title: Comparison of functional annotation schemes for genomes.
abstract: In this paper we survey a number of functional classification schemes applicable to genomes. We present the concepts of depth, breadth and resolution as descriptors of the schemes' scope and architecture and compare selected classifications according to these criteria. We also generate a 'Combined Scheme' against which we map six classifications which we believe are representative of the range currently available. The mapping allows the generation of 'FuncWheels', which are graphical representations of hierarchical classification schemes. They are used to illustrate similarities and differences in functional space coverage. This survey highlights many issues related to the design and implementation of gene product functional classifications, which are discussed in the light of emerging 'second-generation' schemes.
authors.affiliation: Ludwig Institute for Cancer Research, 91 Riding House Street, London, W1P 8BT, UK. rison@biochem.ucl.ac.uk
authors.forename: S C
authors.initials: SC
authors.lastname: Rison
authors.forename: T C
authors.initials: TC
authors.lastname: Hodgman
authors.forename: J M
authors.initials: JM
authors.lastname: Thornton
mesh_terms: D000818:Animals; D003196:Computer Graphics; D030541:Databases, Genetic; D016678:Genome; D016680:Genome, Bacterial; D016681:Genome, Fungal; D018745:Genome, Plant; D023281:Genomics; D020407:Internet; D051379:Mice; D011506:Proteins / Q000145:classification* / Q000502:physiology*; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins