Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Clarify how our annotations get into GO and major public DBs #26

Open
Thyra opened this issue Feb 5, 2019 · 4 comments
Open

Clarify how our annotations get into GO and major public DBs #26

Thyra opened this issue Feb 5, 2019 · 4 comments
Assignees

Comments

@Thyra
Copy link
Member

Thyra commented Feb 5, 2019

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

@Thyra
Copy link
Member Author

Thyra commented Feb 5, 2019

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
Copy link

iacornflake commented Feb 6, 2019

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
Copy link
Member Author

Thyra commented Feb 20, 2019

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
Copy link

wkpalan commented Mar 8, 2019

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants