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fyeco.obo
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format-version: 1.2
date: 30:07:2021 14:14
saved-by: midori
auto-generated-by: OBO-Edit 2.3.1
subsetdef: Grouping_terms "High level terms not used for direct annotation, but for organizing more specific terms in the ontology."
default-namespace: fission_yeast_phenotype_condition
ontology: fyeco
[Term]
id: FYECO:0000001
name: fission yeast phenotype condition
def: "Any aspect of an experiment that the experimenter controls and that does not depend on which strain/organism/cells are used." [PomBase:al]
subset: Grouping_terms
synonym: "phenotype condition" RELATED [PomBase:al]
created_by: antonialock
creation_date: 2012-02-07T11:36:20Z
[Term]
id: FYECO:0000002
name: temperature
def: "Any experimental condition specifying the temperature at which the experiment was performed." [PomBase:al]
subset: Grouping_terms
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-07T12:00:23Z
[Term]
id: FYECO:0000003
name: expression level
def: "The expression level of the gene was altered in the experiment, compared to expressing the gene from the genome and its endogenous promoter." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-07T12:23:02Z
[Term]
id: FYECO:0000004
name: high temperature
def: "The experiment was performed, or cells were grown, at a high temperature (typically exceeding ~32 degrees Celsius)." [PomBase:al]
synonym: "33 degrees Celsius" NARROW [PomBase:al]
synonym: "34 degrees Celsius" NARROW [PomBase:al]
synonym: "35 degrees Celsius" NARROW [PomBase:al]
synonym: "36 degrees Celsius" NARROW [PomBase:al]
synonym: "37 degrees Celsius" NARROW [PomBase:al]
synonym: "38 degrees Celsius" NARROW [PomBase:al]
synonym: "39 degrees Celsius" NARROW [PomBase:al]
synonym: "40 degrees Celsius" NARROW [PomBase:al]
synonym: "41 degrees Celsius" RELATED [PomBase:al]
synonym: "42 degrees Celsius" RELATED [PomBase:al]
synonym: "43 degrees Celsius" RELATED [PomBase:al]
is_a: FYECO:0000132 ! grouping experimental environment
created_by: antonialock
creation_date: 2012-02-07T12:17:29Z
[Term]
id: FYECO:0000005
name: standard temperature
def: "The experiment was performed, or cells were grown in a temperature typically in the range between 25+32 degrees Celsius." [PomBase:al]
synonym: "25 degrees Celsius" NARROW [PomBase:al]
synonym: "26 degrees Celsius" NARROW [PomBase:al]
synonym: "27 degrees Celsius" NARROW [PomBase:al]
synonym: "28 degrees Celsius" NARROW [PomBase:al]
synonym: "29 degrees Celsius" NARROW [PomBase:al]
synonym: "30 degrees Celsius" NARROW [PomBase:al]
synonym: "31 degrees Celsius" NARROW [PomBase:al]
synonym: "32 degrees Celsius" NARROW [PomBase:al]
synonym: "normal temperature" EXACT [PomBase:al]
is_a: FYECO:0000132 ! grouping experimental environment
disjoint_from: FYECO:0000004 ! high temperature
disjoint_from: FYECO:0000006 ! low temperature
created_by: antonialock
creation_date: 2012-02-07T12:17:29Z
[Term]
id: FYECO:0000006
name: low temperature
def: "The experiment was performed, or cells were grown, at a low temperature (typically lower than ~25 degrees Celsius)." [PomBase:al]
synonym: "17 degrees Celsius" NARROW [PomBase:al]
synonym: "18 degrees Celsius" NARROW [PomBase:al]
synonym: "19 degrees Celsius" NARROW [PomBase:al]
synonym: "20 degrees Celsius" NARROW [PomBase:al]
synonym: "21 degrees Celsius" NARROW [PomBase:al]
synonym: "22 degrees Celsius" NARROW [PomBase:al]
synonym: "23 degrees Celsius" NARROW [PomBase:al]
synonym: "24 degrees Celsius" NARROW [PomBase:al]
synonym: "cold" RELATED [PomBase:al]
is_a: FYECO:0000132 ! grouping experimental environment
disjoint_from: FYECO:0000004 ! high temperature
created_by: antonialock
creation_date: 2012-02-07T12:17:29Z
[Term]
id: FYECO:0000007
name: overexpression
def: "The expression level of the gene was increased compared to expressing it from its endogenous promoter in the genome." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-07T12:23:45Z
[Term]
id: FYECO:0000008
name: knockdown
def: "The expression level of the gene was decreased compared to expressing it from its endogenous promoter in the genome." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-07T12:23:45Z
[Term]
id: FYECO:0000009
name: grouping growth medium
def: "Any experimental condition pertaining to the medium in which cells are grown." [PomBase:mah]
subset: Grouping_terms
is_a: FYECO:0000001 ! fission yeast phenotype condition
