OBSOLETION: GO:0090650 cellular response to oxygen-glucose deprivation

[ValWood]

This term seems odd to be a compound term (the extensions should be compounded if necessary with a comma)

i.e. response to gluclose starvation,response to hypoxia

12 EXP mostly IEP

[pgaudet]

From the paper abstracts, oxygen-glucose deprivation is a way to induce ischemia, so a merge with GO:0002931 response to ischemia seems appropriate.

@RLovering @gthayman annotations are by your groups; is this proposal OK for you?

Thanks, Pascale

[RLovering]

yes sounds good. Hopefully no edits required by me?

[pgaudet]

No, not with a merge.

[gthayman]

I don't mean to be difficult, but I can't find a definition for 'ischemia' that doesn't refer to restricted blood flow. What I do find in the 10 papers we have annotated to GO:0090650, involving in vitro experiments, is that nine of them use the phrase 'oxygen-glucose deprivation', so the phrase seems commonly used in the literature. If you're going ahead with this merge, could we at least make sure that we retain 'response to oxygen-glucose deprivation' as an exact or related synonym? We weren't sure whether that happens automatically or not in merges. Thanks.

[RLovering]

This is a good point. especially based on the comment in this term record: Ischemia always results in hypoxia; however, hypoxia can occur without ischemia. Plus, thinking about this a bit more I am not convinced that how often the gene products involved in responding to oxygen deprivation will be the same as those responding to glucose deprivation. Maybe it would be more sensible to just delete the 'oxygen-glucose deprivation' and move all annotations to both parent terms 'oxygen' deprivation and 'glucose' deprivation?

Also based on the comment in the ischemia term record shouldn't this be a child term of GO:0001666 response to hypoxia? Perhaps the response to ischemia should be merged into GO:0001666 response to hypoxia. I guess there may be other aspects to responding to ischemia but I have a feeling that often experiments that cause ischemia are looking at the impact of low oxygen to an area of tissue/cells.

[ValWood]

Oh dear, response to terms...maybe I shouldn't have poked this one.... I always feel that they are only useful if used as extesnions/qualifiers of another term to give them some context (and prevent them being used just for expression changes with IEP). I'm happy for this to close it just seemed a bit odd...

[gthayman]

Sounds good.

[pgaudet]

@RLovering

Are you suggesting we merge

• GO:0090650 cellular response to oxygen-glucose deprivation
• GO:0090649 response to oxygen-glucose deprivation
• GO:0002931 response to ischemia should be merged into GO:0001666 response to hypoxia?

based on the comment in the ischemia term record shouldn't this be a child term of GO:0001666 response to hypoxia?

ischemia causes hypoxia, see https://en.wikipedia.org/wiki/Ischemia, so I don't think this is right?

WRT the merge I propose, PMID: 28064357 "The most frequently used in vitro model of cerebral ischemia is the combined oxygen and glucose deprivation (OGD)." So, this really does sound like this is the same ?

[pgaudet]

Discussing this one with @RLovering She mentions that this is not a normal process, and should be obsoleted.

Maybe some annotations can be rehoused to other terms, but this term is not within the scope of GO.

Thanks, Pascale

[pgaudet]

Dear all,

The proposal has been made to obsolete GO:0090650 cellular response to oxygen-glucose deprivation. The reason for obsoleteion is that this represents an assay to induce ischemia, which is not a normal process. There are 22 annotation left by MGI (2) and RGD (20), see https://github.com/geneontology/go-annotation/issues/4686.

There are no mappings to this term; this term is not present in any subset.

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/21284

Thanks, Pascale