#10991 cellular protection against oxidative stress

[RFoulger]

1/ Following on from our discussions on 'response to oxidative stress' terms, and email discussions with Paola about cell death, I'd like to add in the following terms:

cell death in response to oxidative stress ; GO:NEW1
neuron death in response to oxidative stress ; GO:NEW2
cell death in response to hydrogen peroxide ; GO:NEW3
neuron death in response to hydrogen peroxide ; GO:NEW4

I'll tie them into the existing terms and their children:
programmed cell death in response to reactive oxygen species ; GO:0097468
hydrogen peroxide-mediated programmed cell death ; GO:0010421

As Paola stated, we're not saying anything about the mechanism of cell death here (we don't know how programmed it is, just that it happens in response to an oxidative stress stimulus, but often this is all the paper assays). I'll add comments to warn (but for now, not restrict) against use for direct annotation.

2/ These terms are needed to add in the corresponding regulation terms in TG for annotation of the protectants/antioxidants. Note that I'll be tweaking the names (not the relationships) of the regulation terms to make them human-readable:

negative regulation of oxidative stress-induced cell death
negative regulation of oxidative stress-induced neuron death
negative regulation of hydrogen peroxide-induced cell death (optional)
negative regulation of hydrogen peroxide-induced neuron death (optional)

Therefore I'll add definition comments to each to say that if any evidence is known about the specific mechanism of death, this should be captured using a more granular term (e.g. regulation of apoptosis).

3/ Tweak name of GO:1902175 and children to make it clearer where the stress trigger is acting:
from:
regulation of intrinsic apoptotic signaling pathway in response to oxidative stress
to:
regulation of oxidative stress-induced intrinsic apoptotic signaling pathway

Related SF items:
https://sourceforge.net/p/geneontology/ontology-requests/10927/ (response to oxidative stress)
https://sourceforge.net/p/geneontology/ontology-requests/10878/ (H202 and cell death)
https://sourceforge.net/p/geneontology/ontology-requests/10098/ (cell death)

Listing here for any comments. Will go ahead and edit next week if not.

Thanks!

[RFoulger]

New terms (complete with warning against direct manual annotation):

cell death in response to oxidative stress ; GO:0036473
neuron death in response to oxidative stress ; GO:0036475
cell death in response to hydrogen peroxide ; GO:0036474
neuron death in response to hydrogen peroxide ; GO:0036476

renamed GO:1902175 and children
from: regulation of intrinsic apoptotic signaling pathway in response to oxidative stress
to: :
regulation of oxidative stress-induced intrinsic apoptotic signaling pathway

left to do on this ticket: TG regulation terms

[RFoulger]

TG terms:
id: GO:1903201
name: regulation of oxidative stress-induced cell death

id: GO:1903202
name: negative regulation of oxidative stress-induced cell death

id: GO:1903203
name: regulation of oxidative stress-induced neuron death

id: GO:1903204
name: negative regulation of oxidative stress-induced neuron death

id: GO:1903205
name: regulation of hydrogen peroxide-induced cell death

id: GO:1903206
name: negative regulation of hydrogen peroxide-induced cell death

id: GO:1903207
name: regulation of hydrogen peroxide-induced neuron death

id: GO:1903208
name: negative regulation of hydrogen peroxide-induced neuron death

TO_DO: Just need to look at apoptosis terms-from recent papers...