FP-regulates
Frequently Asked Questions:
Will my parser break?
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.
Can I strip out the inter-ontology links?
We will provide a lightweight script that can do this. In addition, we may deploy a 'dumbed-down' version of the ontology with only is_a and part_of links. This will have the effect of eliminating the inter-ontology regulates links
How do I calculate transitive closure?
Which files will be affected?
Both of the OBO format ontology files (gene_ontology_edit.obo and gene_ontology.obo) will be affected by this change, as will the database. The only files that will be unaffected are the deprecated GO format files.