Suppression of BAX-induced host cell death (PMID: 39400398)

[Hsinyugithub]

I needed a term for this and asked Co-pilot to help. @jseager7 Please let me know if this makes sense.

Proposed PHIPO Term

Label: suppression of BAX-induced host cell death
Definition: A phenotype in which the expression or activity of a pathogen effector results in the inhibition or reduction of host cell death triggered by the heterologous expression of the mammalian pro-apoptotic protein BAX.
Synonyms:

inhibition of BAX-induced cell death
reduction of BAX-mediated programmed cell death

Parent Term: suppression of host programmed cell death (PHIPO:0000008 or similar)
Associated Entities:

Effector: pathogen-derived protein
Host: plant species (e.g., Nicotiana benthamiana)
Assay: transient expression assay or agroinfiltration

[jseager7]

@Hsinyugithub This seems okay to me, but we need to make clear whether 'suppression' means a reduction to some smaller value (decreased) or a reduction to zero (abolished / absent).

If I remember correctly, we tend to have separate terms in PHIPO for 'decreased' and 'absent' phenotypes. This separation also exists in uPheno.

The suggested parent term 'suppression of host programmed cell death' doesn't exist in PHIPO so I guess it's been hallucinated. We do have a few terms in PHIPO that refer to 'host programmed cell death' (like PHIPO:0000461, PHIPO:0000465, and PHIPO:0000477).

I'd recommend checking how this new term relates to the term 'absence of pathogen necrotrophic effector-mediated host programmed cell death' (PHIPO:0000465). Is it broadly equivalent or more specific? Could the parent term of PHIPO:0000465 also be a parent term for this new term?

[Hsinyugithub]

I believe this experiment is more specific and widely used by the community. I would like to ask Kim and @martin2urban about this in the meeting. I also need to rewrite the definition in PHIPO format.

'BAX-induced host cell death absent' and 'BAX-induced host cell death present'

P.S. Co-pilot seems to hallucinate a lot when it comes to PHIPO terms.

[jseager7]

P.S. Co-pilot seems to hallucinate a lot when it comes to PHIPO terms.

This is almost certainly due to the lack of context. I previously suggested passing the entire PHIPO ontology to Copilot but due to the size of the file, that's probably not very efficient.

You could consider pasting in a list of terms from PHIPO after your prompt, or keeping this list saved as a file so you can upload it to Copilot and refer to it in future.

You can use Protégé to copy a tab-indented list of term IDs and labels for a term and all of its children. Just right click a term and select 'Copy sub-hierarchy as tab indented text', then paste that list into Copilot to provide context. If the prompt gets too long you can upload the list as a file.

(I'm not sure if Copilot will be able to parse the structure of the ontology from tab-indentation, but if it only needs to suggest a parent term, that shouldn't matter.)

[Hsinyugithub]

Just did this. Here is the reply:

Parent Term Suggestion:
host cell death phenotype (PHIPO:0000446)
This term encompasses phenotypes related to the death of host cells, which is the broader biological process affected by BAX (a pro-apoptotic protein). Since your term describes a suppression of this process, it fits well under this category.
If PHIPO includes more specific child terms under host cell death phenotype (e.g., “effector-independent host hypersensitive response”), and your term is mechanistically or experimentally linked to such subtypes, we could consider those as well. However, based on the document, host cell death phenotype is the most appropriate general parent.

[Hsinyugithub]

Term: BAX-induced host cell death absent
Definition:
A host cell death phenotype in which the cell death typically triggered by the expression or activity of the pro-apoptotic protein BAX is completely abolished. This phenotype may result from genetic mutations, pathogen effectors, or treatments that block BAX-mediated apoptotic signaling in the host.
Parent Term:

host cell death phenotype (PHIPO:0000446)

Synonyms:

Absence of BAX-induced host cell death
No host cell death in response to BAX
BAX-triggered apoptosis abolished

is_a: PHIPO:0000446 ! host cell death phenotype
has_modifier: absent
has_agent: BAX
has_trigger: host cell death

[Hsinyugithub]

Term: BAX-induced host cell death present
Definition:
A host cell death phenotype in which the expression or activity of the pro-apoptotic protein BAX leads to observable host cell death. This phenotype may be used to confirm the functionality of BAX in triggering apoptosis in host cells, often in experimental systems such as transient expression assays.
Parent Term:

host cell death phenotype (PHIPO:0000446)

Synonyms:

Presence of BAX-induced host cell death
BAX-triggered apoptosis present
Host cell death in response to BAX

is_a: PHIPO:0000446 ! host cell death phenotype
has_modifier: present
has_agent: BAX
has_trigger: host cell death