EXTRACTING AND CONVERTING DATA FROM SEMI-STRUCTURED BIOLOGICAL DATABANKS USING SRS
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30-01-2009, 11:56 PM


One fundamental property underlines most biological databanks; their availability in text format Report gives an approach to retrieve and convert biological data stored in textual flat files into information in formats more suitable for further analysis and use by client applications. Extracted data can be exported into different data structures (CORBA objects, DBMS, C structures, HTML reports). These data structures are loader objects. They are generated based on loader specifications, which specify how to get specific pieces of information and how to package them. This article focuses on CORBA loaders. There is a growing interest for CORBA in the Bio informatics, and more generally the Life Science Research community, because CORBA is seen as a unifying framework that could help the integration of heterogeneous data sources and applications using these data.
The SRS system is one of the most widely used tools in the Bioinformatics and Molecular Biology community for accessing biological information stored in textual flat files. It can be seen as a successful model of collaborative integration, where the SRS system administrators collaborate by exchanging structure descriptions, grammars and loaders for the databanks.
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