created_by: antonialock
creation_date: 2012-02-07T12:28:25Z
[Term]
id: FYECO:0000010
name: absence of chemical
alt_id: FYECO:0000018
def: "The experimental conditions included the absence of a chemical." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-07T02:22:00Z
[Term]
id: FYECO:0000011
name: grouping limited
def: "Any experimental condition pertaining to the presence of one or more substances in a limited amount." [PomBase:mah]
subset: Grouping_terms
is_a: FYECO:0000059 ! chemical added or excluded
created_by: antonialock
creation_date: 2012-02-07T02:23:26Z
[Term]
id: FYECO:0000013
name: grouping defined medium
def: "Any experimental condition that describes a defined growth medium, i.e. one in which all constituent substances and their concentrations are known." [PomBase:mah]
subset: Grouping_terms
is_a: FYECO:0000009 ! grouping growth medium
created_by: antonialock
creation_date: 2012-02-07T12:41:33Z
[Term]
id: FYECO:0000015
name: sporulation medium
def: "Experiments were performed in defined medium promoting mating and sporulation." [PomBase:al]
comment: Use the medium terms to specify the general type of growth medium and its carbon source. If certain chemicals not normally found in the medium were added, please also use the 'chemical added/excluded' terms, for instance 'caffeine added' or 'nitrogen excluded'. If a chemical was added in a much lower quantity than normal, please use the 'limited chemical added' conditions, for instance 'limited adenine added'.
synonym: "malt extract medium" NARROW [PomBase:al]
synonym: "mating medium" RELATED [PomBase:al]
synonym: "SPA medium" NARROW [PomBase:al]
is_a: FYECO:0000013 ! grouping defined medium
created_by: antonialock
creation_date: 2012-02-07T01:35:35Z
[Term]
id: FYECO:0000016
name: high glucose MM
def: "Experiments were performed in minimal medium containing a high concentration of glucose (~5-8% typically) as carbon source, salts and water." [PomBase:al]
comment: Use the medium terms to specify the general type of growth medium and its carbon source. If certain chemicals not normally found in the medium were added, please also use the 'chemical added/excluded' terms, for instance 'caffeine added' or 'nitrogen excluded'. If a chemical was added in a much lower quantity than normal, please use the 'limited chemical added' conditions, for instance 'limited adenine added'.
synonym: "high glucose minimal medium" EXACT [PomBase:al]
is_a: FYECO:0000013 ! grouping defined medium
created_by: antonialock
creation_date: 2012-02-07T12:51:06Z
[Term]
id: FYECO:0000021
name: + limited adenine
def: "An experimental condition in which adenine was added to the medium or assay buffers in a limiting quantity compared to standard medium or assay buffers." [PomBase:al]
comment: Example: 5 mg/L adenine compared to 100 mg/L.
xref: PMID:7565608
is_a: FYECO:0000011 ! grouping limited
created_by: antonialock
creation_date: 2012-02-07T02:34:30Z
[Term]
id: FYECO:0000022
name: absence of P-factor
def: "P-factor, the mating pheromone secreted by P-cells, was absent from the experiment." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-07T02:55:29Z
[Term]
id: FYECO:0000023
name: presence of 3',5'-cyclic AMP
def: "Experiments were performed in the presence of cAMP. Presence can either imply exogenous addition of the chemical or the action of adenylate cyclase." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-07T03:09:38Z
[Term]
id: FYECO:0000024
name: + sugar
def: "An experimental condition in which a sugar was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-07T03:09:38Z
[Term]
id: FYECO:0000025
name: + sorbitol
def: "An experimental condition in which sorbitol was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-07T03:09:38Z
[Term]
id: FYECO:0000026
name: + vanadate
def: "An experimental condition in which vanadate was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "sodium orthovanadate added" EXACT [PomBase:al]
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-07T03:09:38Z
[Term]
id: FYECO:0000027
name: presence of mating pheromone
def: "Experiment was performed in the presence of mating pheromone." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-07T03:09:38Z
[Term]
id: FYECO:0000028
name: + TBC
def: "An experimental condition in which TBC was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: This term was made obsolete because it is not clear what chemical TBC refers to.
