title: NeXO Web: the NeXO ontology database and visualization platform.
abstract: The Network-extracted Ontology (NeXO) is a gene ontology inferred directly from large-scale molecular networks. While most ontologies are constructed through manual expert curation, NeXO uses a principled computational approach which integrates evidence from hundreds of thousands of individual gene and protein interactions to construct a global hierarchy of cellular components and processes. Here, we describe the development of the NeXO Web platform (http://www.nexontology.org)-an online database and graphical user interface for visualizing, browsing and performing term enrichment analysis using NeXO and the gene ontology. The platform applies state-of-the-art web technology and visualization techniques to provide an intuitive framework for investigating biological machinery captured by both data-driven and manually curated ontologies.
authors.affiliation: Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Janusz
authors.initials: J
authors.lastname: Dutkowski
authors.forename: Keiichiro
authors.initials: K
authors.lastname: Ono
authors.forename: Michael
authors.initials: M
authors.lastname: Kramer
authors.forename: Michael
authors.initials: M
authors.lastname: Yu
authors.forename: Dexter
authors.initials: D
authors.lastname: Pratt
authors.forename: Barry
authors.initials: B
authors.lastname: Demchak
authors.forename: Trey
authors.initials: T
authors.lastname: Ideker
mesh_terms: D003196:Computer Graphics; D030541:Databases, Genetic; D004843:Epistasis, Genetic; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D020407:Internet; D025941:Protein Interaction Mapping