Version 27 (modified by antonialock, 10 years ago) (diff)


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)

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
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

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)