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-07T03:09:38Z
[Term]
id: FYECO:0000030
name: + ions
def: "An experimental condition in which ions were added to the assay buffer in excess compared to standard assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
subset: Grouping_terms
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-07T03:09:38Z
[Term]
id: FYECO:0000031
name: + K ions
def: "An experimental condition in which potassium ions were added to the assay buffer in excess compared to standard assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "potassium ions added" EXACT [PomBase:al]
is_a: FYECO:0000030 ! + ions
created_by: antonialock
creation_date: 2012-02-07T03:10:12Z
[Term]
id: FYECO:0000032
name: + Cl ions
def: "An experimental condition in which chloride ions were added to the assay buffer in excess compared to standard assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "chloride ions added" EXACT [PomBase:al]
is_a: FYECO:0000030 ! + ions
created_by: antonialock
creation_date: 2012-02-07T03:10:12Z
[Term]
id: FYECO:0000033
name: + Cd ions
def: "An experimental condition in which cadmium ions were added to the assay buffer in excess compared to standard assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "cadmium ions added" EXACT [PomBase:al]
is_a: FYECO:0000030 ! + ions
created_by: antonialock
creation_date: 2012-02-07T03:10:12Z
[Term]
id: FYECO:0000034
name: + Ca ions
def: "An experimental condition in which calcium ions were added to the assay buffer in excess compared to standard assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "Ca ions added" EXACT [PomBase:al]
synonym: "calcium ions added" EXACT [PomBase:al]
is_a: FYECO:0000030 ! + ions
created_by: antonialock
creation_date: 2012-02-07T03:10:12Z
[Term]
id: FYECO:0000035
name: + Cu ions
def: "An experimental condition in which copper ions were added to the assay buffer in excess compared to standard assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "copper ions added" EXACT [PomBase:al]
is_a: FYECO:0000030 ! + ions
created_by: antonialock
creation_date: 2012-02-07T03:10:12Z
[Term]
id: FYECO:0000036
name: + Pb ions
def: "An experimental condition in which lead ions were added to the assay buffer in excess compared to standard assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "lead ions added" EXACT [PomBase:al]
is_a: FYECO:0000030 ! + ions
created_by: antonialock
creation_date: 2012-02-07T03:10:12Z
[Term]
id: FYECO:0000037
name: + Bi ions
def: "An experimental condition in which bismuth ions were added to the assay buffer in excess compared to standard assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "bismuth ions added" EXACT [PomBase:al]
is_a: FYECO:0000030 ! + ions
created_by: antonialock
creation_date: 2012-02-07T03:10:12Z
[Term]
id: FYECO:0000038
name: + Mg ions
def: "An experimental condition in which magnesium ions were added to the assay buffer in excess compared to standard assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "magnesium ions added" EXACT [PomBase:al]
is_a: FYECO:0000030 ! + ions
created_by: antonialock
creation_date: 2012-02-07T03:10:12Z
[Term]
id: FYECO:0000039
name: + P-factor
def: "An experimental condition in which P-factor was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "P factor added" EXACT [PomBase:al]
is_a: FYECO:0000058 ! + mating pheromone
created_by: antonialock
creation_date: 2012-02-07T03:10:36Z
[Term]
id: FYECO:0000040
name: + M-factor
def: "An experimental condition in which M-factor was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "M factor added" EXACT [PomBase:al]
is_a: FYECO:0000058 ! + mating pheromone
created_by: antonialock
creation_date: 2012-02-07T03:10:36Z
[Term]
id: FYECO:0000041
name: sugar alcohol added
def: "An experimental condition in which a sugar alcohol was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-07T03:11:16Z
[Term]
id: FYECO:0000042
name: + fatty acid
def: "An experimental condition in which a fatty acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:alock]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
subset: Grouping_terms
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-07T03:14:49Z
[Term]
id: FYECO:0000043
name: + palmitic acid
