Hello,

Would it be possible to modify makeOrgPackage to allow for GO that are not currently in the most recent GO.db?

I would be happy to submit a pull request with the functionality, if you think it is reasonable to include, but wanted to check before I made the changes.

On a related note, is there a dedicated bug tracker for AnnotationForge?

Cheers,

Keith

On second thought, it appears that the terms which I thought were being excluded for being too new have actually been deprecated and removed in the past few months, so this functionality is probably not that useful.

Unless anyone else is interested in this, please feel free to ignore for now.

Keith

Related question:

Would it make sense for makeOrgPackage to map GO terms synonyms to primary GO terms? Or should this be left up to the inidividual database creators?

After working on this a bit more, it appears that the main issue is that the GFF which I'm parsing included some (outdated?) secondary GO identifiers.

For example, "GO:0032313" is an alternative identifier for "GO:0043087"

Currently, the term will simply be ignored. It might not be too hard to take the list of terms which are not in keys(GO.db) and check if they are synonyms for terms in the database, and then map to primary terms.

What do you think?

Keith