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microbialphenotypes / OMP-ontology

This repository contains the editors's working copy of OMP and public release files.
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Term for essential genes #163

Open sandylabonte opened 8 years ago

sandylabonte commented 8 years ago

we need terms for essential and nonessential genes or viable vegetative cell population or nonviable vegetative cell population

dsiegele commented 8 years ago

still working on this:

Terms currently in OMP: OMP:0007259 viability phenotype ! A microbial phenotype related to the ability of an organism to survive and/or reproduce. .....OMP:0007260 altered viability ..........OMP:0007261 decreased viability ...............OMP:0007391 abolished viability ..........OMP:0007262 increased viability

Viability phenotypes in other ontologies: PATO:0000169 ! viability
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.

APO:0000111 ! viability The proportion of cells in a sample that are viable, i.e. able to form colonies. Often measured by spotting aliquots of a dilution series on a plate.

FYPO:0000004 ! cell viability
A cell phenotype that consists of the cell's disposition to survive and develop normally.

FYPO:0000124 ! viable cell A viability phenotype in which a cell is able to survive under the specified conditions. (is_a cell viability)

FYPO:0002057 ! cell population viability
A cell population phenotype that reflects the proportion of the population that survive and develop normally.

FYPO:0002058 ! viable cell population A cell population phenotype in which cells in the population are viable. (is_a cell population viability)

CMPO:0000013 ! cell viability phenotype
A phenotype relating to the ability of a cell survive or to develop normally

CMPO:0000160 ! cell population viability phenotype
A phenotype of a cell population relating to the ability of the cells to live and develop normally

dianeoinglis commented 8 years ago

Hello Debby,

Can the xref "APO:0000112 inviable" be added to "OMP:0007391 abolished viability?"

Thank you! Diane

dsiegele commented 8 years ago

Added "APO:0000112 inviable" as xref to "OMP:0007391 abolished viability" and OMP:0007393 nonviable cell."

dsiegele commented 8 years ago

Added terms for viable and nonviable cell populations and vegetative cell populations.

dianeoinglis commented 8 years ago

Hi,

In practice, the APO term that is used is and displayed is "APO:0000113: viable" rather than "APO:0000111 ! viability." By the way, I'll just mention how that term was used for annotations in Cryptococcus.

This term was not used for genes/proteins that had some phenotype as one can infer the mutant strain was viable if a phenotype of some sort was observed. When there was no phenotype whatsover to record, we felt it was important to indicate that a knock-out or mutant has been made and the mutant could be obtained (not an essential gene). Only when there was no phenotype to record did we apply the term "viable."

As an aside, how does one discern the difference between a mutation that would be annotated with "increased viability" vs. a strain that simply proliferates faster? Just curious.

Diane

dsiegele commented 8 years ago

Thank you for the information on how "viable" was used for annotation in Cryptococcus. I'll bring this up for discussion on one of the OMP group calls.

I imagine increased/decreased viability being used to indicate either that a wild-type cell is different viability in two conditions or that a mutant and parent strain have different viability in a given condition. Depending on how the experiment was performed you might not be able to distinguish between a difference in survival and a difference in proliferation rate. Assaying proliferation rate would be a separate phenotype.