Genomic pathways database and biological data management

Abstract

In this paper, we discuss the properties of biological data and challenges it poses for data management, and argue that, in order to meet the data management requirements for 'digital biology', careful integration of the existing technologies and the development of new data management techniques for biological data are needed. Based on this premise, we present PathCase: Case Pathways Database System. PathCase is an integrated set of software tools for modelling, storing, analysing, visualizing and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The novel features of the system include: (i) genomic information integrated with other biological data and presented starting from pathways; (ii) design for biologists who are possibly unfamiliar with genomics, but whose research is essential for annotating gene and genome sequences with biological functions; (iii) database design, implementation and graphical tools which enable users to visualize pathways data in multiple abstraction levels and to pose exploratory queries; (iv) a wide range of different types of queries including, 'path' and 'neighbourhood queries' and graphical visualization of query outputs; and (v) an implementation that allows for web (XML)-based dissemination of query outputs (i.e. pathways data in BIOPAX format) to researchers in the community, giving them control on the use of pathways data.