wiki:PhenotypeConditions

Version 20 (modified by antonialock, 10 years ago) (diff)

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Experimental conditions for phenotype annotation extensions - collect here; Midori will convert to OBO file

Syntax --> condition=condition
E.g. condition=at_high_temperature

Legacy syntax --> annotation_extension=condition(in_minimal_media)

conditiondefinitionexample
at_high_temperatureCultures are grown at temperatures >32 degrees C
at_normal_temperature|Cultures are grown at temperatures 25-32 degrees C
at_low_temperatureCultures are grown at temperatures <25 degrees C
overexpressiongene product is overexpressed
knockdown the expression of the gene product is artificially lowered
plasmid_expression_repressedDeprecated - use knockdown. chromosomal copy deleted and gene is instead expressed from a repressible plasmid
in vitrodeprecated - use ECO 49 instead
in_rich_mediaYE etc media
in_high_[glucose]Cells are grown in 'minimal media' where the concentration of glucose is increased.
in_minimal_mediaminimal media
in_glycerol_carbon_sourceCells are grown with glycerol as the carbon source
nitrogen_starvationCultures are starved of nitrogen
nitrogen_limitationDeprecated + use nitrogen starvation? Nitrogen is limited

note:
We discussed using conditions for high_[substance]_concentration and low_[substance]_concentration (eg cacl2 ions, sucrose etc etc) rather than using the extension in_presence_of(CHEBI:xxx) or in_absence_of(CHEBI:xxx)