- A decent genome assembly.
- A decent reference gene set.
- Gene annotations. Typically in the form of an ontology, and gene to ontology term mappings.
- A community of researchers actually taking measurements in user community for said species.
For species near enough to human for our own cis-regulation interests - practically all vertebrates - vertebrate species, you can help us consider additional species by sending us specific links to rich gene annotation resources unique to your species of interest.
For species more distantly related to human (say fly e.g. drosophila or arabidopsis) we will likely not do the curation ourselves. However, if you are seriously interested and capable, we can consider sharing our file format requirements with you and have you contribute this species into GREAT.
Here's what you'll need to do:
- Pick a reference genome, and describe it to GREAT.
- Pick a reference gene set, and describe it to GREAT.
- Pick a GREAT gene regulatory domain assignment default rule.
- Identify (and/or generate from data) a set of ontologies with high-quality gene annotations for your species of interest.
- For each such ontology:
- Describe the ontology structure to GREAT.
- 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.
- 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.