NTR: decreased level of pyocyanin

[CuzickA]

For curating
PHI-base/curation#34
Fig 2A

toxin biosynthetic process phenotype PHIPO:0000496 add below as children to this single species branch term

-abnormal biosynthesis of pyocyanin
A single organism phenotype in which the biosynthesis of pyocyanin is abnormal (i.e. different than the wild type).

--decreased level of pyocyanin
A single organism phenotype where there is a decreased amount of pyocyanin.

--pyocyanin absent (OR abolished??)
A single organism phenotype where pyocyanin is absent.

[CuzickA]

After todays chat we are unsure of whether

1. above term should fall under biosynthetic process phenotype or altered level of a substance
2. substance absent or abolished

Val to follow up with Midori

Note in CHEBI under pyocyanine

[ValWood]

@mah11 I mailed Midori, but answer can go here.

We looked at FYPO and we think we use altered level as that is what is observed. However, was not sure.

[ValWood]

From Midori:

I would create and use an "abnormal biosynthesis (formation, production, etc.)" term if

a ) you're annotating experiments that actually look at the biosynthesis process somehow;

and b) it's biologically interesting or useful to capture the distinction between synthesis and level (yes, this is woolier than point a).

If experiments only look at levels, especially in a static or snapshot way, it's probably safer to use an "altered level" term.

[ValWood]

So I think for the ones we were looking at we use "level" but level should not be a descendant of biosynthesis terms, only under "altered level of..."

[CuzickA]

Thanks @ValWood @mah11 that makes sense.
I guess for the second question above 'substance absent or abolished' it would be 'substance absent'.

[CuzickA]

under 'altered level of substance in cell' I will need a new grouping term
perhaps 'altered cellular toxin level' or 'altered cellular secondary metabolite level' what do you think @Val?

Then I could add the new pyocyanin terms and move the existing Fusarium mycotoxin deoxynivalenol terms under here.

[ValWood]

I would put altered toxin level here, since we are likely to be annotating a lot of toxins.

[CuzickA]

Thanks @ValWood

under single species branch
-altered level of substance in cell
--NTR: altered cellular toxin level
A single species cell phenotype in which the amount of toxin measured in a cell differs from normal.
---NTR:decreased cellular toxin level
A single species cell phenotype in which the amount of toxin measured in a cell is lower than normal.
----NTR:decreased level of pyocyanin
A single species cell phenotype in which the amount of pyocyanin measured in a cell is lower than normal.
-----NTR:pyocyanin absent
A single species cell phenotype in which the amount of pyocyanin measured in a cell is too low to detect.

Move below DON terms under 'altered cellular toxin level'

[CuzickA]

0d48328 Added altered cellular toxin level terms to single species branch as above

[CuzickA]

36ff067 Moved and updated 'decreased/increased level of DON' and 'DON absent'

[CuzickA]

a170c41
'deoxynivalenol present' moved under 'normal level of substance in cell' under single species branch

Currently unsure as to whether we want his to be 'present' or 'normal'. Therefore have 'present' in term name but 'normal' in text def. May need to see how term is used in annotation before making a decision.

[CuzickA]

88499fd
Note: Also updated PHI branch with 'altered toxin level in pathogen host interaction'