def: "An experimental condition in which palmitic acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-02-07T03:17:46Z
[Term]
id: FYECO:0000044
name: + myristic acid
def: "An experimental condition in which myristic acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-02-07T03:17:46Z
[Term]
id: FYECO:0000045
name: + pentadecanoic acid
def: "An experimental condition in which pentadecanoic acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-02-07T03:17:46Z
[Term]
id: FYECO:0000046
name: + margaric acid
def: "An experimental condition in which margaric acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-02-07T03:17:46Z
[Term]
id: FYECO:0000047
name: + stearic acid
def: "An experimental condition in which stearic acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-02-07T03:17:47Z
[Term]
id: FYECO:0000048
name: + petroselinic acid
def: "An experimental condition in which petroselinic acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-02-07T03:17:47Z
[Term]
id: FYECO:0000049
name: + oleic acid
def: "An experimental condition in which oleic acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-02-07T03:17:47Z
[Term]
id: FYECO:0000050
name: + linoleic acid
def: "An experimental condition in which linoleic acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-02-07T03:17:47Z
[Term]
id: FYECO:0000051
name: + linolenic acid
def: "An experimental condition in which linolenic acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-02-07T03:17:47Z
[Term]
id: FYECO:0000052
name: + arachidic acid
def: "An experimental condition in which arachidic acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-02-07T03:17:47Z
[Term]
id: FYECO:0000053
name: + melissic acid
def: "An experimental condition in which melissic acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-02-07T03:17:47Z
[Term]
id: FYECO:0000054
name: glycerol MM
alt_id: FYECO:0000077
def: "Experiments were performed in minimal medium where glycerol is the sole carbon source (i.e. NO addition of glucose/ethanol etc at all)." [PomBase:al]
comment: Use the medium terms to specify the general type of growth medium and its carbon source. If certain chemicals not normally found in the medium were added, please also use the 'chemical added/excluded' terms, such as 'caffeine added' or 'nitrogen excluded'. If a chemical was added in a much lower quantity than normal, please use the 'limited chemical added' conditions, for instance 'limited adenine added'.
synonym: "glycerol minimal medium" EXACT [PomBase:al]
is_a: FYECO:0000013 ! grouping defined medium
created_by: antonialock
creation_date: 2012-02-07T03:29:51Z
[Term]
id: FYECO:0000055
name: M and P factor produced
def: "Both M-factor and P-factor, endogenously produced by cells, were present in the experiment." [PomBase:al]
synonym: "presence of M-factor and P-factor" EXACT [PomBase:al]
synonym: "presence of mating pheromones" EXACT [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-07T03:37:43Z
[Term]
id: FYECO:0000056
name: + 3,5-cyclic AMP
def: "An experimental condition in which 3'5'-cyclic AMP was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [CHEBI:17489]
comment: Note that this term includes both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
xref: CHEBI:17489 "3',5'-cyclic AMP"
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-07T05:07:31Z
[Term]
id: FYECO:0000057
name: 3'5'-cyclic AMP produced
def: "The experiment was performed under conditions such that cAMP was produced endogenously." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-07T05:10:53Z
[Term]
id: FYECO:0000058
name: + mating pheromone
def: "An experimental condition in which mating pheromone (M factor and P factor) was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
subset: Grouping_terms
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-07T05:25:01Z
[Term]
id: FYECO:0000059
name: chemical added or excluded
alt_id: FYECO:0000017
alt_id: FYECO:0000019
alt_id: FYECO:0000020
def: "Any experimental condition that specifies one or more chemical(s) that are added to, or excluded from, growth medium, assay buffer, etc." [PomBase:mah]
subset: Grouping_terms
synonym: "chemical added" RELATED [PomBase:al]
synonym: "chemicals" RELATED [PomBase:al]
