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Pathogen-Host Interaction Phenotype Ontology
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Edit PHIPO:0001225 'abolished PAMP receptor decoy activity' and PHIPO:0001224 'decreased PAMP receptor decoy activity #336

Closed CuzickA closed 3 years ago

CuzickA commented 3 years ago

For https://github.com/PHI-base/curation/issues/62

Currently image

We would like to model these terms on the metagenotype terms created for https://github.com/PHI-base/phipo/issues/335 for PHI-base/curation#37

i.e. the term 'pathogen modulation of chitin hydrolysis by host present' with related synonym 'PAMP receptor decoy activity present' image

In the fungal protection from hydrolysis studies often using Trichoderma there are papers using a pathogen and host within the paper (https://github.com/PHI-base/curation/issues/37), or just the pathogen and commercially purchased chitinases instead of host (https://github.com/PHI-base/curation/issues/62). Therefore sometimes these expt will be curated using PHI terms and sometimes singles species terms.

CuzickA commented 3 years ago

Edit PHIPO:0001225 abolished PAMP receptor decoy activity -> chitin hydrolysis present change def from A single species molecular function phenotype in which the occurrence of recognition, binding and sequestering of PAMP ligands in order to prevent them from binding and activating the host PAMP receptor is abolished (was present and is now absent). to A single species molecular function phenotype, in which a pathogen effector does not prevent the hydrolysis of chitin by chitinases. related synonyms: abolished PAMP receptor decoy activity, PAMP receptor decoy activity absent

PHIPO:0001224 decreased PAMP receptor decoy activity -> increased chitin hydrolysis present change def from A single species molecular function phenotype in which the occurrence of recognition, binding and sequestering of PAMP ligands in order to prevent them from binding and activating the host PAMP receptor is decreased. to A single species molecular function phenotype, in which the occurrence of a pathogen effector preventing the hydrolysis of chitin by chitinases is decreased (chitin hydrolysis is increased). related synonym: decreased PAMP receptor decoy activity

Please let me know what you think of these @ValWood

Should they stay under molecular function or move under metabolic process like the PHI branch term? image

CuzickA commented 3 years ago

edits to PHIPO:0001225 and PHIPO:00012254 360ce6b

NTR: chitin hydrolysis absent 7d38593 A single species molecular function phenotype, in which a pathogen effector prevents the hydrolysis of chitin by chitinases. related synonyms: PAMP receptor decoy activity present

Now looks like this image

@ValWood do you think this is okay under 'molecular function' or should it be under a 'metabolic process' parent to mirror the PHI branch version of the terms? (see screenshot below)

Also I think the grouping 'abnormal molecular function' is not correct here because we have absent and present terms listed underneath it.

image

ValWood commented 3 years ago

I think it should be under process.

CuzickA commented 3 years ago

moved 'chitin hydrolysis' terms under metabolic process parent (also updated term defs to reflect this) 93f31ac

Now looks like this

image