Flexible Integration of Molecular-Biological Annotation Data: The GenMapper Approach

Molecular-biological annotation data is continuously being collected, curated and made accessible in numerous public data sources. Integration of this data is a major challenge in bioinformatics. We present the GenMapper system that physically integrates heterogeneous annotation data in a flexible way and supports large-scale analysis on the integrated data. It uses a generic data model to uniformly represent different kinds of annotations originating from different data sources. Existing associations between objects, which represent valuable biological knowledge, are explicitly utilized to drive data integration and combine annotation knowledge from different sources. To serve specific analysis needs, powerful operators are provided to derive tailored annotation views from the generic data representation. GenMapper is operational and has been successfully used for large-scale functional profiling of genes

Kleisli, its Exchange Format, Supporting Tools, and an application in Protein Interaction Extraction

We describe the Pizzkell/Kleisli suite of software for bioinformatics data integration. We also present a protein interaction extraction system to illustrate the power of this software in rapid construction of bioinformatics applications. 1 Summary "Until recently, biological sequence databases were built by biologists. When sequence databases were first created the amount of data was small and it was important that the database entries were human readable. Database entries were constructed, therefore, as flat files, that is, text entries with the information ordered in a specific way. Indeed, it is probably more accurate to describe these databases as data repositories. As new types of data were captured or created, new data repositories were created using a variety of flat file formats. The result of this effort has been to create a large number of different databases, all in different formats, typically using non-standard data query software, and only really properly accessible to..