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  1. Pick a reference genome, and describe it to GREAT.
  2. Pick a reference gene set, and describe it to GREAT.
  3. Pick a GREAT gene regulatory domain assignment default rule.
  4. Identify (and/or generate from data) a set of ontologies with high-quality gene annotations for your species of interest.
  5. For each such ontology:
    1. Describe the ontology structure to GREAT.
    2. Map the ontology gene annotations to the reference gene set you chose in #2 (in case they are tagged with another reference gene set from yours). This step can be tricky.
    3. Provide a format to link from GREAT to a term details page for each term in the ontology.

And that's it. Interested parties are welcome to contact us for more detailed instructions.