is_a: FYECO:0000001 ! fission yeast phenotype condition
created_by: antonialock
creation_date: 2012-02-07T05:36:48Z
[Term]
id: FYECO:0000060
name: chemical produced
def: "Chemical was endogenously produced in the experiment." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-07T05:37:05Z
[Term]
id: FYECO:0000061
name: + xenobiotic substrate
def: "An experimental condition in which a xenobiotic substrate was added to the medium or assay buffer in excess compared to standard medium or assay buffers. A xenobiotic substrate is a macromolecular substrate which is not synthesised by S. pombe." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-10T11:50:01Z
[Term]
id: FYECO:0000062
name: absence of nitrogen
def: "Nitrogen was absent from the experiment." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-08T07:33:48Z
[Term]
id: FYECO:0000063
name: absence of 3'5'-cyclic AMP
def: "3'5'-cyclic AMP was absent from the experiment." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-10T12:15:58Z
[Term]
id: FYECO:0000064
name: + inositol
def: "An experimental condition in which inositol was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-13T02:35:48Z
[Term]
id: FYECO:0000065
name: absence of adenine
def: "Adenine was absent from the experiment." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-13T02:53:59Z
[Term]
id: FYECO:0000066
name: absence of inositol
def: "Inositol was absent from the experiment." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-14T03:15:13Z
[Term]
id: FYECO:0000067
name: + lauric acid
def: "An experimental condition in which lauric acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-02-14T03:18:35Z
[Term]
id: FYECO:0000068
name: + vaccenic acid
def: "An experimental condition in which vaccenic acid was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-02-14T03:21:32Z
[Term]
id: FYECO:0000069
name: + caffeine
def: "An experimental condition in which caffeine was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term includes both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-15T12:28:11Z
[Term]
id: FYECO:0000070
name: absence of uracil
def: "Uracil was absent from the experiment." [PomBase:al]
is_obsolete: true
created_by: antonialock
creation_date: 2012-02-15T12:40:35Z
[Term]
id: FYECO:0000071
name: + 1-Na-PP1
def: "An experimental condition in which 1-Na-PP1 was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "1-Na-PP1 present" EXACT [PomBase:al]
synonym: "4-amino-1-tert-butyl-3-(1'-naphthyl)pyrazolo[3,4-d]pyrimidine added" EXACT [CHEBI:52310]
synonym: "4-amino-1-tert-butyl-3-(1'-naphthyl)pyrazolo[3,4-d]pyrimidine present" EXACT [CHEBI:52310]
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-19T10:45:53Z
[Term]
id: FYECO:0000072
name: glycerol MM with trace glucose
def: "Experiments were performed in minimal medium where glycerol is the main carbon source, but the medium also contained trace amounts of glucose (<0.1%)." [PomBase:al]
comment: Use the medium terms to specify the general type of growth medium and its carbon source. If certain chemicals not normally found in the medium were added, please also use the 'chemical added/excluded' terms, for instance 'caffeine added' or 'nitrogen excluded'. If a chemical was added in a much lower quantity than normal, please use the 'limited chemical added' conditions, for instance 'limited adenine added'.
synonym: "glycerol main carbon source + very low glucose MM" EXACT [PomBase:al]
synonym: "glycerol minimal medium with trace glucose" EXACT [PomBase:al]
is_a: FYECO:0000013 ! grouping defined medium
created_by: antonialock
creation_date: 2012-02-27T12:12:17Z
[Term]
id: FYECO:0000073
name: DHA minimal medium
def: "Experiments were performed in minimal medium where DHA (dihydroxyacetone) is the main carbon source." [PomBase:al]
comment: Use the medium terms to specify the general type of growth medium and its carbon source. If certain chemicals not normally found in the medium were added, please also use the 'chemical added/excluded' terms, for instance 'caffeine added' or 'nitrogen excluded'. If a chemical was added in a much lower quantity than normal, please use the 'limited chemical added' conditions, for instance 'limited adenine added'.
