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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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obsolete: GO:0052161 modulation by symbiont of defense-related host cell wall thickening #18726

Closed ValWood closed 4 years ago

ValWood commented 4 years ago

GO:0052161 modulation by symbiont of defense-related host cell wall thickening Definition (GO:0052161 GONUTS page) Any process in which an organism modulates the frequency, rate or extent of host processes resulting in the thickening of its cell walls, occurring as part of the defense response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.

This term, and its descendants GO:0052105 induction by symbiont of defense-related host cell wall thickening is_a GO:0052189 modulation by symbiont of defense-related host cell wall callose deposition should be obsoleted.

They don't make sense because this is a plant PTI (pathogen triggered immunity) response. The plant increases callose deposition as a defense response an infected cell. I think this is to contain the pathogens to prevent them spreading to surrounding cells.

There are appropriate plant terms for this process. GO:0052542 defense response by callose deposition

But, this (GO:0052161) is not an evolved process for the pathogen. It happens in the plant as a result of the plant detecting the pathogen.

Can we search for any other terms under "response to host defenses" which have Any process in blah ......occurring as part of the defense response of the host organism ?as it is unlikely that any of these are valid, the 2 statements are logically inconsistent.

again, no annotations, no reference....

ValWood commented 4 years ago

Double checking @mgiglio99 ?

I think I have seen papers where the cell wall is made thinner by the pathogen, but not thicker?

mgiglio99 commented 4 years ago

Hi Val, I agree with obsoleting these. Michelle

pgaudet commented 4 years ago

Dear all,

The proposal has been made to obsolete

The reason for obsoletion is that this is a host, not a symbiont process, but is formulted as a symbiont process.

There are no annotations, no mappings to those terms. Those terms are no present in any subsets.

https://github.com/geneontology/go-ontology/issues/18726.

We are opening a comment period for this proposed obsoletion. Since there are a few annotations we’d like to proceed and obsolete this term on February 7th, 2020. Unless objections are received by February 7th, 2020, we will assume that you agree to this change.

Thanks, Pascale

pgaudet commented 4 years ago

Another term to obsolete in this branch: GO:0075048 cell wall strengthening in symbiont involved in entry into host No annotations, no mapping, not in any subsets.

See #18725

genegodbold commented 4 years ago

Val wrote: "But, this (GO:0052161) is not an evolved process for the pathogen. It happens in the plant as a result of the plant detecting the pathogen."

Yep, along with a suite of other responses that arise from the transcriptional activation that results (or is a hallmark of) PTI (the mild reaction to pathogen detection) and ETI (effector-triggered immunity) the stronger reaction to pathogen detection.