How to create the following files using SQL queries in R from GO.db, org.Sc.sgd.db, and org.Hs.eg.db, respectively.

gene_ontology.obo

gene_association.sgd

gene_association.goa_human

Please help me.

It seems you can get those files from geneontology directly:

http://www.geneontology.org/ontology/gene_ontology.obo

http://www.geneontology.org/gene-associations/

Is there a particular reason why you want to create them using SQL queries from GO.db, org.Sc.sgd.db, and org.Hs.eg.db?