Databases and Systems

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Broker Architecture [18]) is an open standard considered a good solution for the
development of Client/Server applications in distributed heterogeneous environments
(different computers, different operating systems, different programming languages).
Our CORBA wrappers allow client applications (e.g. visualization tools) to access
SRS servers remotely (through the Internet) through an Object Request Broker
(ORB). These wrappers are generated based on ‘loaders’ defined in Icarus by SRS
administrators on the server side.
We might also consider a more flexible model of client-server, in which the client
application can send to the server information about the granularity of requested
information, and negotiate dynamically a communication protocol by sending a
loader specification from the client side. This would be very useful in a field where
client applications are developed by groups that have little interaction with the
database maintainers. Finally, we are studying the integration of object oriented and
relational database management systems. This will allow mirrored data from external
sources to be kept in flat files, while local data are handled by a database system. The
interfaces should allow work on both systems in the same way, with hybrid query
resolution and query optimization routing the query to the more appropriate system.
References
1. Interpreter of Commands And Recursive Syntax
http://srs.ebi.ac.uk:5000/man/srsman.html
2. Stoehr, P.J. and Cameron, G.N., The EMBL Data Library, Nucleic Acids Res.,
1991, pp.2227-2230
3. Burks, C., Cassidy, M., Cinosky, M.J., Cumella, K.E., Gilna, P., Hayden, J.E.-D,
Keen, G.M., Kelley, T.A., Kelly, M., Kristoffersson, D. and Ryals, J., Genbank,
Nucleic Acids Res., 1991, pp. 2221-2225
4. Johnson, S., YACC: Yet Another Compiler Compiler, Supplementary Documents
1. University of California, Berkeley, 1986
5. Lesk and Schmidt, A Lexical Analyzer Generator, UNIX Programmer’s Manual:
Supplementary Documents 1. University of California, Berkeley, 1986
6. Wirth, N., CompilerBau. B.G. Teubner, Stuttgart, 1984, pp.34-44
7. Bairoch, A. and Boeckmann, B., The SWISS-PROTprotein sequence data bank,
Nucleic Acids Res., 1991, pp.2247-2249
8. Abola, E. E., Bernstein, F.C. and Koetzle, T.F., The Protein Data Bank,
Computational Molecular Biology. Sources and Methods for Sequence
Analysis., 1988, pp. 69-81
9. Etzold, T. et al, SRSWWW version 5.1 at EMBL-EBI. http://srs.ebi.ac.uk:5000/
10. Etzold, T., Ulyanov, A. and Argos, P., SRS: Information Retrieval for Molecular
Biology Databanks, Methods In Enzymology, 1996, pp. 114-128
11. Etzold, T. and Verde, G., Using Views for Retrieving Data from Extremely
Heterogeneous Databanks, Pac. Symp. Biocomput., 1997, pp. 134-141.