How to curate WT pathogen antifungal target?

[CuzickA]

Needed for #36

In this paper they are using an enzyme assay to screen a small molecule-library for inhibitors of pathogen PptA activity.

They found 3 compounds that were potent inhibitors of PptA and calculated the half-maximal inhibitory concentrations (IC50).

This is really useful info to capture as it provides the baseline information of WT sensitivity to these drugs. If these drugs are used in the future, there may eventually be studies to identify Pathogen PptA mutations that lead to increased resistance or increased sensitivity to these drugs. For curation the alleles could be recorded and a phenotype annotated.

In this paper they have NOT assessed a PptA mutant with the chemistry, so there is no shift in R/S to chemical compared to WT to annotate with a phenotype.

I have had a try at curating this, see below. The parent 'increased sensitivity to chemical' does not seem right as this is the WT. (In the lower annotations they add the chemical to see if pathogen growth is inhibited).

@ValWood what do you think?

[ValWood]

I agree this is useful to capture and it is important.

We haven't been able to capture this so far for PomBase. What is the publication and I'll take a look.

I'm sure we can come up with something, even if not immediatly.

[ValWood]

PMID: 28720735?

probably
WT gene
phosphopantetheinyl transferase inhibitor activity
with chemical in condition if this is what the assay is showing?

We have not been able to do this for PomBase because we don't curate wild type features, and these types of papers haven''t been a priority for us, but in PHI-Canto this is allowed...

and also the decreased population growth terms in the way you have done them.

[CuzickA]

Yes this could work thanks @ValWood .

It may need to be
phosphopantetheinyl transferase inhibitor activity present

Where would I put this is PHIPO?
Maybe it would be a child of 'decreased catalytic activity' in the single species branch ??

[ValWood]

Actually my suggestion isn't quite right. I'll have a think how we should do this. Hold on for this one.

[ValWood]

My original suggestion was incorrect. It should have been:

decreased phosphopantetheinyl transferase activity

with the chemical as a condition

[CuzickA]

09734b1 done