What methods are used for automatic annotation in GOA?
At present, GOA has five independent methods for automatic annotation. Four of these methods use mappings of concepts from external database systems that have been manually indexed to equivalent GO terms. The mappings used by GOA are of InterPro signatures, Enzyme Commission numbers, Swiss-Prot keywords and HAMAP families to GO terms. Further information on mapping files can be found at: http://www.geneontology.org/GO.indices.shtml. In addition GOA has recently provided a new electronic annotation technique in collaboration with the Ensembl group. Using the gene orthology obtained from the Ensembl Compara pipeline, GO terms from a source species have been projected onto one or more target species. This method has provided over 30,000 annotations to the human, mouse, rat, chicken, dog, bovine and Anopheles gambiae proteomes. Only one to one and apparent one to one orthologies are used and only manually-annotated GO terms with an evidence type of IDA, IEP, IGI, IMP or IPI are projected.