synonym: "DHA MM" EXACT [PomBase:al]
synonym: "dihydroxyacetone MM" EXACT [PomBase:al]
synonym: "dihydroxyactone minimal medium" EXACT [PomBase:al]
is_a: FYECO:0000013 ! grouping defined medium
created_by: antonialock
creation_date: 2012-02-27T12:15:46Z
[Term]
id: FYECO:0000074
name: + NAD+
def: "An experimental condition in which NAD+ was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-27T01:14:00Z
[Term]
id: FYECO:0000075
name: + NADP+
def: "An experimental condition in which NADP+ was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-27T01:14:35Z
[Term]
id: FYECO:0000076
name: + dihydroxyacetone
def: "An experimental condition in which dihydroxyacetone was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "DHA added" EXACT [PomBase:al]
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-27T04:02:57Z
[Term]
id: FYECO:0000078
name: + H2O2
def: "An experimental condition in which hydrogen peroxide was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "hydrogen peroxide added" EXACT [PomBase:al]
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-02-29T03:06:23Z
[Term]
id: FYECO:0000079
name: + thiabendazole
def: "An experimental condition in which thiabendazole was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "TBZ added" EXACT [PomBase:al]
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-03-12T02:59:23Z
[Term]
id: FYECO:0000080
name: grouping rich medium
def: "Any experimental condition that describes a rich growth medium, i.e. one in which not all constituent substances and their concentrations are specified, and some are present in excess." [PomBase:mah]
comment: Rich media typically support faster growth than defined media.
subset: Grouping_terms
is_a: FYECO:0000009 ! grouping growth medium
created_by: antonialock
creation_date: 2012-03-14T01:33:58Z
[Term]
id: FYECO:0000081
name: low glucose YES
def: "Experiments were performed in rich medium containing yeast extract and other components. The concentration of glucose is very low (eg around 0.1%)." [PomBase:al]
comment: Use the medium terms to specify the general type of growth medium and its carbon source. If certain chemicals not normally found in the medium were added, please also use the 'chemical added/excluded' terms, for instance 'caffeine added' or 'nitrogen excluded'. If a chemical was added in a much lower quantity than normal, please use the 'limited chemical added' conditions, for instance 'limited adenine added'.
synonym: "low glucose rich medium" RELATED [PomBase:al]
synonym: "low glucose YE" RELATED [PomBase:al]
is_a: FYECO:0000080 ! grouping rich medium
created_by: antonialock
creation_date: 2012-03-14T01:35:45Z
[Term]
id: FYECO:0000082
name: + arginine
def: "An experimental condition in which arginine was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term includes both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-03-22T08:21:12Z
[Term]
id: FYECO:0000084
name: + glutamate
def: "An experimental condition in which glutamate was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-03-22T08:28:47Z
[Term]
id: FYECO:0000085
name: + glutamine
def: "An experimental condition in which glutamine was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-03-22T08:29:26Z
[Term]
id: FYECO:0000086
name: + ornithine
def: "An experimental condition in which ornithine was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-03-22T08:29:44Z
[Term]
id: FYECO:0000087
name: + pro
def: "An experimental condition in which proline was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "proline added" EXACT [PomBase:al]
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-03-22T08:30:19Z
[Term]
id: FYECO:0000088
name: + 2-OG
def: "An experimental condition in which 2-oxoglutarate was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term includes both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "2-OG present" EXACT [PomBase:al]
synonym: "2-oxoglutarate added" EXACT [PomBase:al]
synonym: "2-oxoglutarate present" EXACT [PomBase:al]
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-03-22T08:30:35Z
[Term]
id: FYECO:0000089
name: + Na oleate
def: "An experimental condition in which sodium oleate was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "sodium oleate added" EXACT [PomBase:al]
is_a: FYECO:0000042 ! + fatty acid
created_by: antonialock
creation_date: 2012-03-22T08:52:53Z
[Term]
id: FYECO:0000090
name: + limited nitrogen
def: "An experimental condition in which nitrogen was added to the medium or assay buffers in a limiting quantity compared to standard medium or assay buffers." [PomBase:al]
synonym: "nitrogen starvation" RELATED [PomBase:al]
is_a: FYECO:0000011 ! grouping limited
created_by: antonialock
creation_date: 2012-03-26T11:47:41Z
[Term]
id: FYECO:0000091
name: + cisplatin
def: "An experimental condition in which cisplatin was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term includes both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-04-18T05:05:41Z
