Gene Ontology: tool for the unification of biology

Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

[1]  M. Wigler,et al.  Functional homology of mammalian and yeast RAS genes , 1985, Cell.

[2]  D. Botstein,et al.  Yeast: an experimental organism for modern biology. , 1988, Science.

[3]  B. Barrell,et al.  Life with 6000 Genes , 1996, Science.

[4]  Tim J. P. Hubbard,et al.  SCOP: a structural classification of proteins database , 1998, Nucleic Acids Res..

[5]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL , 1997, Nucleic Acids Res..

[6]  M. Boguski,et al.  Genome cross-referencing and XREFdb: Implications for the identification and analysis of genes mutated in human disease , 1997, Nature Genetics.

[7]  K. Gould,et al.  Myb-Related Schizosaccharomyces pombe cdc5p Is Structurally and Functionally Conserved in Eukaryotes , 1998, Molecular and Cellular Biology.

[8]  J. Berg.  Genome sequence of the nematode C. elegans: a platform for investigating biology. , 1998, Science.

[9]  Andrew Smith.  Genome sequence of the nematode C-elegans: A platform for investigating biology , 1998 .

[10]  J. Cherry,et al.  Arabidopsis thaliana: a model plant for genome analysis. , 1998, Science.

[11]  Michael Ruogu Zhang,et al.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.

[12]  B. Tye.  MCM proteins in DNA replication. , 1999, Annual review of biochemistry.

[13]  Dmitrij Frishman,et al.  MIPS: a database for genomes and protein sequences , 1999, Nucleic Acids Res..

[14]  Kara Dolinski,et al.  Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure , 1999, Nucleic Acids Res..

[15]  Miguel A. Andrade-Navarro,et al.  Automated genome sequence analysis and annotation , 1999, Bioinform..

[16]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[17]  A. Munnich,et al.  Conservation of the Caenorhabditis elegans timing gene clk-1 from yeast to human: a gene required for ubiquinone biosynthesis with potential implications for aging , 1999, Mammalian Genome.

[18]  Rolf Apweiler,et al.  A novel method for automatic functional annotation of proteins , 1999, Bioinform..

[19]  Stephen M. Mount,et al.  The genome sequence of Drosophila melanogaster. , 2000, Science.

[20]  R. Lin,et al.  Biochemical and Genetic Conservation of Fission Yeast Dsk1 and Human SR Protein-Specific Kinase 1 , 2000, Molecular and Cellular Biology.

[21]  Peter B. McGarvey,et al.  The Protein Information Resource (PIR) , 2000, Nucleic Acids Res..

[22]  Janan T. Eppig,et al.  GXD: a Gene Expression Database for the laboratory mouse: current status and recent enhancements , 2000, Nucleic Acids Res..

[23]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[24]  Michael Y. Galperin,et al.  The COG database: a tool for genome-scale analysis of protein functions and evolution , 2000, Nucleic Acids Res..

[25]  Amos Bairoch,et al.  The ENZYME database in 2000 , 2000, Nucleic Acids Res..

[26]  Michael E. Cusick,et al.  The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information , 2000, Nucleic Acids Res..

[27]  Judith A. Blake,et al.  The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse , 2000, Nucleic Acids Res..

[28]  Kara Dolinski,et al.  Integrating functional genomic information into the Saccharomyces Genome Database , 2000, Nucleic Acids Res..

[29]  Evelyn Camon,et al.  The EMBL Nucleotide Sequence Database , 2000, Nucleic Acids Res..

[30]  Hideaki Sugawara,et al.  DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams , 2000, Nucleic Acids Res..

[31]  Dmitrij Frishman,et al.  MIPS: a database for genomes and protein sequences , 1999, Nucleic Acids Res..