'pathogen-induced host substance level phenotypes -> host defense-induced

[ValWood]

Thes labels: 'decreased level of host callose deposition induced by pathogen' 'decreased level of host reducing sugar in apoplast induced by pathogen' 'decreased level of host RNA involved in a pathogen interaction' etc

might read better as 'decreased level of pathogen-interaction induced host callose deposition ' 'decreased level of pathogen-interaction induced host reducing sugar in apoplast' 'decreased level of pathogen-interaction induced host RNA'

(I prefer pathogen-interaction induced too, because then it is clearer that this is a host response to the pathogen, rather than that pathogen is evolved to induce the host process.

[ValWood]

Or even "pathogen-infection" induced?

[ValWood]

Or decreased level of host defense-induced callose deposition This might be much better because it distinguishes from a single species phenotype and is much clearer that the host is doing the inducing.

[ValWood]

label "pathogen-induced host oxidative burst level phenotype" would become label "host defense-induced oxidative burst level phenotype"

[ValWood]

I think this would be much clearer. If you agree this entire branch would be labelled in this way.

[ValWood]

There is a precedence for this term label pattern: 'host defense induced acidification in phagolysome present' 'host defense induced alkalization present'

I would use throughout for all host defense induced process instead of pathogen-induced host process which is ambiguous if you do not read the definition.

[ValWood]

label "pathogen host interaction host tissue phenotype" -> host defense-induced host tissue phenotype

'host chlorosis phenotype in presence of pathogen' ->'host defense-induced chlorosis phenotype'

[CuzickA]

I think we have discussed this before and decided that we needed to have both "pathogen" and "host" within the PHI-branch term names to avoid confusion with any similar terms in the single species branch.

I agree that "host defense-induced blah" reads better than the current labels. But, the difficulty is that we will gradually be adding more "host only" terms to the single species branch and in some cases the same phenotypes may be seen in the "host only" as the "pathogen and host" branch terms. The "host only" expt may have a chemistry condition added to trigger a defense response or perhaps the host genotype alteration results in HR cell death WITHOUT a pathogen. We have an example of the host only HR terms here

This option with both "pathogen" and "host" could work

'decreased level of pathogen-interaction induced host callose deposition ' 'decreased level of pathogen-interaction induced host reducing sugar in apoplast' 'decreased level of pathogen-interaction induced host RNA'

[ValWood]

I think we have discussed this before and decided that we needed to have both "pathogen" and "host" within the PHI-branch term names to avoid confusion with any similar terms in the single species branch.

This is true for the terms where this confusion might exist. I can't immediately think of an example though for the terms which are "host defense induced". If they are 'defense induced" they must be part of a pathogen-host interaction mustn't they?

To me ->'host defense-induced chlorosis phenotype' is easier for a human to parse than host chlorosis phenotype in presence of pathogen'

and 'decreased level of host defense-induced callose deposition ' easier than 'decreased level of pathogen-interaction induced host callose deposition '

(but they are semantically equivalent and the existing labels could. be exact synonyms.

and there is no ambiguity "defense-induced" == "in presence of pathogen" and the definitions would reiterate this.

If it were a host-only phenotype it would need to be decreased level of host callose deposition

I think the defense-induced labels are easier for people working outside the pathogen-host interaction space to understand too (as we discovered from the discussions with Ensembl the word 'interaction is very loaded). Although if you think it doesn't help then you can keep as it is.

[CuzickA]

Yes, I agree the "defense-induced" terms are easier to understand.

I realise that the terms that are throwing me are the chlorosis terms. 'host chlorosis phenotype in presence of pathogen' ->'host defense-induced chlorosis phenotype'

Chlorosis can occur for a variety of reasons

I think we chose to say '... in the presence of pathogen' as it might be unclear as to whether the host-defence is activated or whether the pathogen is causing the chlorosis.

[ValWood]

Yes you are right, the pathogen could be causing the chlorosis, (most likely?). So we can only do this in the cases where the phenotype is always a defense response (based on current knowledge), maybe that is not often?

[CuzickA]

This is currently what the "pathogen-induced host substance level phenotypes" branch looks like

[CuzickA]

PHIPO:0001196 pathogen-induced host substance level phenotype (add as exact synonym) -> host defence-induced substance level phenotype 58cf11d

[CuzickA]

Edit term labels for callose terms b14f009

PHIPO:0001015 decreased level of host callose deposition induced by pathogen -> decreased level of host defense-induced callose deposition

PHIPO:0001014 increased level of host callose deposition induced by pathogen -> increased level of host defense-induced callose deposition

PHIPO:0001083 pathogen-induced callose deposition in host present -> host defense-induced callose deposition present

[CuzickA]

Edit term labels for reducing sugar terms 53a4132

PHIPO:0001226 decreased level of host reducing sugar in apoplast induced by pathogen -> decreased level of host defense-induced reducing sugar in apoplast

PHIPO:0001227 increased level of host reducing sugar in apoplast induced by pathogen -> increased level of host defense-induced reducing sugar in apoplast

