ROS production

[ValWood]

PHIPO:0001156 | increased level of pathogen reactive oxygen species production within host and PHIPO:0001155 | decreased level of pathogen reactive oxygen species production within host

are confusing terms, and are not used.

They initially prevented me locating the term I needed

PHIPO:0000927 | pathogen induced host reactive oxygen species present

Do you know what they were added for? If not I suggest obsoletion (as an aside I'm not sure that the source of the ROS in a host can really be differentiated, but host is always assumed)

[CuzickA]

I think these terms were added to describe the ROS production within the pathogen during host colonization rather than the host produced ROS whne challenged with a pathogen.

[CuzickA]

Does this help @ValWood

[ValWood]

Yes but is the level of pathogen ROS production ever observed? Do you have an example (have pathogens evolved to increase ROS production sometimes to activate the host immune system?).

[CuzickA]

Hmm I remember talking with Martin in the past about a paper where the pathogen ROS production was observed. I can't remember which session though.

If these terms have not been used perhaps I should obsolete them? PHIPO:0001156 | increased level of pathogen reactive oxygen species production within host and PHIPO:0001155 | decreased level of pathogen reactive oxygen species production within host

[ValWood]

I think I would obsolete to avoid confusion unless we have a real case where we know this is part of the PHI. Pathogenes will increase ROS production when they increase respiration but I'm not sure that alone is a reason to include.

[CuzickA]

I have just checked the list of used terms from James and found this

@jseager7 please could you let me know which curation session this term has been used in?

[ValWood]

That's weird. I loaded the used term ontology and searched for these but did not find this?

[jseager7]

@ValWood The term should be in the used terms ontology that I sent you, since I can find it:

You might want to use the search function in Protege (Cmd+F) and search for 'PHIPO:0001155'. Make sure you've got 'Search in annotation values' enabled:

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please could you let me know which curation session this term has been used in?

@CuzickA Oddly enough it doesn't appear in the export, which implies it's not used in any curation sessions. Maybe it was something that was in use when I produced the ontology but has been removed since. If you notice many more problems like this, that might point to something being wrong with my methods.

[CuzickA]

What did we decide to do here?

[ValWood]

I think we first need to see find an example of

PHIPO:0001156 | increased level of pathogen reactive oxygen species production within host

(I'm interested how it is possible to tell which species is producing the ROS!)

[CuzickA]

So we still need to track down the session where i used

PHIPO:0001155 | decreased level of pathogen reactive oxygen species production within host

[jseager7]

So we still need to track down the session where i used PHIPO:0001155

The only session is PMID:17041146.

[ValWood]

OK I get it now. It's the one where a pathogen enzyme increases host ROS production. I was thinking it was referring to ROS production in the pathogen.

( I think, because the way the term is worded:

" increased level of pathogen reactive oxygen species production within host"

I wiondefr if we need to differentiate at the pehnotype level

In some terms we call it PHIPO:0000927 | pathogen-induced host reactive oxygen species present which is much clearer.

[CuzickA]

Here is the annotation. The top annotation refers to pathogen ROS, whereas the control annotation below refers to host ROS??

[ValWood]

OK yes sorry it makes sense how it is.

[CuzickA]

I still think this second annotation is a bit odd as a control. Maybe it should be 'NTR: pathogen ROS production within host present' or similar?

[ValWood]

That might be better. They are a bit of a mouthful either way ;)

[CuzickA]

@ValWood Do you think the three 'ROS' terms need a grouping term?

Still need to update above annotation once NTR loaded.

[ValWood]

maybe wait, it can be added later if needed.

[CuzickA]

session updated with NTR