A logical approach to working with biological databases

It has been argued before that Prolog is a strong candidate for research and code develop-ment in bioinformatics and computational biology. This position has been based on boththe intrinsic strengths of Prolog and recent advances in its technologies. Here we strengthenthe case for the deployment and penetration of Prolog into bioinformatics, by introduc-ingbiodb, a comprehensive and extensible system for working with biological data. Wefocus on databases that translate between biological products and product-to-productinteractions, the latter of which can be visualised as graphs. This library allows easy ac-cess to high quality data in two formats: as Prolog fact files and as SQLite databases.On-demand downloading of prepacked data files in these two formats is supported in alloperating system architectures as well as reconstruction from latest data files from thecurated databases. The methods used to deliver the data are transparent to the user andthe data are delivered in he familiar format of Prolog facts