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.
You can find the number of terms on each of the ontologies by going to AmiGO:
Under the 'Advanced Search' section in the middle of the page, use the drop-down menu to choose "Ontology". You don't need to type anything on the 'Quick search' box.
This action will send you to the 'Information about Ontology search' page. There, open the 'Ontology source' filter menu on the left. You will see that as of October-27-2015 the number of terms on per ontology were:
AmiGO is under constant development and our suggestion is that you frequently check back for the most recent information (and code, accordingly). The most recent proposal for a stable API is available from the
AmiGO 2 wiki manual.
Search results can be filtered using the filter menu on the left-hand side of the results page of an AmiGO search. Using the drop-down menu a variety of evidence codes or evidence code combinations can be added or removed to filter the set.
The GO Consortium has developed AmiGO for searching and browsing the Gene Ontology and the gene products that member databases have annotated using GO terms. Entering a search term into the quick search menu and choosing an auto-completed choice from the drop-down will return the summary page for that gene product or term. Alternatively terms can be entered by free text and the user will be allowed to choose whether the search will return genes, terms or annotations.