wiki:PhenotypeConditions

Version 27 (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_temperatureCultures are grown at temperatures 25-32 degrees C
at_low_temperatureCultures are grown at temperatures <25 degrees C
overexpressiongene product is overexpressed
knockdownthe expression of the gene product is artificially lowered
in_rich_mediaCultures are grown in rich media such as YE
in_high_[glucose]Cells are grown in 'minimal media' where the concentration of glucose is increased.
in_minimal_mediaCultures are grown in minimal media
in_glycerol_carbon_sourceCultures are grown with glycerol as the carbon source
nitrogen starvationCultures are starved of nitrogen


deprecated termsdefinitioncondition to use instead
nitrogen_limitationnitrogen_starvation
in vitroin vitro 'artificial' experiment (using, for instance, artificial substrates)use eco49 instead
plasmid_expression_repressedchromosomal copy deleted and gene is instead expressed from a repressible plasmidknockdown

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)