GSO: A semantic web ontology to capture 3D genome structure

More and more evidences indicate that the 3D conformation of eukaryotic genome plays important functional role in the cell. While extensive experimental investigations have been performed to study such structurefunction relationships using techniques such as Hi-C methods, there is no data standard to capture the 3D conformation of the genome. In previous work, we have developed an object-oriented framework, Genome3D, to integrate, model and visualize human genome in 3-dimension. We report here about a high level ontology, Genome Structure Ontology (GSO), to capture the 3D conformation of eukaryotic genome. GSO captures the structural organization of eukaryotic genome at levels ranging from chromosome, to 30nm fiber, to nucleosome and then to the atomic level of DNA. We believe such ontology could play a significant role in annotating, analyzing and describing molecular data for the 3D conformation of eukaryotic genome.