Kleisli is a modern data integration system that has made a significant impact on bioinformatics data integration. The primary query language provided by Kleisli is called CPL, which is a functional query language whose surface syntax is based on the comprehension syntax. Kleisli is itself implemented using the functional language SML. This paper describes the influence of functional programming research that benefits the Kleisli system, especially the less obvious ones at the implementation level. 1 Introduction The Kleisli system [14] is an advanced broad-scale integration technology that has proved useful in the bioinformatics arena. Many bioinformatics problems require access to data sources that are high in volume, highly heterogeneous and complex, constantly evolving, and geographically dispersed. Solutions to these problems usually involve multiple carefully sequenced steps and require information to be passed smoothly between the steps. Kleisli is designed to handle these req...

We consider the problem of extracting, manipulating, and managing

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...

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(Note: parts of text also to appear in Biotech Hobbyist Magazine)

We consider the problem of extracting, manipulating, and managing pathways, especially protein-protein interaction pathways. We discuss here the Protein Interaction Extraction System (PIES). The PIES is contructed on top of three main technologies: Kleisli, BioNLP, and Graphviz. Kleisli is a broad-scale data integration system that we use for downloading Medline abstracts and for general manipulation and management of pathway/interaction databases. BioNLP is a natural language-based information extraction module that we use for analysing Medline abstracts and to extract precise protein-protein and other interaction information. Graphviz is a graphically layout package developed for directed graphs that we use for visualization of the extracted pathways. The PIES can be augmented with means for extracting protein interaction information from sequence databases, for example, by using Kleisli's power to integrate sequence comparison tools to detect gene fusion events in sequence ...