Rename host chlorosis terms

[jseager7]

The current host chlorosis terms don't follow the naming convention for presence and absence that other terms use. Consider the following:

host chlorosis absent in presence of pathogen (PHIPO:0000213)

This could be more conventionally expressed as follows:

absence of host chlorosis in presence of pathogen

Or, if the chlorosis is assumed to be induced by the pathogen:

absence of pathogen-induced host chlorosis

In this case, we probably don't need to mention 'host' either, since 'pathogen-induced' should be enough to imply that the chlorosis relates to the host, which reduces the term name to:

absence of pathogen-induced chlorosis

The term definition can explain the phenotype in full to prevent any confusion.

@CuzickA If you agree with any of the above term names, I'll make the changes.

See also: #188

[CuzickA]

Hi @jseager7, I think I would go with 'absence of host chlorosis in presence of pathogen' and 'presence of host chlorosis in presence of pathogen' (does it sound odd using 'presence' twice?). Just re-reading tickets #118 and #346 and it looks like we decided that we could not state 'pathogen-induced' or 'host-defence induced' as we do not know whether it is the pathogen or the host causing the host chlorosis within the interaction.

Currently looks like this

[jseager7]

does it sound odd using 'presence' twice?

I do think it sounds a bit odd. We could use "with pathogen present" if we can't decide on a better solution, but I've not too keen on that wording either.

we decided that we could not state 'pathogen-induced' or 'host-defence induced' as we do not know whether it is the pathogen or the host causing the host chlorosis within the interaction.

I'm struggling to understand how this distinction is useful. The pathogen may not be the proximate (immediate) cause but it is surely the ultimate cause, since presumably chlorosis would have never occurred if the pathogen was not present (if chlorosis did occur in the absence of a pathogen, then it would be a host phenotype).

More generally, "with pathogen present" is a bit ambiguous since 'presence' doesn't necessarily imply infection, only that the pathogen is probably in the same location as the host (not just within it). This could be interpreted as the pathogen inducing chlorosis remotely, e.g. through secreting chemicals into the environment.

It might be better to frame these terms as part of a process, namely a pathogen-host interaction, since it seems like that's all we can guarantee here if we don't want to add additional terms for the proximate causes (pathogen-induced vs host-induced). So maybe:

• host chlorosis phenotype during pathogen-host interaction
• absence of host chlorosis during pathogen-host interaction

…and so on. This might also be easier to map to uPheno's patterns in future, since it follows the pattern "absence of x during biological process".