This project seeks to create a web-accessible resource called the Genome KnowledgeBase (GKB). It will be a process-level annotation of the human genome, organized around integrated descriptions of molecular processes relevant to human biology. The GKB will take the form of a set of """"""""summations"""""""", a short electronic summary of what is known in a field analogous to a review article or book chapter, and written by an expert in the field. Each summation will be associated with a set of assertions that present the core facts of the field using a controlled vocabulary and grammar, as well as diagrams, animations and other graphics. The set of summations, including assertions and associated materials, will be stored in a relational database. Bench biologists will be able to browse the GKB like a book, or search the assertion database using a templating system. Bioinformaticians will be able to access the database directly in order to perform more sophisticated searches of the knowledgebase. The system will be extensively linked with other genomic databases.
Specific Aims : 1. To create software for authoring and editing GKB summations. 2. To create a database for storing these summations. 3. To create a web site infrastructure for displaying and searching summations. 4. To develop a management infrastructure for authoring 30 new summations per year, and updating 40 existing summations per year. 5. To publish 140 summations over the course of 5 years
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| Vastrik, Imre; D'Eustachio, Peter; Schmidt, Esther et al. (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biol 8:R39 |
| Joshi-Tope, G; Gillespie, M; Vastrik, I et al. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 33:D428-32 |
| Coghlan, Avril; Eichler, Evan E; Oliver, Stephen G et al. (2005) Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends Genet 21:673-82 |
| Joshi-Tope, G; Vastrik, I; Gopinath, G R et al. (2003) The Genome Knowledgebase: a resource for biologists and bioinformaticists. Cold Spring Harb Symp Quant Biol 68:237-43 |
