All binary interactions evidences in the IntAct database, including those generated by Spoke expansion of co-complex data, are clustered to produce a non-redundant set of protein pairs. Each binary pair is then scored, using a simple addition of the cumulated value of a weighted score for the interaction detection method and the interaction type for each interaction evidence associated with that binary pair.
It is possible and usually expected for a single gene / gene product to be associated with more than one GO term. The fact that you may have found that there are two or more different GO terms associated with a single gene / gene product in your results should not be a cause for concern.
The Gene Ontology allows users to describe a gene / gene product in detail, considering three main aspects: its molecular function, the biological process in which it participates, and its cellular location:
This very useful BIOSTARS thread clarifies "How Do I Do Simple GO Term Lookup Given A Gene (Or mRNA) Identifier?"
You might find these responses useful when trying to simply create a list of GO terms associated with a given ID- and when you are not looking to conduct enrichment analyses - using a programatic approach.
These are some of the differences between EBI-GOA (QuickGO) and GO Central (AmiGO) when it comes to entities.
GO Central recommends that GAF annotations are made to genes, that is 1:1 equivalents. In GOA (and consequently in QuickGO) annotations are made to proteins, and there may be multiple proteins per gene, sometimes representing different isoforms. You will see this reflected in different numbers for mouse annotations for example.
The filtered version available on the GO Download's site (gene_association.goa_uniprot_noiea ) does not contain annotations for
those species where a different Consortium group is primarily responsible