wiki:PhenotypeConditions

Version 19 (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)

conditionsynonymsexplanation
plasmid_expression_repressedchromosomal copy deleted and gene is instead expressed from a repressable plasmid
in_rich_mediaYE etc media
in_high_[glucose]High [glucose], otherwise MM
in_minimal_mediaMM media and derivatives
in_glycerol_carbon_source
at_high_temperatureAL uses above 32 for high
at_normal_temperatureAL only uses this if specifying high and low temp. Perhaps it is redundant
at_low_temperatureAL uses below 25 for low
overexpressiongene product is overexpressed. Probably only used for plasmid expression
knockdown the expression of the gene product is artificially lowered
in vitrodeprecated - use ECO 49 instead
nitrogen_starvation-
nitrogen_limitationonly 3 use cases dso far, need to check if "in minimal media" would be sufficient

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)