I want to use the database files but...

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The *.txt files must be imported into a MySQL instance using mysqlimport. They are not intended to be loaded into excel or parsed using custom tools. Why are so many of the .txt files empty?

For some exports of the GO database, some tables will necessarily be empty. For example, the termdb dump by design omits any data on genes or gene associations, so the corresponding tables are mepty. MySQL requires a file be present for every table, hence there will be some tables with 0 rows in the .txt files.