[Term]
id: FYECO:0000092
name: + Na ions
def: "An experimental condition in which sodium ions were added to the assay buffer in excess compared to standard assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "sodium ions added" EXACT [PomBase:al]
is_a: FYECO:0000030 ! + ions
created_by: antonialock
creation_date: 2012-04-23T01:01:11Z
[Term]
id: FYECO:0000093
name: + Li ions
def: "An experimental condition in which lithium ions were added to the assay buffer in excess compared to standard assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
synonym: "lithium ions added" EXACT [PomBase:al]
is_a: FYECO:0000030 ! + ions
created_by: antonialock
creation_date: 2012-04-23T01:04:46Z
[Term]
id: FYECO:0000094
name: grouping sequential growth conditions
def: "Any series of two or more different sets of conditions used in a single experiment." [PomBase:mah]
subset: Grouping_terms
is_a: FYECO:0000238 ! grouping condition combinations
created_by: antonialock
creation_date: 2012-04-23T03:15:51Z
[Term]
id: FYECO:0000095
name: 24-48h nitrogen starvation followed by 4-7 day recovery in rich medium
def: "Recovery from nitrogen starvation: cells are first grown in minimal medium containing no nitrogen for 24-48h. This medium is then replaced with rich medium containing nitrogen and cells allowed to grow for 4-7 days." [PomBase:al]
is_a: FYECO:0000110 ! nitrogen starvation and recovery
created_by: antonialock
creation_date: 2012-04-23T03:17:23Z
[Term]
id: FYECO:0000096
name: 24-48h nitrogen starvation followed by 5-12h recovery in rich medium
def: "Recovery from nitrogen starvation: cells are first grown in minimal medium containing no nitrogen for 24-48h. This medium is then replaced with nitrogen containing rich medium and cells are allowed to grow for 5-12h." [PomBase:al]
is_a: FYECO:0000110 ! nitrogen starvation and recovery
created_by: antonialock
creation_date: 2012-04-24T01:48:26Z
[Term]
id: FYECO:0000097
name: 24-48h nitrogen starvation followed by 12-24h recovery in rich medium
def: "Recovery from nitrogen starvation: cells are first grown in minimal medium containing no nitrogen for 24-48h. This medium is then replaced with nitrogen containing rich medium and cells are allowed to grow for 12-24h." [PomBase:al]
is_a: FYECO:0000110 ! nitrogen starvation and recovery
created_by: antonialock
creation_date: 2012-04-24T01:52:54Z
[Term]
id: FYECO:0000098
name: 72h-7days nitrogen starvation followed by 12-24h recovery in rich medium
def: "Recovery from nitrogen starvation: cells are first grown in minimal medium containing no nitrogen for 72h-7days. This medium is then replaced with nitrogen containing rich medium and cells are allowed to grow for 12-24h." [PomBase:al]
is_a: FYECO:0000110 ! nitrogen starvation and recovery
created_by: antonialock
creation_date: 2012-04-24T01:55:58Z
[Term]
id: FYECO:0000099
name: 72h-7days nitrogen starvation followed by 4-7 days recovery in rich medium
def: "Recovery from nitrogen starvation: cells are first grown in minimal medium containing no nitrogen for 72h-7days. This medium is then replaced with nitrogen containing rich medium and cells are allowed to grow for 4-7 days." [PomBase:al]
is_a: FYECO:0000110 ! nitrogen starvation and recovery
created_by: antonialock
creation_date: 2012-04-25T12:31:19Z
[Term]
id: FYECO:0000100
name: water medium
def: "Experiments were performed in medium containing water only." [PomBase:al]
is_a: FYECO:0000013 ! grouping defined medium
created_by: antonialock
creation_date: 2013-01-09T17:56:46Z
[Term]
id: FYECO:0000101
name: medium texture
def: "Any experimental condition specifying the physical texture of the growth medium." [PomBase:al]
subset: Grouping_terms
is_obsolete: true
created_by: antonialock
creation_date: 2012-05-04T07:51:30Z
[Term]
id: FYECO:0000102
name: agar plates
def: "Cells were grown on agar plates." [PomBase:al]
synonym: "solid agar plates" EXACT [PomBase:al]
is_a: FYECO:0000009 ! grouping growth medium
disjoint_from: FYECO:0000103 ! liquid culture
created_by: antonialock
creation_date: 2012-05-04T07:53:03Z
[Term]
id: FYECO:0000103
name: liquid culture
def: "Cells were grown in liquid culture." [PomBase:al]
is_a: FYECO:0000009 ! grouping growth medium
created_by: antonialock
creation_date: 2012-05-04T07:53:10Z
[Term]
id: FYECO:0000104
name: low glucose MM
def: "Experiments were performed in minimal medium containing a low concentration of glucose (~0.5%) as carbon source, salts and water." [PomBase:al]
comment: Use the medium terms to specify the general type of growth medium and its carbon source. If certain chemicals not normally found in the medium were added, please also use the 'chemical added/excluded' terms, for instance 'caffeine added' or 'nitrogen excluded'. If a chemical was added in a much lower quantity than normal, please use the 'limited chemical added' conditions, for instance 'limited adenine added'.
