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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Obsolete cell wall strengthening in symbiont involved in entry into host and (regulation) children ? #18056

Closed pgaudet closed 4 years ago

pgaudet commented 4 years ago

Hello,

Related to #17987

The following terms have no references and no annotations. When I google 'cell wall strengthening host entry', I find the host cell wall strengthening, for example: https://www.researchgate.net/publication/237165677_Plant_cell_wall_reinforcement_in_the_disease-resistance_response_Molecular_composition_and_regulation

But I cannot find anything that talks about the symbiont's cell wall strengthening for entry into host.

@mgiglio99 Do you know what this was supposed to represent ?

Thanks, Pascale

mgiglio99 commented 4 years ago

I just read about this process in the symbiont somewhere - but now I can't find it. I'll keep looking. Basically what I remember reading is that the plant sends out compounds/enzymes to attack the walls of pathogens to kill them and the pathogens toughen their walls in response. Hopefully I can find it.

ValWood commented 4 years ago

But this does not sound like it is involved directly in "entry into host". It sounds more like "cell wall thickening involved in avoidance of host defenses"

mgiglio99 commented 4 years ago

Yes, that's true. Did I read somewhere about fungal hyphae thickening their walls to penetrate cells? Or is it only that they make those penetrating structures?

ValWood commented 4 years ago

I think you are correct, I'm sure that invasive hyphae are thicker.

I think I could call this "invasive hyphae formation" and could be defined to cover all of the various processes that happen in a hyphae ( the septal ring does something and the hyphae thickens and constricts, so there is a lot going on)

Things like "cell wall thickening" will probably attributed to specific activities 'like "beta-glucan synthase".

So I think it's better to add when we are annotating. This way you can understand the current model and figure out how the term fits with existing terms and where things should be grouped more logically (i.e which things are Molecular functions, and which are Biological Processes).

pgaudet commented 4 years ago

So I could merge 'GO:0075048 cell wall strengthening in symbiont involved in entry into host' and obsolete the 'modulation' terms ?

Pascale

mgiglio99 commented 4 years ago

Merging into 'entry into host' or 'cell wall thickening'?

pgaudet commented 4 years ago

I thought to merge into "invasive hyphae formation" but I see @ValWood was proposing to change the term label - "invasive hyphae formation" does not exist.

What do you think @mgiglio99

mgiglio99 commented 4 years ago

I guess I'd merge into 'entry into host' And obsoleting the modulation terms sounds fine.

pgaudet commented 4 years ago

ok very good, thanks!

pgaudet commented 4 years ago

Dear all,

The proposal has been made to obsolete

The reason for the obsoletion is that there is no evidence that those processes exist.

There are no annotations or mappings to those terms. Those terms are not present in any subsets.

Any comments can be added to the issue: https://github.com/geneontology/go-ontology/issues/18056

We are opening a comment period for this proposed obsoletion. We’d like to proceed and obsolete this term on October 31st, 2019. Unless objections are received by October 31st, we will assume that you agree to this change.

Thanks, Pascale