Networks for Knowledge

Biological networks are exploited in many ways for gaining new knowledge about biological systems. Graph analysis of networks may provide useful characteristics about the design principles and mechanisms of pathways and regulation processes. Building networks as an object of scientific study, however, may prove to be a painstaking task, calling for elaborate database and literature surveying in order to get a comprehensive network representation in a topological correct format. We have used such elaborate approaches for instance for building logical models with predictive power for anti-cancer drug efficacy. Alternatively, the Semantic Web brings promises of enhanced sharing and use of biological knowledge. Semantic Systems Biology (SSB) aims to utilise semantic web resources as an additional toolkit for integrative and modeling approaches aiming to analyse and understand biological systems. The SSB group at the Norwegian University of Science and Technology works towards ways to reach out to end-users/biologists in order to create some user-pull to direct further implementations of semantic web resources. One of our efforts resulted in the construction of a resource for gene expression regulation analysis: the Gene eXpression Knowledge Base GeXKB. GeXKB provides a resource for finding novel network candidates potentially involved in gene expression regulation. The construction of GeXKB prompted us to start efforts in the direction of `semantifying´ data from the source: the curation of Transcription Factor information from scientific literature. This resulted in the TFcheckpoint database (www.tfcheckpoint.org), and the publication of a set of curation guidelines for other volunteer curators to join in this effort. This work inspired us to see if we could bring together the global community interested in the domain of transcription regulation research, and we are in the process of initiating GRECO: the Gene Regulation Consortium. GRECO aims to facilitate communica- ion between resource and technology providers, paving the way to develop one virtual integrated high quality knowledge resource that could be used for instance in the field of regulatory network building and analysis.