I'm trying to map lists of proteins to GO slim chembl terms (http://www.geneontology.org/page/go-slim-and-subset-guide). In QuickGO (https://www.ebi.ac.uk/QuickGO/slimming) one can list all gene associations to a selected GO slim, resulting in 394,897,572 associations in the case of goslim_chembl. I could use these annotations to look up my proteins and extract the GO terms, however one can only download up to 50000 annotations.
Does anybody know how to obtain a (GAF) file with all goslim_chembl annotations? Or another way to do the mapping? I have hundreds of lists of proteins, so I need to do it programmatically, not by manually entering protein lists in a user interface.