While working on issue #147 I recognized a difference in how resistance to stress phenotype terms were organized in OMP compared to FYPO. In OMP, terms for altered resistance or sensitivity to an environmental stress were descendants of 'OMP:0000173 response to stress'. For example, 'OMP:0005122 altered resistance to oxidative stress' was a child of 'OMP:0005038 response to oxidative stress phenotype', which is a child of 'OMP:0000173 response to stress phenotype'.
In FYPO 'resistance to stress' and 'response to stress' are separate branches of the ontology. FYPO phenotype terms for increased or decreased resistance to a stress are descendants of 'FYPO_0002046 resistance to stress', which is defined as "A phenotype in which cells in a population show decreased sensitivity to a stress. Typically, a cell population are deemed resistant to a stress if cells in the population grow and divide when exposed to the stress at an intensity at which wild-type cells stop growing (and may die)." The comment for FYPO:0002046 includes the recommendation: "Use a descendant of this term if you have assayed growth of cells exposed to a stress in culture. If you have assayed the response to the stress at the subcellular or molecular level, consider annotating to a descendant of 'abnormal cellular response to stress' (FYPO:0000162)."
The FYPO terms for 'normal cellular response to stress' (FYPO_0005191) and 'abnormal cellular response to stress' (FYPO_0000162) are descendants of 'cellular response phenotype' (FYPO_000xxx), which has a logical definition that includes a cross-product with 'cellular response to stress' (GO_0033554). The definition of GO:0033554 is: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)."
The definitions for the existing altered resistance to a stress terms in OMP were already consistent with the definition of resistance to stress in FYPO. But to make the organization of OMP compatible with that of FYPO, I needed to change the parentage of these terms.
i) I created a high-level term 'resistance to stress phenotype' (OMP:0007568). (Note: The definition of this term was edited after I posted to issue #147 . The newer definition is: 'A population growth phenotype related to the resistance or sensitivity that microbes in a population show to a stress. Typically, a population is deemed resistant to a stress if microbes in the population grow and multiply when exposed to the stress. A population is deemed sensitive to a stress if microbes in the population stop growing and multiplying (and may die) when exposed to the stress.')
ii) I created child terms of 'resistance to stress phenotype' for individual stresses, including 'OMP:xx resistance to oxidative stress phenotype,' 'OMP:xx resistance to heat phenotype,' and 'OMP:xx resistance to cold phenotype.'
iii) I moved the existing 'altered resistance to a particular stress' terms to the appropriate parent from (ii) and edited the definitions.
iv) I moved 'OMP:0000173 response to stress phenotype' and its descendants to be children of biological process phenotype. We should discuss whether this is the right place for it to be or whether it should be a child of cellular process phenotype. Issue: Can OMP terms with the parent 'cellular process phenotype' be applied to viruses? I think so because virus reproduction occurs at the cellular/subcellular level.
v) I edited the descendants of 'OMP:xx response to stress phenotype' to make sure the term names include 'response to.' I am still in the process of editing the definitions.
Note: This explanation is also relevant to NTR #102 and NTR #112.
While working on issue #147 I recognized a difference in how resistance to stress phenotype terms were organized in OMP compared to FYPO. In OMP, terms for altered resistance or sensitivity to an environmental stress were descendants of 'OMP:0000173 response to stress'. For example, 'OMP:0005122 altered resistance to oxidative stress' was a child of 'OMP:0005038 response to oxidative stress phenotype', which is a child of 'OMP:0000173 response to stress phenotype'.
In FYPO 'resistance to stress' and 'response to stress' are separate branches of the ontology. FYPO phenotype terms for increased or decreased resistance to a stress are descendants of 'FYPO_0002046 resistance to stress', which is defined as "A phenotype in which cells in a population show decreased sensitivity to a stress. Typically, a cell population are deemed resistant to a stress if cells in the population grow and divide when exposed to the stress at an intensity at which wild-type cells stop growing (and may die)." The comment for FYPO:0002046 includes the recommendation: "Use a descendant of this term if you have assayed growth of cells exposed to a stress in culture. If you have assayed the response to the stress at the subcellular or molecular level, consider annotating to a descendant of 'abnormal cellular response to stress' (FYPO:0000162)."
The FYPO terms for 'normal cellular response to stress' (FYPO_0005191) and 'abnormal cellular response to stress' (FYPO_0000162) are descendants of 'cellular response phenotype' (FYPO_000xxx), which has a logical definition that includes a cross-product with 'cellular response to stress' (GO_0033554). The definition of GO:0033554 is: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)."
The definitions for the existing altered resistance to a stress terms in OMP were already consistent with the definition of resistance to stress in FYPO. But to make the organization of OMP compatible with that of FYPO, I needed to change the parentage of these terms.
i) I created a high-level term 'resistance to stress phenotype' (OMP:0007568). (Note: The definition of this term was edited after I posted to issue #147 . The newer definition is: 'A population growth phenotype related to the resistance or sensitivity that microbes in a population show to a stress. Typically, a population is deemed resistant to a stress if microbes in the population grow and multiply when exposed to the stress. A population is deemed sensitive to a stress if microbes in the population stop growing and multiplying (and may die) when exposed to the stress.')
ii) I created child terms of 'resistance to stress phenotype' for individual stresses, including 'OMP:xx resistance to oxidative stress phenotype,' 'OMP:xx resistance to heat phenotype,' and 'OMP:xx resistance to cold phenotype.'
iii) I moved the existing 'altered resistance to a particular stress' terms to the appropriate parent from (ii) and edited the definitions.
iv) I moved 'OMP:0000173 response to stress phenotype' and its descendants to be children of biological process phenotype. We should discuss whether this is the right place for it to be or whether it should be a child of cellular process phenotype. Issue: Can OMP terms with the parent 'cellular process phenotype' be applied to viruses? I think so because virus reproduction occurs at the cellular/subcellular level.
v) I edited the descendants of 'OMP:xx response to stress phenotype' to make sure the term names include 'response to.' I am still in the process of editing the definitions.
Note: This explanation is also relevant to NTR #102 and NTR #112.