I there to all, I have some issue trying to retrieve all go terms for some uniprot entries. I have a vector of nearly 12000 uniprot entries, some are swissprot,some are trembl etc etc. And I want to retrieve for all of them the corresponding go terms.
When i run the R command:
major_proteins_GO_terms = getBM(attributes = c("uniprotsptrembl","go_id","name_1006","namespace_1003"),filters = c('uniprotsptrembl'),values = unlist(major_proteins_ids),mart = ensembl)
I get only a fraction of them. But the strange things is that if I select the entries non found, and launch another query like:
not_found_GO_terms = getBM(attributes = c("uniprotsptrembl","go_id","name_1006","namespace_1003"),filters = c('uniprotsptrembl'),values = not_found_proteins,mart = ensembl)
I can retrieve the GO terms i want. However also this element is not complete, and i have to launch recursively until the go terms for all the entries I want. This seems very strange, and I wanna know if someone has some knowledge on how to deal with that.
Someone has any ideas? This is happening, both with swissprot but also with trembl...
Thanks a lot!