wiki:PhenotypeConditions

Version 12 (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 --> annotation_extension=condition(in_minimal_media)

conditionsynonymsexplanation
plasmid expression repressedplasmid_expression_repressedchromosomal copy deleted and gene is instead expressed from a repressable plasmid
in rich mediain_rich_mediaYE, lots of glucose etc
in minimal mediain_minimal_medialow glucose
at high temperatureat_high_temperatureAL uses above 32 for high
at normal temperatureat_normal_temperatureAL only uses this if specifying high and low temp. Perhaps it is redundant
at low temperatureat_low_temperatureAL uses below 25 for low
overexpression-gene product is overexpressed. Probably only used for plasmid expression
in vitro-deprecated - use ECO 49 instead
nitrogen starvation-
nitrogen limitation-only 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)