Make edits to AE 'infective ability' terms used in gene-for-gene annotations

[CuzickA]

28_09_2020 (maybe remove pathogen and host from labels in future)

rename 'host resistance absent' and update def Functional host resistance gene absent A phenotype where ability of a host to be resistant to a pathogen, via the recognition of a pathogen effector by a specific host resistance gene, is absent

rename 'host resistance present' and update def Functional host resistance gene present A phenotype where ability of a host to be resistant to a pathogen, via the recognition of a pathogen effector by a specific host resistance gene, is present

rename 'loss of host resistance' and update def Loss of functional host resistance gene A phenotype where the ability of a host to be resistant to a pathogen, via the recognition of a pathogen effector by a specific host resistance gene is abolished (resistance was present and is now absent).

rename 'gain of host resistance' and update def Gain of functional host resistance gene A phenotype where the ability of a host, to be resistant to a pathogen, via the recognition of a pathogen effector by a specific host resistance gene is acquired (resistance was absent and is now present). Comment: gain of function may result from engineering or a natural variant or transformation

New parent: pathogen effector phenotype A phenotype that is relevant to pathogen effectors

rename 'pathogenicity absent', move under new parent and update def Functional pathogen effector absent A phenotype where the ability of a pathogen effector to produce an infectious disease is absent. Comment: this may mean that the effector is not present or the effector is present but not recognised.

rename 'pathogenicity present', move under new parent and update def Functional pathogen effector present A phenotype where the ability of a pathogen effector to produce an infectious disease is present.

Loss of functional pathogen effector (NEW TERM) (need list where 'loss of pathogenicity' term used in gene-for-gene annotation, need to move over to this new term) A phenotype where the ability of a pathogen effector to produce an infectious disease is abolished.

rename 'gain of pathogenicity', move under new parent and update def Gain of functional pathogen effector (double check to make sure not used in non gene-for-gene curation sessions) A phenotype where the ability of a pathogen effector to produce an infectious disease is acquired.

Further changes can be made once the gene-for-gene workflow decided upon. Also need to decide on whether to keep loss of/gain of within these terms or whether to merge with absence/presence

[CuzickA]

15c69c3 edits made to host resistance terms

[CuzickA]

From James Here's the sessions that contain 'gain of pathogenicity', based on the term ID given above (current as of 28 September).

https://canto.phi-base.org/curs/f41d30e250b8f9b0 gene for gene https://canto.phi-base.org/curs/326646a152a66e68 https://canto.phi-base.org/curs/59484877a87d5786 gene for gene https://canto.phi-base.org/curs/87e386b652573063 https://canto.phi-base.org/curs/bd02fdb6831712ca gene for gene

I will need to review the two non-gene-for-gene sessions before changing 'gain of pathogenicity'

[CuzickA]

New parent: pathogen effector phenotype A phenotype that is relevant to pathogen effectors c5feef8

[CuzickA]

rename 'gain of pathogenicity', move under new parent and update def Gain of functional pathogen effector (double check to make sure not used in non gene-for-gene curation sessions) A phenotype where the ability of a pathogen effector to produce an infectious disease is acquired.

Suggest leave 'gain of pathogenicty' for now and create a new term called 'gain of functional pathogen effector' only to be used in the gene-for-gene work flow.

[CuzickA]

[14:12] James Seager

PHIPO:0000008 'pathogenic ability absent':

https://canto.phi-base.org/curs/f41d30e250b8f9b0 gene-for-gene https://canto.phi-base.org/curs/59484877a87d5786 gene-for-gene https://canto.phi-base.org/curs/69e99b22bfebf3b0 gene-for-gene https://canto.phi-base.org/curs/bd02fdb6831712ca gene-for-gene https://canto.phi-base.org/curs/6dd9062354648dc7 gene-for-gene https://canto.phi-base.org/curs/87e386b652573063 old session needs updating, temp moved AE into term suggestion

[CuzickA]

PHIPO:0000007 'pathogenic ability absent':

https://canto.phi-base.org/curs/bd02fdb6831712ca gene-for-gene https://canto.phi-base.org/curs/87e386b652573063 old session needs updating, temp moved AE into term suggestion https://canto.phi-base.org/curs/3b2c44b436098af1 old session needs updating, temp moved AE into term suggestion

[CuzickA]

rename 'pathogenicity absent', move under new parent and update def Functional pathogen effector absent A phenotype where the ability of a pathogen effector to produce an infectious disease is absent. Comment: this may mean that the effector is not present or the effector is present but not recognised.

rename 'pathogenicity present', move under new parent and update def Functional pathogen effector present A phenotype where the ability of a pathogen effector to produce an infectious disease is present.

Done b5ccd62

Next make new terms for Loss of / gain of functional pathogen effector

[CuzickA]

e9161e4 made NTRs Loss of / gain of functional pathogen effector

[CuzickA]

current infective ability branch after changes

[CuzickA]

Next i) Check terms load correctly into PHI-Canto AE infective ability. _DONE ii) Create ticket on curation tracker to document when the gene-for-gene curation sessions have been updated/checked for usage of these terms. https://github.com/PHI-base/curation/issues/82

[ValWood]

I think these are more precise now. Something is really odd about these terms- this is a consequence trying to fit the old PHI high-level terms into the new schema.

Now we changed the term names these don't really seem to be phenotypes at all, but information about the genotype? or, it's information about the genetic interaction, but it isn't a phenotype.....

[CuzickA]

I think these are more precise now. Something is really odd about these terms- this is a consequence trying to fit the old PHI high-level terms into the new schema.

Now we changed the term names these don't really seem to be phenotypes at all, but information about the genotype? or, it's information about the genetic interaction, but it isn't a phenotype.....

Yes, it is really the information about the potential of the pathogen genotype and the host genotype within the metagenotype interaction.