NTR: 'cell viability phenotype' and re-structure

PHI-base / phipo

Pathogen-Host Interaction Phenotype Ontology

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NTR: 'cell viability phenotype' and re-structure #298

Open CuzickA opened 3 years ago

CuzickA commented 3 years ago

A single species cell phenotype that consists of the cell's disposition to survive and develop normally.

FYPO:0000004

ac678c8

CuzickA commented 3 years ago

Move terms under 'cell viability phenotype' 771f774

now looks like this

@jseager please could you let me know if below term been used in any sessions PHIPO:000939 asexual spore lysis absent

@ValWood what else did we want to change here?

CuzickA commented 3 years ago

Note the term 'PHIPO:0000513 inviable population' from the population branch corresponds to the high level PHI-base term 'lethal' NOT the 'inviable cell' level term above

ValWood commented 3 years ago

@ValWood what else did we want to change here?

I think it is OK for now we can move other things if we come across them.

CuzickA commented 3 years ago

@jseager please could you let me know if below term been used in any sessions PHIPO:000939 asexual spore lysis absent

If this term has not been used I will obsolete it and move the 'cell lysis' group under 'inviable cell'

CuzickA commented 3 years ago

@jseager please could you let me know if below term been used in any sessions PHIPO:000939 asexual spore lysis absent

If this term has not been used I will obsolete it and move the 'cell lysis' group under 'inviable cell'

CuzickA commented 3 years ago

See #297

CuzickA commented 3 years ago

Hi @jseager7 please could you let me know if below term been used in any sessions PHIPO:000939 asexual spore lysis absent

jseager7 commented 3 years ago

@CuzickA PHIPO:0000939 hasn't been used in any curation sessions, as of the time of writing.

CuzickA commented 2 years ago

Add exact synonym 'cytolysis' to 'cell lysis' and add 'GO:0019835' cytolysis to definition.

CuzickA commented 2 years ago

Discussion from https://github.com/PHI-base/curation/issues/107

Val's comment

@ValWood Should these terms be merged?

The host term annotations from the ATR1/RPP1 paper. These terms were always a bit tricky. Does it make sense to remove the information about the 'cause' of the cell death

Changing the presence of effector-independent host hypersensitive response -> inviable cell ?? for the first annotation and removing the second and third annotations?

However, only some of the cells within the leaf tissue will be undergoing HR.

ValWood commented 2 years ago

I don't understnad the question fully. I think you can keep these terms.

Don't you only need to change the label of "host cell death phenotype" to "cell death phenotype"

The descendants are OK.

CuzickA commented 2 years ago

The definition states it in the host and it looks like it is in subset 'host'

CuzickA commented 2 years ago

Hi @ValWood, are you suggesting 1) removing 'host' from the term label 2) removing 'host' from the definition 3) removing the in_subset 'host_phenotype' 4) would these 'cell death phenotypes' be grouped under 'cell viability phenotype'?