cell growth and viability phenotypes

[ValWood]

For sensitivity and lethality phenotypes, I recommend that you mirror the FYPO ontology, since these are already logically defined.

• FYPO has a high level split for “population level phenotypes” and “cell level phenotypes”
• Viability phenotypes can be “cell level” or population level”
• Most users are interested in “population level” phenotypes for viability.
  We refer to “inviable population” inviable phenotypes have the synonym “lethal”
• Some viability terms are cell level phenotypes. This gives us the ability to capture for instance “cell lysis” or “mitotic catastrophe” with a penetrance 40% if 40% of cells die, (this would still be a “viable population”).
• We can also capture reduced growth and viability.
• Chemical sensitivities and resistances are also captured as “population phenotypes” (cell growth assay evidence)

I would begin your ontology development with the “population phenotypes” branch, as you can largely mirror the FYPO logical refs, and just copy the terms you need, and add any missing ones.

Do not worry if some of your “high level terms” become somewhat buried. We can make these more prominent in the curtain tool longer term using “ontology subsets”

NB. Many "viability calls" are in a “grey area” where they are conditionally lethal depending on environment and nutrients.

[CuzickA]

One of our nine high level phenotype terms is 'lethal'
Here is the past definition

As discussed this has been split into cell level 'inviable cell' and population level 'inviable cell population'

@ValWood you mention above that * “inviable population” inviable phenotypes have the synonym “lethal” so would this term be the equivalent of our high level 'lethal' term above? Does the cell level 'inviable cell' not have the 'lethal' synonym?

[ValWood]

We do:

synonym: "lethal in cell" EXACT [PomBase:mah] to name: inviable cell
synonym: "lethal in vegetative cell" EXACT [PomBase:mah]
synonym: "lethal in cell population" EXACT [PomBase:mah] to name: inviable cell population

I would also add
synonym: "lethal” BROAD to these important terms.
This will hopefully make these main terms most prominent in the search ( if not we can tweak this).
We will aim to make these terms be at the top of the suggestion list if anyone types “lethal”. If users can see these 2 terms
inviable cell
inviable cell population

together at the top of the term suggestions search results it is much clearer which term to use. I notice that for FYPO these terms are currently a bit buried in the search, and our users often select the wrong one (or curate only the cell level phenotype and not the population level phenotype....it's the population level term that most people want when distinguishing lethal/non-lethal )

[ValWood]

actually, I think you will only be able to logically define the "cell level inviable"

@mah11 has done
intersection_of: PATO:0000718 ! lethal (sensu genetics)
intersection_of: inheres_in CL:0000334 ! vegetative cell (sensu Fungi)
relationship: inheres_in CL:0000334 ! vegetative cell (sensu Fungi)

but you will obviously need a more general cell term.

It seems that @mah11 has not yet logically defined the population level terms > Is that correct?

[mah11]

It seems that @mah11 has not yet logically defined the population level terms > Is that correct?

It's entirely theoretically possible to have a logical definition for 'inviable cell population', but in practice I haven't figured out what to use to refer to a 'cell population'. I should have another look at the Population and community ontology again some time ... maybe along with the POTATO refactoring ...

[ValWood]

So @CuzickA in general, at this stage you only need to think about logical defs for terms which are clearly derived from GO, SO or CHEBI + PATO. I wouldn't worry about logical definitions which don't fit these patterns at present. It is likely that the ontology will not be too complex in these areas so the benefits for ontology maintenance won't probably be worth the effort of trying to define them until much later. My rule of thumb would be if @mah11 hasn't logically defined the equivalent term in FYPO, than it's likely to be a bit tricker.

Sometime this year @mah11 will be working on refactoring FYPO to align with POTATO Unified Phenotype Ontology, not the plant!), so we can let you know if any design patterns change substantially.

[CuzickA]

As discussed in this mornings meeting
We would like to identify when altering a gene product is 'essential for life' and there is no pathogen to take forward into experiments compared to when eg a chemical is added to a pathogen that kills it.
We have used the PHI-base phenotype 'lethal' to describe the 1st situation. It is possible that we may want to capture the 'essential for life' information as an AE to 'inviable cell population'.

[CuzickA]

Closing ticket for now.
We currently have PHIPO:0000513
'inviable population' with exact synonym 'lethal' and related 'essential'