wiki:PhenotypeConditions

Version 32 (modified by val_wood, 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)

Note, I have made the names with underscores synonymns (these can be treated as exact during parsing, in the ontology we will use phrases without underscroes so we may as well use these now....)

conditionsynonymsdefinitionexample
at high temperature at_high_temperatureCultures are grown at temperatures >32 degrees C
at normal temperatureat_normal_temperatureCultures are grown at temperatures 25-32 degrees C
low temperatureat_low_temperatureCultures are grown at temperatures <25 degrees C
overexpression-gene product is overexpressed
knockdown-the expression of the gene product is artificially lowered
in rich mediain_rich_mediaCultures are grown in rich media such as YE
in high [glucose]in_high_[glucose]Cells are grown in 'minimal media' where the concentration of glucose is increased.
in minimal mediain_minimal_mediaCultures are grown in minimal media
in glycerol carbon sourcein_glycerol_carbon_sourceCultures are grown with glycerol as the carbon source
nitrogen starvationnitrogen_starvationCultures are starved of nitrogen
in presence of TBCin_presence_of_TBC-


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)