Difference between revisions of "Help:FAQ"
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The 'decreased phenotype X' would be used when a phenotype is decreased, but can still be detected. For example, OMP:0000002 decreased cell motility would be used to describe the phenotype of a mutant strain that is less motile than the parent strain, but still retains some motility. Either OMP:0000002 or OMP:0007000 abolished cell motility could be used to describe the phenotype of a mutant that has no detectable motility because abolished motility is the limit case of decreased motility | The 'decreased phenotype X' would be used when a phenotype is decreased, but can still be detected. For example, OMP:0000002 decreased cell motility would be used to describe the phenotype of a mutant strain that is less motile than the parent strain, but still retains some motility. Either OMP:0000002 or OMP:0007000 abolished cell motility could be used to describe the phenotype of a mutant that has no detectable motility because abolished motility is the limit case of decreased motility | ||
| − | == Why | + | == Why not use the term 'absence of X' to describe a mutant phenotype?== |
| − | + | OMP uses the 'absence of X' to annotate an independent phenotype<ref name='PMID:25433798'/>, i.e. it provides information about an organism without reference to any other information. The phenotype of a mutant strain is typically being observed as a relative difference observed between the phenotypes of at least two separate genotypes. If a member of a newly identified bacterial taxon were observed to move, it would have the independent phenotype “presence of cell motility”. However, if a mutant strain was isolated that was less motile, then that strain would be described by the dependent phenotype “decreased cell motility,” which is relative to the strain used as a reference. An organism that was non-motile, such as Klebsiella pneumonia, would have the independent phenotype “absence of cell motility” | |
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== References == | == References == | ||
Latest revision as of 19:07, 16 March 2015
What is the difference between 'decreased phenotype X' and 'abolished phenotype X'?
The 'decreased phenotype X' would be used when a phenotype is decreased, but can still be detected. For example, OMP:0000002 decreased cell motility would be used to describe the phenotype of a mutant strain that is less motile than the parent strain, but still retains some motility. Either OMP:0000002 or OMP:0007000 abolished cell motility could be used to describe the phenotype of a mutant that has no detectable motility because abolished motility is the limit case of decreased motility
Why not use the term 'absence of X' to describe a mutant phenotype?
OMP uses the 'absence of X' to annotate an independent phenotype[1], i.e. it provides information about an organism without reference to any other information. The phenotype of a mutant strain is typically being observed as a relative difference observed between the phenotypes of at least two separate genotypes. If a member of a newly identified bacterial taxon were observed to move, it would have the independent phenotype “presence of cell motility”. However, if a mutant strain was isolated that was less motile, then that strain would be described by the dependent phenotype “decreased cell motility,” which is relative to the strain used as a reference. An organism that was non-motile, such as Klebsiella pneumonia, would have the independent phenotype “absence of cell motility”
References
See Help:References for how to manage references in OMPwiki.
- ↑ Chibucos, MC et al. (2014) An ontology for microbial phenotypes. BMC Microbiol. 14 294 PubMed OMPwiki page
