If I am understanding what you want correctly you could use bioMart to query this information. You would probably want to apply some filters on evidence type etc. but you should be able to get what you want from the GO database. Something like this would work in R:
library("biomaRt") # Select appropriate database ensembl <- useMart("ensembl") ensembl <- useDataset("hsapiens_gene_ensembl", mart=ensembl) # set up any filters and their appropriate values filters <- c("hgnc_symbol") gene <- c("PTEN", "PRLR") values <- as.list(gene) # select attributes to return attributes <- c("hgnc_id", "namespace_1003", "name_1006", "go_id", "go_linkage_type", "definition_1006") # perform biomart query getBM(attributes=attributes, filters=filters, values=values, mart=ensembl)
or you could use biomarts web resource.