The GO is heavily reliant on the Web Ontology Language (OWL) for the construction and ongoing maintenance of the ontology. By using many tools developed by the OWL community, such as automated reasoning engines like Elk, we are able to automate tasks such as making sure edges in the graph are complete, and avoiding erroneous edges.
Our current procedures for using OWL are described in the conference paper Use of OWL within the Gene Ontology presented at the Proceedings of the 11th International Workshop on OWL: Experiences and Directions (OWLED 2014).
The OWL version of GO is available from the Ontology Download Page. The edition which is described in the OWLED paper is called "go-plus", and this includes not only the core GO, but also a network of relationships connecting GO to other ontologies.