Open jseager7 opened 4 years ago
ValWood
commented
4 years ago This is a good example
Pathogen induced is better wording.
chlorosis loss of the normal green coloration of leaves of plants, caused by iron deficiency in lime-rich soils, disease, or lack of light.
so presumably to be an interaction the pathogen must be affecting the chlorosis.
Therefore pathogen-induced chlorosis seems correct. and no need to mention 'host' in terms which use 'pathogen induced'
jseager7
commented
4 years ago I've gone through the terms that use 'induced', and my corrections to their labels are shown below. @ValWood or @CuzickA can you check these and let me know if there are any problems? I've followed Val's advice of removing reference to 'host', since 'pathogen-induced' should imply this already.
| term | old label | new label |
|---|---|---|
| PHIPO:0000190 | delayed host hypersensitive response induced by pathogen during biotrophy | delayed pathogen-induced hypersensitive response during biotrophy |
| PHIPO:0000192 | presence of host hypersensitive response induced by pathogen during biotrophy | presence of pathogen-induced hypersensitive response during biotrophy |
| PHIPO:0000461 | host programmed cell death phenotype induced by pathogen presence | pathogen-induced programmed cell death phenotype |
| PHIPO:0000462 | abolished host programmed cell death induced by pathogen during necrotrophy | abolished pathogen-induced programmed cell death during necrotrophy |
| PHIPO:0000465 | absence of host programmed cell death induced by pathogen during necrotrophy | absence of pathogen-induced programmed cell death during necrotrophy |
| PHIPO:0000466 | host necrotic cell death by pathogen induced hypersensitive response | necrotic cell death caused by pathogen-induced hypersensitive response |
| PHIPO:0000476 | gain of host programmed cell death induced by pathogen during necrotrophy | gain of pathogen-induced programmed cell death during necrotrophy |
| PHIPO:0000477 | presence of host programmed cell death induced by pathogen during necrotrophy | presence of pathogen-induced programmed cell death during necrotrophy |
| PHIPO:0000516 | gain of host hypersensitive response induced by pathogen during biotrophy | gain of pathogen-induced hypersensitive response during biotrophy |
| PHIPO:0000924 | pathogen induced host oxidative burst phenotype | pathogen-induced oxidative burst phenotype |
| PHIPO:0000927 | presence of pathogen induced host reactive oxygen species production | presence of pathogen-induced production of reactive oxygen species |
| PHIPO:0000928 | absence of pathogen induced host reactive oxygen species production | absence of pathogen-induced production of reactive oxygen species |
| PHIPO:0001014 | increased level of host callose deposition induced by pathogen | increased level of pathogen-induced callose deposition |
| PHIPO:0001015 | decreased level of host callose deposition induced by pathogen | decreased level of pathogen-induced callose deposition |
| PHIPO:0001083 | presence of pathogen induced callose deposition in host | presence of pathogen-induced callose deposition |
| PHIPO:0001109 | abnormal pathogen induced host pH | abnormal pathogen-induced change in pH |
| PHIPO:0001110 | pathogen induced decrease in host pH | pathogen-induced decrease in pH |
| PHIPO:0001111 | pathogen induced increase in host pH | pathogen-induced increase in pH |
| PHIPO:0001113 | pathogen induced pH decrease in host phagolysome | pathogen-induced decrease in phagolysome pH |
| PHIPO:0001161 | absence of pathogen induced host phenolic compound | absence of pathogen-induced phenolic compound |
| PHIPO:0001169 | altered level of pathogen induced host substance | altered level of pathogen-induced production of substance |
| PHIPO:0001172 | normal level of pathogen induced host substance | normal level of pathogen-induced production of substance |
jseager7
commented
4 years ago There's one term in this set that I didn't include: 'host effector triggered immunity signaling induced hypersensitive response activated by pathogen' (PHIPO:0001141). This term combines so many causal factors that I'm not sure if it should exist as a single term. It's certainly never going to map to uPheno patterns in its current state.
The current definition is as follows (with some clarification that I've added):
"A cell signaling pathway phenotype where the host effector-triggered immunity signaling pathway is induced by a pathogen [in order] to activate a plant hypersensitive response and induce necrosis"
My best attempt at a new term label is as follows:
'necrotic cell death induced by hypersensitive response activated by pathogen-induced effector-triggered immunity signaling'
From the above label it's more evident that this term can be broken down into multiple causally-related events:
I think this is way too much information for a single term. I feel like we could commute this phenotype to 'necrotic cell death caused by pathogen-induced hypersensitive response': the pathogen still plays some part in the induction of the hypersensitive response, even if it's only transitive. We could then merge PHIPO:0001141 into PHIPO:0000466, for which I've already suggested the new label 'necrotic cell death caused by pathogen-induced hypersensitive response'.
CuzickA
commented
4 years ago Hi @jseager7 Thanks for your above comments and term label suggestions. @ValWood and I are actively working on the branches for these terms as part of the PHI-branch overhaul. We will consider your suggestions above as we work through them.
I still prefer to keep 'host' in the above terms to make it really clear whether the change is in the pathogen or the host eg a pH change could happen in the pathogen or the host.
If we decide on using 'pathogen-induced' perhaps it would be faster to add the hyphen to the text file rather than to individual terms using Protege.
jseager7
commented
4 years ago I still prefer to keep 'host' in the above terms to make it really clear whether the change is in the pathogen or the host eg a pH change could happen in the pathogen or the host.
To clarify, we were only proposing removing 'host' in the case where it's mentioned in the same term label as 'pathogen-induced'.
I think it would be better if we use 'pathogen-induced' to always imply a pathogen-induced change in the host, because if we have the opposite – a pathogen-induced change in the pathogen – then that presumably makes it a single-species phenotype, as I'd expect the phenotype could occur in the absence of a real host.
If we have the complex case of a pathogen inducing a change in the host that then induces a change in the pathogen, I'd recommend that we don't create singular terms to capture these cases. If we end up with cases like this, it would be better to create two terms to capture both sides of the induction, then use an annotation extension to causally link the two phenotype annotations. Although, this might depend on what approach GO chooses if they decide to capture these sorts of processes.
ValWood
commented
4 years ago I think we should keep this explictly for now. We do have examples of pathogen changes in the pathogen -host interaction branch (for instance with entry into host and invasiveness). I don't think we would use 'pathogen-induced' here though.
I think if a user read "altered level of pathogen induced substance" or " absence of pathogen induced ROS production" they could easily overlook these terms were only for the host processes because the same processes also apply to the pathogen.
CuzickA
commented
3 years ago See ticket #346 Some terms have now been changed to 'host defense-induced'
There's numerous different ways in which PHIPO describes phenotypes where the pathogen is a causative factor, specifically when a pathogen has induced some host phenotype. Examples below:
I think the above examples would be easier to understand if they followed the form of 'pathogen-induced x', where x is a phenotype of some sort. For example:
Note that I'm not sure if PHIPO:0000215 means 'pathogen-induced chlorosis'; you can ignore this if the term isn't meant to imply any causative link between chlorosis and the presence of a pathogen.