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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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resistance to cold stress and heat stress phenotypes need editing #249

Open dsiegele opened 6 years ago

dsiegele commented 6 years ago

The resistance to cold stress and resistance to heat stress terms need editing to clarify the difference between these terms and the terms for microbial population growth at low and high temperature. Use definitions in FYPO as a guide. cold stress should be renamed cold shock and defined heat stress should be renamed heat shock and defined

dsiegele commented 6 years ago

Consider wording from FYPO to distinguish between growth in condition that is not optimal, but is still not lethal for the designated control.

FYPO_0001989 sensitive to low pH def. A cell phenotype observed in the vegetative growth phase of the life cycle in which cells show increased sensitivity to pH lower than that of standard S. pombe growth media (about 5.8). Cells stop growing (and may die) at a pH that allows wild type cells to grow. [ http://www.pombase.org/spombe/result/mah ]

jimhu-tamu commented 6 years ago

Also check on shift phenotypes for nutrients

dianeoinglis commented 5 years ago

Hi.

I'd like to comment that terms for heat stress when applied to a culture as a pulse at a higher/lower than normal temperature for the organism is considered a "shock" stress that is a type "heat stress" but not the other way around. So, if heat stress is edited to heat shock, will there be terms for population growth at higher/lower than normal temperature?

Survival at mammalian host temperature (37 degrees C) is a common temperature assay for pathogens that is definitely not a "heat shock" but is a "heat stress." This assay is not performed in non-pathogenic model yeasts such as S. pombe or S. cerevisiae as it is a lethal temperature and can only be assessed as a shock-type heat stress in these yeasts.

While browsing, I found the following terms are related in the wrong parent/child order as "heat shock" is_a "heat" but not the other way around as defined. OMP: 0007585 altered resistance to heat is_a OMP: 0007579 resistance to heat shock phenotype

The following term does not make sense, at all as "thermotolerance" is an adaption state/phenpotype of the organism, not the condition that it responds to. Consider rewording to "response to heat stress phenotype" OMP: 0005082 response to thermotolerance stress phenotype

It will be great to see the terms edited for clarity and the parentages in accurate order.

Thanks, Diane

dianeoinglis commented 5 years ago

By the way, the term thermotolerance is not a simple resistance to high temp. It is a phenotype that is acquired after some prior exposure to stress.