The GOBASE: an information management system for Gene Ontology

Recent research in biology has discovered that a large portion of genes that are responsible for core biological functions are conserved in most or all living cells. This has initiated development of, and emphasizes the importance of, common annotation facilities for biological knowledge, as features and functions of an unknown gene can be related to or inferred from those of a similar and well-studied gene. The gene ontology (`GO´), a collection of three ontologies each defining a specialization hierarchy of biological terms, has been an extraordinary focus of this effort. This paper describes GOBASE, a publicly-available graph database for query and visualization of GO information. There are existing browsers for visualizing GO information, but GOBASE provides a more powerful interface, allowing both interactive query and interactive annotation of GO terms with other data sources. We focus on how GOBASE achieves interactive annotation and query and its tight interactions with backend databases