'interaction with host' (GO:0051701) and 'interaction with symbiont' (GO:0051702) are essentially the same class

[dillerm]

'interaction with host' = An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.

'interaction with symbiont’ = An interaction between two organisms living together in more or less intimate association. The term symbiont is used for the smaller (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.

Moreover, this definition was assigned to two new IRIs, as it previously was the definition for ‘symbiosis, encompassing mutualism through parasitism’ (GO:0044403).

[ValWood]

To the editors, I collected these tickets with some of my previous tickets and added the label "multi-species process". Part way I realized there was an existing label "viruses and symbionts" but this is only used twice. You might want to standardize this set on a single label.

[pgaudet]

Hi @dillerm

These terms have been in the ontology since 2005, and IRIs or IDs have not changed since, as far as I can tell. Looking at the children, I think these terms are OK (at least in the current structure of the ontology).

What changes do you suggest we make ?

Thanks, Pascale

[dillerm]

Ah, I guess I didn't catch that earlier, but the issue is that they both have the same definition, which therefore makes them the same class with two different IRIs. If you look at it at the instance level, you would essentially end up having a single interaction between a symbiont and a host instantiating two classes, which is problematic since the instance-of relation is restricted to having a one-to-one correspondence between a particular and a type.

[pgaudet]

Hello,

A few thoughts on this:

'interaction with host'

The definition, "An interaction between two organisms (...) , sounds like we are annotating organisms, not gene products. To annotate gene products, the most appropriate term right now is 'symbiont process', "A process carried out by symbiont gene products that enables the interaction between two organisms living together in more or less intimate association."

'interaction with symbiont'

We need to look at this one a bit more closely, but most terms could be re-housed under immune response:

Term	Number of EXP
positive regulation by host of viral transcription	19
negative regulation by host of viral transcription	17
positive regulation by host of viral process	11
interaction with symbiont	10
negative regulation by host of viral genome replication	9
positive regulation by host of viral genome replication	8
neutrophil mediated killing of gram-negative bacterium	7
killing by host of symbiont cells	6
modification by host of symbiont morphology or physiology via secreted substance	6
negative regulation by host of viral process	5
positive regulation by host of viral release from host cell	5
interaction with symbiont via secreted substance involved in symbiotic interaction	4
cytolysis by host of symbiont cells	3
maintenance of symbiont-containing vacuole by host	3
modulation by host of viral RNA genome replication	3
negative regulation by host of symbiont molecular function	3
positive regulation by host of symbiont cAMP-mediated signal transduction	3
recognition of symbiont	3
lectin-induced modified bacterial internalization	2
modulation by host of viral transcription	2
negative regulation by host of viral exo-alpha-sialidase activity	2
negative regulation by host of viral glycoprotein metabolic process	2
neutrophil mediated killing of bacterium	2
neutrophil mediated killing of fungus	2
neutrophil mediated killing of gram-positive bacterium	2
positive regulation by host of cytolysis of symbiont cells	2
positive regulation of neutrophil mediated killing of fungus	2
catabolism by host of symbiont cell wall chitin	1
catabolism by host of symbiont protein	1
disruption by host of symbiont cells	1
host-mediated regulation of intestinal microbiota composition	1
modification by host of symbiont morphology or physiology	1
modulation by host of RNA binding by virus	1
modulation by host of symbiont signal transduction pathway	1
modulation by host of viral RNA-binding transcription factor activity	1
modulation by host of viral genome replication	1
modulation by host of viral process	1
positive regulation by host of symbiont catalytic activity	1
positive regulation of neutrophil mediated killing of gram-negative bacterium	1

regulation of neutrophil mediated killing of gram-negative bacterium

Would that work ?

[deustp01]

Haven't looked at any actual annotations but most of the terms, even if they could include aspects of immune response, look mostly like they would not fit well under an immune response parent. @addiehl ?

[pgaudet]

Haven't looked at any actual annotations but most of the terms, even if they could include aspects of immune response, look mostly like they would not fit well under an immune response parent.

I think you are probably right - but the annotations, ie what the curator was trying to capture, probably could.

I'll gather examples.

Thanks, Pascale

[pgaudet]

I am thinking of terms like

neutrophil mediated killing of gram-negative bacterium | 7 killing by host of symbiont cells

those likely have a counterpart in the immune response branch... ?