synonym: "low glucose minimal medium" EXACT [PomBase:al]
is_a: FYECO:0000013 ! grouping defined medium
created_by: antonialock
creation_date: 2012-05-11T02:53:00Z
[Term]
id: FYECO:0000105
name: + limited thiamine
def: "An experimental condition in which thiamine was added to the medium or assay buffers in a limiting quantity compared to standard medium or assay buffers." [PMID:12653111]
xref: PMID:12653111
is_a: FYECO:0000011 ! grouping limited
created_by: antonialock
creation_date: 2012-05-11T03:00:02Z
[Term]
id: FYECO:0000106
name: + thiamine
def: "An experimental condition in which thiamine was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-05-11T03:02:06Z
[Term]
id: FYECO:0000107
name: + aminopyrimidine
def: "An experimental condition in which aminopyrimidine was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term includes both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-05-11T03:02:21Z
[Term]
id: FYECO:0000108
name: + thiazole
def: "An experimental condition in which thiazole was added to the medium or assay buffer in excess compared to standard medium or assay buffers." [PomBase:al]
comment: Note that this term can be used both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
is_a: FYECO:0000109 ! grouping excess
created_by: antonialock
creation_date: 2012-05-11T03:03:12Z
[Term]
id: FYECO:0000109
name: grouping excess
def: "Any experimental condition that describes the presence of one or more substances at higher than default levels in growth medium, assay buffer, etc." [PomBase:mah]
comment: Note that this term includes both when the chemical is not normally present in the buffer, or when the buffer normally contains much lower quantities of the chemical so that the chemical is added 'in excess'.
subset: Grouping_terms
is_a: FYECO:0000059 ! chemical added or excluded
created_by: antonialock
creation_date: 2012-05-11T03:03:45Z
[Term]
id: FYECO:0000110
name: nitrogen starvation and recovery
def: "Cells are first grown in minimal medium lacking nitrogen and are then allowed to recover in rich medium." [PomBase:al]
synonym: "recovery from nitrogen depletion" EXACT [PomBase:al]
synonym: "recovery from nitrogen starvation" EXACT [PomBase:al]
is_a: FYECO:0000094 ! grouping sequential growth conditions
created_by: antonialock
creation_date: 2012-05-11T03:31:01Z
[Term]
id: FYECO:0000111
name: + limited myo-inositol
def: "An experimental condition in which myo-inositol was added to the medium or assay buffers in a limiting quantity compared to standard medium or assay buffers." [PomBase:al]
comment: Mating and sporulation is very inefficient in media containing 1 mg/L of myo-inositol, compared to 10 mg/L which is the most efficient myo-inositol concentration observed for mating and sporulation.
synonym: "limited inositol added" RELATED [PomBase:al]
xref: PMID:9560432
is_a: FYECO:0000011 ! grouping limited
created_by: antonialock
creation_date: 2012-05-17T12:11:53Z
[Term]
id: FYECO:0000112
name: + limited phosphate
def: "An experimental condition in which phosphate was added to the medium or assay buffers in a limiting quantity compared to standard medium or assay buffers." [PomBase:al]
is_a: FYECO:0000011 ! grouping limited
created_by: antonialock
creation_date: 2012-05-18T09:21:48Z
[Term]