makeOrgPackage: possible to add option to allow GO terms now in GO.db?
2
0
Entering edit mode
Keith Hughitt ▴ 180
@keith-hughitt-6740
Last seen 4 weeks ago
United States

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

annotationforge makeorgpackage go • 1.2k views
ADD COMMENT
0
Entering edit mode
Keith Hughitt ▴ 180
@keith-hughitt-6740
Last seen 4 weeks ago
United States

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

ADD COMMENT
0
Entering edit mode
Keith Hughitt ▴ 180
@keith-hughitt-6740
Last seen 4 weeks ago
United States

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After working on this a bit more, it appears that the main issue is that the GFF which I'm parsing included some (outdated?)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

ADD COMMENT

Login before adding your answer.

Traffic: 929 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6