Gene Ontology (GO) Knowledgebase
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A Gene Ontology (GO) Knowledgebase is an Ontology of Genes and Gene Products produced by the GO Gene Ontology Project.
- AKA: GO Gene Ontology|GO, GO Gene Ontology|Gene Ontology Database.
- Context:
- Example(s):
- AmiGO 2,
- ...
- Counter-Example(s):
- See: Entity Database, Uniprot Database, OBO Foundry, Database, Knowledgebase, Digital Repository.
References
2009
- (Gene Ontology, 2009) ⇒ http://www.geneontology.org/GO.downloads.database.shtml and http://www.geneontology.org/GO.doc.shtml#not
- It is important to clearly state the scope of GO, and what it does and does not cover. The preceding section explained the domains covered by GO; the following areas are outside the scope of GO, and terms in these domains would not appear in the ontologies.
- Gene products: e.g. cytochrome c is not in the ontologies, but attributes of cytochrome c, such as oxidoreductase activity, are.
- Processes, functions or components that are unique to mutants or diseases: e.g. oncogenesis is not a valid GO term because causing cancer is not the normal function of any gene.
- Attributes of sequence such as intron/exon parameters: these are not attributes of gene products and will be described in a separate sequence ontology (see the OBO website for more information).
- Protein domains or structural features.
- Protein-protein interactions.
- Environment, evolution and expression.
- Anatomical or histological features above the level of cellular components, including cell types.
- GO is not a database of gene sequences, nor a catalog of gene products. Rather, GO describes how gene products behave in a cellular context.
- GO is not a dictated standard, mandating nomenclature across databases. Groups participate because of self-interest, and cooperate to arrive at a consensus.
- GO is not a way to unify biological databases (i.e. GO is not a 'federated solution'). Sharing vocabulary is a step towards unification, but is not, in itself, sufficient. Reasons for this include the following:
- Knowledge changes and updates lag behind.
- Individual curators evaluate data differently. While we can agree to use the word 'kinase', we must also agree to support this by stating how and why we use 'kinase', and consistently apply it. Only in this way can we hope to compare gene products and determine whether they are related.
- GO does not attempt to describe every aspect of biology; its scope is limited to the domains described above.
- It is important to clearly state the scope of GO, and what it does and does not cover. The preceding section explained the domains covered by GO; the following areas are outside the scope of GO, and terms in these domains would not appear in the ontologies.
2006
- (Blake & Bult, 2006) ⇒ JA Blake, CJ Bult. (2006). “Beyond the Data Deluge: data integration and biontologies.” In: Journal of Biomedical Informatics
- Keywords_: Biomedical Text Mining, GO Gene Ontology.
2005
- (Doms & Schroeder, 2005) ⇒ Andreas Doms, and Michael Schroeder. (2005). “GoPubMed: exploring PubMed with the gene ontology.” In: Nucl. Acids Res., 33(suppl 2). doi:10.1093/nar/gki470
2004
- (Camon et al., 2004) ⇒ Evelyn Camon, Michele Magrane, Daniel Barrell, Vivian Lee, Emily Dimmer, John Maslen, David Binns, Nicola Harte, Rodrigo Lopez, and Rolf Apweiler. (2004). “The Gene Ontology Annotation (GOA) Database: Sharing Knowledge In Uniprot With Gene Ontology.” In: Oxford Journals Life Sciences Nucleic Acids Research, 32.