, so that scientist will be able to use the FRED as a laboratory notebook. At the same time, and in the same environment, they will link their experimental data to public reference data coming from the TED. This permits to use the FRED as a single editorial interface to multiple genomic databases at once.
The power of the IGD approach is in using genral tools rather than ad-hoc solutions to accomplish concrete tasks. The open design will simplify rapid evolution and incorporation of new features and resources provided by third parties.

Funding Scheme

CSC - Cost-sharing contracts
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Coordinator

GERMAN CANCER RESEARCH CENTER
Address
Im Neuenheimer Feld 280
69120 Heidelberg
Germany

Participants (3)

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE
France
Address
Route De Mende 1919
34293 Montpellier
Imperial Cancer Research Fund (ICRF)
United Kingdom
Address
Clare Hall Laboratories Blanche Lane South Mimms
EN6 3LD Potters Bar
MEDICAL RESEARCH COUNCIL
United Kingdom
Address
Babraham Bioincubator
CB2 4AT Cambridge