There are several, each with design for specific and general uses (geneontology.org/docs/download-ontology/).
I am trying to solve your problem also, and I haven't been able to use the relations file yet. There must be a way to map relations to the OBO file (you may be able to use the "part_of" row in the OBO, I am unsure).
Here are all the unique labels in purl.obolibrary.org/obo/go.obo:
format-version, data-version, subsetdef, synonymtypedef, default-namespace, ontology, property_value, [Term], id, name, namespace, def, synonym, is_a, alt_id, subset, xref, disjoint_from, comment, is_obsolete, consider, relationship, intersection_of, created_by, creation_date, replaced_by, [Typedef], is_transitive, transitive_over, inverse_of, holds_over_chain, is_metadata_tag, is_class_level
The "relationship" row may be your best best for creating links in the graph.