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      Gene Ontology: tool for the unification of biology

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          Abstract

          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.

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          The COG database: a tool for genome-scale analysis of protein functions and evolution.

          R. L. Tatusov (2000)
          Rational classification of proteins encoded in sequenced genomes is critical for making the genome sequences maximally useful for functional and evolutionary studies. The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on a phylogenetic classification of the proteins encoded in 21 complete genomes of bacteria, archaea and eukaryotes (http://www. ncbi.nlm. nih.gov/COG). The COGs were constructed by applying the criterion of consistency of genome-specific best hits to the results of an exhaustive comparison of all protein sequences from these genomes. The database comprises 2091 COGs that include 56-83% of the gene products from each of the complete bacterial and archaeal genomes and approximately 35% of those from the yeast Saccharomyces cerevisiae genome. The COG database is accompanied by the COGNITOR program that is used to fit new proteins into the COGs and can be applied to functional and phylogenetic annotation of newly sequenced genomes.
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            Cluster analysis and display of genome-wide expression patterns

            M. B. Eisen, P. T. Spellman, P. O. Brown … (1999)
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              The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

              A Bairoch, R. Apweiler (2000)
              SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include format and content enhancements, cross-references to additional databases, new documentation files and improvements to TrEMBL, a computer-annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDSs) in the EMBL Nucleotide Sequence Database, except the CDSs already included in SWISS-PROT. We also describe the Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT. SWISS-PROT is available at: http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/
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                Author and article information

                Journal
                Title: Nature Genetics
                Abbreviated Title: Nat Genet
                Publisher: Springer Science and Business Media LLC
                ISSN (Print): 1061-4036
                ISSN (Electronic): 1546-1718
                Publication date Created: May 2000
                Publication date (Print): May 2000
                Volume: 25
                Issue: 1
                Pages: 25-29
                Article
                DOI: 10.1038/75556
                SO-VID: 34aa5ab9-db72-4e8d-b42d-84626f797984
                Copyright © © 2000
                License:

                http://www.springer.com/tdm

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