search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
223 stars 40 forks source link

GO:0009627 systemic acquired resistance #18736

Open ValWood opened 4 years ago

ValWood commented 4 years ago

From conversation with PHI . base collaborators @CuzickA and Kim Hammond-Kosack

GO:0009627 systemic acquired resistance The salicylic acid mediated response to a pathogen which confers broad spectrum resistance.

salicylic acid-dependent systemic resistance | exact

Problems

  1. systemic aquired resistance is not always salicylic acid mediated although sometimes is
  2. Definition isn't clear.

Wikipedia definition: Systemic acquired resistance (SAR) is a "whole-plant" resistance response that occurs following an earlier localized exposure to a pathogen. SAR is analogous to the innate immune system found in animals, and there is evidence that SAR in plants and innate immunity in animals may be evolutionarily conserved.[1]

So a key part of this seems to be following earlier localized exposure?

Should this term also be realted to

GO:0090714 innate immunity memory response Definition (GO:0090714 GONUTS page) An immune response mediated by the innate immune system and directed against a previously encountered immunologic stimulus, being quicker and quantitatively better compared with the initial response to that stimulus. PMID:26086132

pgaudet commented 4 years ago

The definition of GO:0009627 systemic acquired resistance seems incorrect, since we have the child GO:0009862 systemic acquired resistance, salicylic acid mediated signaling pathway

Should we merge into the most precise ??? @tberardini There are many TAIR annotations to those two terms (and their regulation).

Thanks, Pascale

ValWood commented 4 years ago

That would work for me. def of GO:0009627 looks like a cut/past error, but if the annotations were made to the def, merging down would be OK.

~@tberardini not that GO:0009862 systemic acquired resistance, salicylic acid mediated signaling pathway also has a parent GO:0009863 salicylic acid mediated signaling pathway is this involved with no "immune response" parent does salicylic acid have non-immune roles~

roles in plant growth and development, photosynthesis, transpiration, ion uptake and transport

@pgaudet has response to drug and response to antibiotic parentage. Is that a reasoner problem?

pgaudet commented 3 years ago

@tberardini can you have a look at this one?

tberardini commented 3 years ago

@lreiser Can you weigh in, please? Your ID is on the def :).

http://amigo.geneontology.org/amigo/term/GO:0009627

Definition The salicylic acid mediated response to a pathogen which confers broad spectrum resistance. Source: GOC:lr, ISBN:0521436125

image

It seems like SAR should have more parts than just the one. Salicylic acid signaling is involved in more than response to pathogen.

https://www.sciencedirect.com/science/article/pii/B9780128115626000086

lreiser commented 3 years ago

Clearly defined that a long time ago ( I think) SAR occurs when a localized infection triggers an immune response in tissues distal to the initial triggering event. It involves long distance signaling molecules.

https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.15068 suggests it has the parts

  1. production of signal (at the site of localized infection)
  2. transmission of signal (from site of infection)
  3. perception of signal (at distal sites) 4