Hi,  I've collected annotations of a large number of genes from GO, and propagated annotations back to the GO ancestors.  Now I am trying to use these annotations for a general-purpose genomic functional graph (similar to genomic KG, etc. that are recently developed).  The problem is that those top-level terms (e.g., on levels 0 and 1) really don't make sense.  However, I don't really know at which level I should be cutting off the GO terms... And there are also papers cutting off terms based on the number of genes associated with such terms.  

Can someone recommend some papers or approaches that contain details on essentially trimming GO terms w.r.t GO level or #genes associated (whether before or after propagation of GOAs), etc.?

Maybe I should ask @go 
Suggestion from GO staff:

>I would suggest you use one of the GO subsets available http://geneontology.org/docs/download-ontology/

>The 'Generic GO subset' is one that should be broadly useful for your case, giving enough granularity to map genes to meanful classes. Organism-specific subsets are also available.
