GO slims are cut-down versions of the GO ontologies. I need to delete some terms with low confidence(inferred from electronic annotation), but I cannot find the file including both the GOslim terms and evidence codes from the following links(http://downloads.yeastgenome.org/curation/literature/goslimmapping.tab). How to solve it except clustering the terms and inferring the evidence from the original GO annotation? Thanks a lot!
It sounds like you want to modify the Yeast GO slim based on the evidence used to assign GO terms to the yeast genes. In which case the file you want is the one describing the assignment of the GO terms ('gene_association.sgd.gz' available from SGD Downloads). Additional details of the Yeast GO slim, and other GO slims can be found on the GO web site. You may also want to look at the Yeast UniProt-GOA which is available from GOA.
Just wanted to confirm, from the Saccharomyces Genome Database, that Hamish is correct that mappings to GO Slim terms don't include evidence codes; the evidence codes are assigned to the original GO annotations and can be seen in the complete GO annotation file 'gene_association.sgd.gz'at the link that he cites. If you have more questions, we're happy to help. Please contact us at sgd-helpdesk@lists.stanford.edu.
