Changes to PHIPO_EXT terms

[CuzickA]

After todays meeting with @ValWood and Kim H-K discussing the GfG curation of Avrstb6/stb6 https://canto.phi-base.org/curs/69e99b22bfebf3b0
we decided on the following

PHIPO_EXT:0000004 functional host resistance gene absent (unchanged)

PHIPO_EXT:0000005 loss of functional host resistance gene ->compromised host resistance gene
(this will cover cases where the gene is absent due to a genetic deletion as well as transient assays where the gene is present but expression is knocked down using VIGS)

PHIPO_EXT:0000006 functional host resistance gene present (unchanged)

PHIPO_EXT:0000006 gain of functional host resistance gene (unchanged)

Question: do we still want 'functional' in the above term labels?

[CuzickA]

For the pathogen effector terms

Effectors can have two functions i) to cause disease ii) to be recognised by host R gene. We will choose to capture ii). Very few experiments record whether the 'effector' is functioning to cause disease, most expt report on whether an effector (avirulence determinant) is recognised by host R gene.

PHIPO_EXT:0000008 functional pathogen effector absent -> recognisable pathogen effector absent

PHIPO_EXT:0000009 loss of functional pathogen effector -> 'loss of recognisable pathogen effector' or 'compromised recognisable pathogen effector'

PHIPO_EXT:0000010 functional pathogen effector present -> recognisable pathogen effector present

PHIPO_EXT:0000011 gain of functional pathogen effector -> gain of recognisable pathogen effector

Compound terms will also need to be adjusted accordingly for all above and definitions reviewed.

[CuzickA]

@jseager7 how should I edit these terms for PHIPO_EXT? Should I make edits directly to the term creator sheet?

[jseager7]

@CuzickA If you're not adding new term IDs then you shouldn't run into any problems editing the OBO file directly. Having said that, it will probably still be easier and faster to make the edits to the term creator sheet. I think it makes more sense to treat the term creator sheet as the master copy of the ontology for the time being, at least while the ROBOT templates provide everything we need: if we take the opposite approach of editing the ontology directly, then we'll have to keep the term creator sheet synced up with our changes, which is somewhat more work compared to deriving the ontology from a spreadsheet.

One minor comment on the changes: I think we should prefer international (US) spellings for '-isa-', so 'recognizable' instead of 'recognisable'.

[CuzickA]

First pass at term edits and defs. These can be refined as required during review of curated G-f-G sessions.

PHIPO_EXT:0000008 functional pathogen effector absent -> recognizable pathogen effector absent
old def
A phenotype where the ability of a pathogen effector to produce an infectious disease is absent.
new def
A phenotype where the ability of a pathogen effector to be recognized by a specific host resistance gene is absent.

PHIPO_EXT:0000010 functional pathogen effector present -> recognizable pathogen effector present
old def
A phenotype where the ability of a pathogen effector to produce an infectious disease is present.
new def
A phenotype where the ability of a pathogen effector to be recognized by a specific host resistance gene is present.

PHIPO_EXT:0000009 loss of functional pathogen effector -> compromised recognizable pathogen effector
synonym: loss of recognisable pathogen effector
old def
A phenotype where the ability of a pathogen effector to produce an infectious disease is abolished.
new def
A phenotype where the ability of a pathogen effector to be recognized by a specific host resistance gene is abolished (recognition was present and is now absent).

PHIPO_EXT:0000011 gain of functional pathogen effector -> gain of recognizable pathogen effector
old def
A phenotype where the ability of a pathogen effector to produce an infectious disease is acquired.
new def
A phenotype where the ability of a pathogen effector to be recognized by a specific host resistance gene is acquired (recognition was absent and is now present).

[CuzickA]

PHIPO_EXT:0000005 loss of functional host resistance gene ->compromised host resistance gene
old def (keep this for now)
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).

[CuzickA]

The term below, developed for the avrSen1/Sen1 paper will now need further review. We have changed the function of an effector from 'to cause disease' to 'be recognised by host R gene'.
PHI-base/curation#65

PHIPO_EXT:0000029 compatible interaction, functional host resistance gene present

A pathogen host interaction phenotype where the gene-for-gene relationship between the pathogen and plant host results in disease susceptibility. 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 present. (The presence of a functional pathogen effector is unknown due to a lack of data showing whether it is able to cause disease).

[CuzickA]

Above changes made and terms are currently being loaded.

Next

1. review G-f-G sessions
   AvrSen1/Sen1 follow up above query (it may be possible to use the new triple component terms now rather than the double component term)
   AvrStb6/Stb6 make sure new terms make sense here (term edits were devised based on this session) looks fine 08_01_2021
   Atr1/RPP1 not yet discussed with Val and Kim - I think I may need to reannotate based on altered effector function (changed 'to cause disease' to 'be recognised by host R gene')
   Tox1/Snn1 not yet discussed with Val and Kim - how do these terms fit with NE and susceptibility locus?

2. review definitions for PHIPO_EXT terms

3. discuss with @ValWood whether these changes on capturing effector function in the PHIPO_EXT impact any of the other PHIPO or GO effector terms where we have recorded the normal effector function is to cause disease.

[CuzickA]

The term below, developed for the avrSen1/Sen1 paper will now need further review. We have changed the function of an effector from 'to cause disease' to 'be recognised by host R gene'.
PHI-base/curation#65

PHIPO_EXT:0000029 compatible interaction, functional host resistance gene present

A pathogen host interaction phenotype where the gene-for-gene relationship between the pathogen and plant host results in disease susceptibility. 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 present. (The presence of a functional pathogen effector is unknown due to a lack of data showing whether it is able to cause disease).

I think we could obsolete this 2-component term and use the newly updated 3-component terms - to discuss in the next Gene-for-gene curation meeting.

[CuzickA]

see #305

Once loaded, new GfG AE terms need to be added to necrotroph sessions
PHI-base/curation#22
PHI-base/curation#91

[CuzickA]

Closing this ticket as out of date.