Databases and Systems

20 EBI: CORBA AND THE EBI
DATABASES
Introduction
Kim Jungfer, Graham Cameron and Tomas
Flores
EMBL Outstation - Hinxton, The European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton,
Cambridge CBIO lSD, United Kingdom
The European Bioinformatics Institute (EBI) is a major center for biological data.
Research groups have collected genome-related data for the last 15 years, during
which the amount of data has grown exponentially. There are now more than 300
publicly available collections of highly interrelated data. The more the size and
complexity of molecular biology data grow, the more important become automatic
tools for management, querying and analysis. The current limitations in using this
wealth of information are not due to missing technology but to lack of
standardization. Biologists utilize every possible hardware platform, operating
system, database management system and programming language. The de facto
standard CORBA [9] [10] [11] offers the opportunity to make such differences
transparent and thereby helps to combine disparate data sources and application
programs.
Molecular biology data have traditionally been stored in simple text files often
referred to as flat-files. Flat-files are the minimalist storage mechanism, adopted for
small data sets and simple programs – easily distributed and readily comprehensible.
Even large volumes of complex data, although managed in database management
systems, are often distributed as flat-file "entries". This leads biologists to see the
flat-file as the basic data representation. The advent of the World Wide Web [2]
strengthened this view. Flat files can easily be transformed to hypertext by turning
references into hypertext links. The Sequence Retrieval System SRS [7] is a well-
known example of this approach. Flat-files became the center of the data flow in
molecular biology. Every data collection has to provide a flat-file version in order to
distribute the data and most analysis programs use flat-files as their data source.