'pathogen host interaction organism/tissue level phenotype'

[ValWood]

'pathogen host interaction organism level phenotype'

is this term used? It is a stub, with no children and it isn't very specific so I suspect ~now~ not.

I think we want to move away from cell/tissue/organism level groupings because they become hard to maintain. If possible I suggest obsoleting this therm (or provide examples where it will be required)

[ValWood]

same question to label "pathogen host interaction host tissue phenotype"

[CuzickA]

we had a ticket to review these terms #179

In PHI-branch we have

In Single species branch we have

[ValWood]

Do the all of the descendants of pathogen host interaction organism level phenotype and pathogen host interaction organism level phenotype have alternative parents?

If not, which terms do not have a different parent? I imagine they will all the host ones will group under some host defense-related phenotype. If we can make sure they are alternatively housed (or even just have them sitting at a high level for now until we need to group them), I think it would improve the organization.

I don't think these groupings are useful (I remember why we had them, because in fission yeast we are so used to working with cell level only phenotypes),I think I thought they would be necessary, but I think we should avoid this axis of classification. It would be over-complicated, and unnecessary- there are way more important features to group by.

[CuzickA]

Current 'pathogen host interaction host tissue phenotype' branch

1) These terms have no other parents. As discussed in #346 they would not really fit under 'host defense-induced'

2) Some of these terms have alternative parents, listed below 'effector-mediated suppression of host effector triggered immunity present' also has parent 'effector-mediated immune suppression phenotype' 'absence of pathogen necrotrophic effector-mediated host programmed cell death' also has parent 'pathogen effector mediated modulation of host immune system process' 'decreased extent of host-defence induced lesion by host hypersensitive response' also has parent ''presence of host-defense induced lesion by host hypersensitive response'' (Within this same branch) 'delayed host-defence induced lesion formation by host hypersensitive response' also has parent ''presence of host-defense induced lesion by host hypersensitive response'' (Within this same branch) 'presence of pathogen necrotrophic effector-mediated host programmed cell death' also has parent 'pathogen effector mediated modulation of host immune system process'

3)These terms are also housed under 'pathogen colonization of host phenotype' so could easily be moved out of tissue level

[CuzickA]

Current organism level branch

None of these terms have alternative parents

[ValWood]

Right, I would remove these terms. We might eventually end up adding a single grouping back but I think this would need to depend on the logical defs of all of the descendant terms, once they are added. There is clearly a problem enforcing a boundary to call chlorosis 'tissue level" and 'pigmentation' organism level.

Also these is a problem because the def A pathogen host interaction phenotype that is observed at the level of an individual organism (eg a worm host).

doe not state explicitly if we are referring here to the pathogen, or host tissue (of course usually this will be the host, but there are multicellular pathogens).

[CuzickA]

Move PHIPO:0001080 altered pathogen pigment accumulation within host and PHIPO:0001070 host organism viability with pathogen phenotype directly under 'pathogen host interaction phenotype' f47424e

obsolete PHIPO:0001067 pathogen host interaction organism level phenotype 92d4563

Now looks like this

[CuzickA]

Remove parent ''pathogen host interaction host tissue phenotype' from PHIPO:0001159 pathogen tissue to tissue migration within host phenotype 8109226

Now terms just under colonization

[CuzickA]

Move PHIPO:0000200 host chlorosis phenotype in presence of pathogen and PHIPO:0000445 pathogen host interaction host lesion formation phenotype directly under 'pathogen host interaction phenotype' 0a744a0

obsolete PHIPO:0000512 pathogen host interaction host tissue phenotype e0f1082

PHI branch now looks like this

[ValWood]

That looks good. We might eventually group the pathogen phenotypes and the host phenotypes in some way. This makes more sense logically and biologically, but we can do this at the end once we can see the full scope.

[CuzickA]

Great. I'll close this ticket for now.