[BioC] Why not protein ids for GO resp. GOstats?

[Kai Schlamp]

Hello, everyone,

sorry if my quesition is a bit silly, I am new to bioinformtics and 
Bioconductor.
Why does GOstats resp. the GO annotation package use entrez gene ids?
I thought, that GO terms are associated with proteins. And cause one 
gene can be translated to diffenent proteins, analyzation only with gene 
ids will perhaps be problematic.
Especially if the data consists of miRNAs or Proteins and you have to 
convert it back to gene ids.
So why does Bioconductor not use the annotation data from the Gene 
Ontology website. For example in the human annotation file, there are 
Uniprot and IPI identifiers annotated.

Best regards,
Kai