Clarify how our annotations get into GO and major public DBs

[Thyra]

Here are instructions by GO: http://www.geneontology.org/page/contributing-go

[Thyra]

According to this article, the established group working with an organism should maintain and submit all of the species' annotations in one master dataset (also removing duplications etc.). There are two columns in the GAF file, one should refer to whoever generated the annotations (us, maybe GOMAP etc.), the other column to the database maintaining them.

• [ ] We would have to find out when the sync dates are for each of our partner groups and try to have the annotations done before then.
• [ ] We should also contact the GOC to discuss our plans with them, but it doesn't list an email address or anything anywhere on that page, it simply refers back to the contributing-go guide which then refers to the contact page again. If we tell them about that we should also let them know that the page http://geneontology.org/contribute-annotations referenced by http://www.geneontology.org/faq/how-do-i-submit-annotations-go returns an access denied.
• [ ] It states in several places that when we submit annotations, they should all have at least one PMID referencing the publication about how these data were produced. We would like to have the annotations in the databases though before our paper is published. How do we do that?
• [ ] We have to create NCBI & UniProt mappings as best as possible.
• [ ] Should we include something like a GOMAP version in our annotations? I'm asking because if we for example ever upgrade the pipeline to use PANNZER2 or PSI-Blast the results would be different and I want to avoid confusion about how these annotations were generated. I asked Gokul about it but he doesn't want to introduce versioning until his paper is submitted. See this issue.

[iacornflake]

We can create a biorxiv publication in advance of submission to the journal so there is a DOI <<how do I make this specifically associated with, "* It states in several places that when we...">>

[Thyra]

Carolyn is in touch with Chris Mungall and we're figuring out how to submit the annotations while we are still writing the paper. One result already: Submitting the annotations to GOC will propagate to all other dbs, so that's all we need to worry about.

[wkpalan]

What is the db for wheat, rice, and cotton?