Frequently Asked Questions:
Which files will be affected?
The new relationships will only be present in the file:
The other OBO format ontology files (gene_ontology_edit.obo, gene_ontology.1_2.obo, gene_ontology.1_0.obo and gene_ontology.obo) will remain unaffected by this change, as will the database.
Your parser or tool should NOT break unless it has been written such that it makes the assumption there are no inter-ontology links.
Even if the parser does not break, tools and databases may behave differently in that they may automatically classify gene products under an MF node where they previously did not.