NeXO is a gene ontology inferred directly from large-scale molecular networks. A gene ontology provides structured knowledge about the cellular components, processes, and functions encoded by genes. While most ontologies – including the highly successful Gene Ontology Database (GO) – are constructed through manual expert curation, NeXO is a data-driven gene ontology inferred directly from ‘omics data. NeXO (The Network Extracted Ontology) uses a principled computational approach which integrates evidence from hundreds of thousands of individual gene and protein interactions to construct a complete hierarchy of cellular components and processes. This data-derived ontology aligns with known biological machinery in the GO Database and also uncovers many new structures.

Documentation

• NeXO Website

Developer Resources

• Developer Resources
• Code Repository

How to Cite

• A gene ontology inferred from molecular networks. Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T., Nature Biotechnology 2013 Jan;31(1):38-45.
• NeXO Web: the NeXO ontology database and visualization platform. Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T., Nucleic Acids Res. 2014 Jan;42(Database issue).