Nathan Dunn

incorporate frameshifts

20

==== - (mostly . . . allow exons to overlap), just for specific isoforms ==== as @cmdcolin noted, we have a bunch of code for frameshifts and they are in...

allow export of GO Annotations within GFF3

5

The idea is to allow a user to write their own export class if they have a different version of GFF3, Chado, etc. and then have that available the Sequence...

tighten up GO rules

1

- implement GO rules / restrictions: http://geneontology.org/docs/go-annotations/ - https://github.com/geneontology/go-site/tree/master/metadata/rules

add annotation extensions to GO spec and GPI output

2

from #2137 / #1134 I think these are important, but I think they can also come afterwards

add the ability to annotate "phenotype"

1

FYI @selewis add anything as you see fit.

The extra line return at the end of the fasta file causes extra space line error. ``` File /opt/temporary/apollo/113449-uploadme does not exist 2019-08-20 09:47:44,679 [http-nio-8080-exec-8] WARN apollo.TrackService - File /opt/temporary/apollo/113449-uploadme...

allow many-to-many gene to transcript

1

In some organisms a transcript may belong to multiple genes.

add Github Authentication

3

Similar to #115, but for using the github authentication. Can probably just copy this type of PR: https://github.com/geneontology/termgenie/pull/100

Deleting annotations from an organism as called from this service: https://github.com/GMOD/Apollo/blob/master/docs/web_services/examples/groovy/delete_annotations_from_organism.groovy calls this service: https://github.com/GMOD/Apollo/blob/master/grails-app/services/org/bbop/apollo/OrganismService.groovy#L58 This piece of code is very slow. It should be replaced with code that does,...