How to represent "delivery mechanism"

[ValWood]

I might need 2 new conditions, or they might exist with another nameand I didn't locate them.

"transgenic host expression" (or similar)
pombase/canto#2049

where the pathogen gene is transfected into the host

"host cell suspension" where the assay is done in a host cell suspension, not actually in vivo

[CuzickA]

I haven't had time to add to the conditions ontology in a while. This ticket would be a useful place to collect 'conditions' for adding in the future.

Where the assay is done in a ''host cell suspension'' would we still have this host in the metagenotype and add 'cell culture' as tissue type AE or is it better to have metagenotype and add ''host cell suspension'' to conditions? @ValWood
#18 PMID:30220500 Suppression of Plant Immunity by Fungal Chitinase-like Effectors. Also contains host cell suspension expts.

[CuzickA]

Some of these are a bit tricky and may not really fit into conditions but are still important to capture.

How the pathogen protein is delivered into the host is important, has a purified protein been infiltrated into a plant leaf or has the pathogen asexual spore germinated on the leaf tissue, used a penetration structure to enter and then secreted pathogen proteins into host etc?

In some expt the host tissue may need to be wounded to enable the pathogen to enter.

@ValWood perhaps we can we talk through conditions on Monday.

[ValWood]

It does. But its an odd one.

Often multiple mechanisms are used to get the protein into the plant will be used but then the same assays will be perfomed. This prevents us from using the normal set of methods to describe the experiment. It would be cumbersome to have:

cell growth assay after purified protein infiltrated onto plant leaf
enzyme assay data after purified protein infiltrated onto plant leaf
etc

In reality, we know that we probably need to extend the phenotype curation interface to include a method for "delivery mechanism" but .that requires a lot of changes and we need to capture this information now, in a way that allows the curation sessions to be approved, and makes them easy to locate. ....So this is more of a short-term stop-gap whilst we figure out what to do.

[ValWood]

@CuzickA actions

We need t to collect a new datatype "delivery mechanism"
Temporarily we will add "delivery mechanisms" as "conditions.
Begin a spreadsheet with links to the sessions + types of delivery mechanism, so we can build up a list which covers most options (keeping quite general).
Then these will need to be in a small vocabulary somewhere.
Once we have a the list, and providing we don't identify any further issues , we can open a Canto tracker ticket with a mockup.

@jseager7 James it might be better for us to keep this ticket on the curation tracker for now?

[ValWood]

List so far:
infiltration on plant leaf
endogenous delivery mechanism using transgenic species (there is probably a better way to say this?)
pathogen gene expressed by transgenic host

[ValWood]

delivery mechanism required for
#44

@CuzickA we should prioritise to discuss this ticket next week

[CuzickA]

https://docs.google.com/spreadsheets/d/1D39pqcpO5mxr_wVCgYWtVGEujqV3Pq1LJZTug3WF4TI/edit#gid=0

Started spreadsheet. Required for #19

[CuzickA]

See #91 want to annotate expts with i)purified pathogen effector infiltrated into host and ii) effector delivered naturally by pathogen inoculation.

and #89 transient and stable transgenic hosts containing pathogen gene (and then inoculated with wild type pathogen)

[CuzickA]

This is what we currently have in PHI-ECO

[CuzickA]

Also have these terms under 'grouping excess'

[CuzickA]

Would it be clearer for the 'delivery mechanism terms' to have this as a term prefix? @ValWood

eg
delivery mechanism: agrobacterium
delivery mechanism: culture infiltration

I think this would be helpful whilst terms still listed under 'conditions' but may not be necessary once we have a new selector option for 'delivery mechanism'.

[CuzickA]

I think we need this NTR condition for #89
'pathogen gene expressed by transgenic host'

[ValWood]

That would probably help. The mechanisms might be a bit 'obscure' but it the text can indicate the help test can indicate start typing "delivery mechanism" that would help and could be removed from term names later.

[CuzickA]

Now looks like this

[CuzickA]

Closing ticket for now as we have decided to keep the 'delivery mechanism' within the 'conditions' option. The term prefix 'delivery mechanism:' makes searches for these terms much easier. We will add some help text.