A query language for biological networks

Many areas of modern biology are concerned with the management, storage, visualization, comparison, and analysis of networks. For instance, networks are used to model signal transduction and metabolic pathways, gene regulation, and interaction of molecules in general. A large number of databases have emerged that collect and provide information on cellular networks and protein interaction. However, most users and applications are not concerned with entire databases, but search for specific subsets of the data. For these purposes, it is essential to be able to describe the desired subnetwork as specific as necessary and as simple as possible. Despite the increased importance of network data in biology, there still exists no proper language for describing and retrieving specific parts of a network. In this paper, we introduce the pathway query language (PQL) for retrieving specific parts of large, complex networks. The language is based on a simple graph data model with extensions refle...

• Type: Conference
• Year: 2005
• Where: ECCB
• Authors: Ulf Leser
• Keywords: ECCB 2005, Pathway Query Language, PQL Query, Specific Parts