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Siegele: /* Why not use the term 'absence of X' to describe a mutant phenotype? */

2015-03-17T00:07:13Z

‎Why not use the term 'absence of X' to describe a mutant phenotype?

Siegele at 00:06, 17 March 2015

2015-03-17T00:06:15Z

Siegele: /* What is the difference between 'decreased phenotype X' and 'abolished phenotype X'? */

2015-03-16T23:50:50Z

‎What is the difference between 'decreased phenotype X' and 'abolished phenotype X'?

Siegele at 23:48, 16 March 2015

2015-03-16T23:48:37Z

Azweifel at 19:14, 30 June 2011

2011-06-30T19:14:52Z

JimHu: /* Why not use the non-X term, e.g. nonmotile or catalase negative */

2011-06-06T21:32:13Z

‎Why not use the non-X term, e.g. nonmotile or catalase negative

JimHu at 21:28, 6 June 2011

2011-06-06T21:28:30Z

JimHu: Created page with ' Category:Help'

2011-06-06T21:21:52Z

Created page with ' Category:Help'

New page

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 == Why not use the term 'absence of X' to describe a mutant phenotype?==
-OMP uses the 'absence of X' to annotate an independent phenotype, 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”
+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”
 == References ==

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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
-== Why would you describe a complete loss as decreased X, which a child of X positive? ==
+== Why not use the term 'absence of X' to describe a mutant phenotype?==
-Example:
+OMP uses the 'absence of X' to annotate an independent phenotype, 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 ==

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 == 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:xx 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:xx or OMP:xx 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 would you describe a complete loss as decreased X, which a child of X positive? ==

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-== Why is there no term for abolished X? ==
+== What is the difference between 'decreased phenotype X' and 'abolished phenotype X'?==
-PATO has a quality named "abolished".  We consider abolished to be the limit case of decreased.  Use decreased X.
+The 'decreased phenotype X' would be used when a phenotype is decreased, but can still be detected.  For example, OMP:xx 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:xx or OMP:xx 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 would you describe a complete loss as decreased X, which a child of X positive? ==

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	== Why is there no term for abolished X? ==		== Why is there no term for abolished X? ==

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 == Why not use the non-X term, e.g. nonmotile or catalase negative ==
+We use terms like nonmotile and catalase negative to annotate properties of a species, while decreased motility or decreased catalase activity are used for mutants where there is less of X than in the reference strain (wt or a parent), which is motile and catalase positive.
 == References ==

← Older revision		Revision as of 21:28, 6 June 2011
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		+	== Why is there no term for abolished X? ==
		+	PATO has a quality named "abolished". We consider abolished to be the limit case of decreased. Use decreased X.
		+
		+	== Why would you describe a complete loss as decreased X, which a child of X positive? ==
		+	Example:
		+	* decreased motility is a child of motile
		+	* decreased catalase activity is a child of catalase activity
		+
		+	== Why not use the non-X term, e.g. nonmotile or catalase negative ==
		+
		+
		+	== References ==
		+	{{RefHelp}}
		+	<references/>

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