Hello, I want a way to generate a gene ontology term (GO term) and gene id association file. On the gene ontology website, I think I can get gene id and GO term associations, but only the most specific GO term is associated with the gene id. The web app Funcassociate2 (http://llama.mshri.on.ca/funcassociate_client/html/) allows downloading a file (from the Download Go Associations button) that has the same format.
However, what I am looking for is a file that gives all GO terms associated with a gene higher up in the hierarchy as well. That is, if a GO term "A" annotates a gene, then the file should give that all parents "A" annotate the gene as well. I'm looking for a tab separated file (or similar like XML) similar to the file format from Funcassociate2 that lists each of these GO terms and gene associations.
I know that I could write a program myself to do this with the information that I have, but what I really want to know is if there is an existing tool that will produce the file in the format that I am looking for. If a program could produce this information from a given set of genes, that'd be great.