There are several ways to do this:
- directly query the GO MySQL database
- use the GO::Parser perl module
- use the Bioconductor GO.db package
- use owltools

using mysql:

SELECT DISTINCT
 child.acc AS child_acc,
 child.name AS child_name,
 rel.acc AS rel,
 parent.acc AS parent_acc,
 parent.name AS parent_name
FROM
 term AS child,
 term AS parent,
 term AS rel,
 graph_path
WHERE  
    child.id=graph_path.term2_id AND
    parent.id=graph_path.term1_id AND
    rel.id = graph_path.relationship_type_id AND
    child.acc  in ("GO:0007049", "GO:0007050") AND
    parent.acc  in ("GO:0007049", "GO:0007050") AND
    child.acc!=parent.acc

;

example:

$ mysql -hmysql.ebi.ac.uk -ugo_select -pamigo -P4085 go_latest -A < input.sql

child_acc   child_name  rel parent_acc  parent_name
GO:0007050  cell cycle arrest   negatively_regulates    GO:0007049  cell cycle
GO:0007050  cell cycle arrest   part_of GO:0007049  cell cycle
GO:0007050  cell cycle arrest   regulates   GO:0007049  cell cycle