[CuzickA]

Edit term labels for some ROS terms 573a1d5

PHIPO:0000924 pathogen-induced host oxidative burst level phenotype -> host defense-induced oxidative burst level phenotype

PHIPO:0001192 decreased level of pathogen-induced host reactive oxygen species -> decreased level of host defense-induced reactive oxygen species

PHIPO:0001193 increased level of pathogen-induced host reactive oxygen species -> increased level of host defense-induced reactive oxygen species

PHIPO:0000928 pathogen-induced host reactive oxygen species absent -> host defense-induced reactive oxygen species absent

PHIPO:0000927 pathogen-induced host reactive oxygen species present -> host defense-induced reactive oxygen species present

Just to note we also have terms for pathogen ROS production within host

single species terms

[CuzickA]

Edit term labels for phenolic compound terms 736f712

PHIPO:0001161 pathogen-induced host phenolic compound absent -> host defense-induced phenolic compound absent

PHIPO:0001230 pathogen-induced host phenolic compound absent -> host defense-induced phenolic compound present

[CuzickA]

Edit term labels for some RNA terms 85e69b4

PHIPO:0001174 decreased level of host RNA involved in a pathogen interaction -> decreased level of host defence-induced RNA

PHIPO:0001104 increased level of host RNA involved in a pathogen interaction -> increased level of host defence-induced RNA

PHIPO:0001231 host RNA involved in a pathogen interaction present -> host defence-induced RNA present

[CuzickA]

PHIPO:0000991 increased level of host protein involved in a pathogen host interaction -> increased level of host defence-induced protein

7a43a72

[CuzickA]

Hi @ValWood

I've made some changes to the term labels for this branch, please could you have a check though.

I haven't changed these three terms yet. Should I switch out the '-related' for '-induced' to make the terms uniform? I think in these example that the literature commonly uses '-related' but this would still be available as an exact synonym. 'decreased level of host defense-related RNA involved in a pathogen interaction' 'host defense-related RNA involved in a pathogen interaction present' 'increased expression of a host defense-related protein involved in a pathogen interaction'

[ValWood]

Yes I think defence-induced is more consistent, and as you say related will be a synonym. Although they are called defence-related they become 'defence-induced' once increased expression is observed.

All looking good, there term labels in general are becoming much more understandable for a user (well at least to me!), and the structure overall is much improved.

[CuzickA]

@ValWood Should the below terms be merged? There is a subtle difference in the definitions which has been overlooked in adding 'host defense-induced'. The former terms relate to host defense substance whilst the latter refer to a host substance which may not be related to defense.

PHIPO:0001144 'decreased level of host defense-related RNA involved in a pathogen interaction' Def: A pathogen host interaction phenotype, in which the level of host defense-related RNA usually present during infection is lower than normal. -> PHIPO:0001174 decreased level of host defense-induced RNA Def: A pathogen host interaction phenotype, in which the level of host RNA usually present during infection is lower than normal.

PHIPO:0001235 'host defense-related RNA involved in a pathogen interaction present' Def: A pathogen host interaction phenotype, in which the host defense-related RNA usually present during infection is normal (i.e. indistinguishable from wild type). -> PHIPO:0001231 host defense-induced RNA present Def: A pathogen host interaction phenotype, in which the host RNA usually present during infection is normal (i.e. indistinguishable from wild type).

PHIPO:0000992 'increased expression of a host defense-related protein involved in a pathogen interaction' Def: A pathogen host interaction phenotype, in which the level of host defense-related protein usually present during infection is higher than normal. ->PHIPO:0000991 increased level of host defense-induced protein Def: A pathogen host interaction phenotype, in which the level of host protein usually present during infection is higher than normal.

@jseager7 please could you look up whether the following terms have been used in annotations (or if they are just grouping terms) PHIPO:0001174 decreased level of host defense-induced RNA PHIPO:0001231 host defense-induced RNA present PHIPO:0000991 increased level of host defense-induced protein

[jseager7]

@CuzickA here's the publications annotated with these terms:

• PHIPO:0001174 'decreased level of host defense-induced RNA'
  • PMID:27819043
  • PMID:31804478
• PHIPO:0001231 'host defense-induced RNA present'
  • PMID:28720735
  • PMID:22241993
  • PMID:31804478
• PHIPO:0000991 'increased level of host defense-induced protein'
  • (no sessions)

[ValWood]

There is a subtle difference in the definitions which has been overlooked in adding 'host defense-induced'. The former terms relate to host defense substance whilst the latter refer to a host substance which may not be related to defense.

Right, but if they are increased in response to the pathogen, then they are also defence induced aren't they?

[CuzickA]

Okay, so I should be able to merge the above terms.

[CuzickA]

@ValWood Just wanted to check whether these new term labels still make sense for the necrotrophs?

PMID:27819043 Snn1 is a host susceptibility locus

PMID:22241993 Just to note that the inverse GfG AE is really important here to indicate whether the outcome was disease (compatible) or no disease (incompatible) and the term label itself could be misleading.