Review annotations using extension 'regulates_o_occurs_in'

[pgaudet]

Hello,

We would like to stop relying on GO_REL, and start by removing relations that don't meet GO-CAM specifications.

Please review annotations using the relation 'regulates_o_occurs_in' in extensions:

https://docs.google.com/spreadsheets/d/1nNj09d_gs0Dv2u_Esq3MRMxwzJmy9FQl0mpjovNfuag/edit#gid=0

Impacted groups:

Assigned by
ARUK-UCL	975
BHF-UCL	39
FlyBase	2
MGI	3167
ParkinsonsUK-UCL	51
SynGO-UCL	1
UniProt	108
WB	2

Thanks, Pascale

[milarolo]

Do we have to delete the extension or replace it?

[pgaudet]

This is how we are planning to convert the annotations using extension 'regulates_o_occurs_in'.
If this correctly represents the data, you can just leave them and when we import these annotations into Noctua, they will be automatically converted:

Thanks, Pascale

[RLovering]

An example to curate?
PMID:21752258
Wnt is released from astrocyte (CL:0000127) and 'negative regulation of oxidative stress-induced neuron death' in midbrain dopaminergic neuron (CL:2000097). This would be captured in the AE field with:
? relation astrocyte (CL:0000127) and
occurs_in midbrain dopaminergic neuron (CL:2000097) rather than regulates_o_occurs_in
Added this example to the has_agent ticket #2618
Thanks
Ruth

[BarbaraCzub]

Related questions in this ticket: geneontology/noctua-models#44

[pgaudet]

See my answer in the other ticket #2618

[ukemi]

I believe this is out of date. We have a method for importing chain relations into GO-CAM models. These annotations can stay for now.

[RLovering]

Great I will remove my name and Barbara's from these
Best
Ruth

[ukemi]

Double check with @vanaukenk, but I think these all pass the import tests.

[pgaudet]

All done