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Next: The TAMBIS Ontology Up: A Survey of Current Previous: The Ontology for Molecular

The Gene Ontology

The Gene Ontology (GO), like the MBO, has database annotation as its main purpose. GO, however, has grown up from within a group of databases, rather than being proposed from outside. GO's scope is also narrower; instead of attempting to describe the whole of molecular biology captured in the community's databases, GO seeks to capture information about the role of gene products within an organism. The classification of gene function by Riley [17] has a similar scope, but for E. coli only. GO was initially created to reflect Drosophila gene function via the Flybase database [18], but has expanded to encompass mouse yeast and gene expression databases, and is expected to expand further. Thus, the main use of GO is as a controlled vocabulary for conceptual annotation of gene product function, process and location in databases.

GO lacks any upper-level organising ontology. It is essentially composed of three hierarchies, representing the function of a gene product; the process in which it takes place and cellular location and structure. GO contains a wide range of concepts, and provides a rich level of detail in its three hierarchies. It uses the `is a kind of' and `is part of ' relationships to describe the role of gene products. It currently has over 5000 concepts within the ontology.

GO defines a fine level of conceptual detail: Double stranded DNA binding proteins; Transcription factors; cytosolic chaperones; muscle motor protein; learning and memory; blood coagulation; male genital morphogenesis; ventral pattern formation; and many pathways, transport and signal transduction systems. GO uses multiple inheritance in the `is a kind of' hierarchy in forming some of the concepts and there is some use of an `is part of' relationship. Many of the relationships held by concepts, however, remain implicit in GO. For example, the concept `succinate (cytosol) to fumarate (mitochondrion) transporter' implicitly holds properties about location and orientation in the mitochondrial membrane etc.


next up previous
Next: The TAMBIS Ontology Up: A Survey of Current Previous: The Ontology for Molecular
Robert Stevens 2001-07-19