wiki:PhenotypeConditions

Version 55 (modified by gomidori, 9 years ago) (diff)

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Experimental conditions for phenotype annotation extensions - original set collected here; Antonia and Midori have converted to OBO file.

Phenotype conditions ontology (PCO) in PomBase subversion repository: http://pombase.svn.sourceforge.net/viewvc/pombase/phenotype_ontology/pco.obo

Request additions or changes via the FYPO tracker

Current syntax: condition=PCO:nnnnnnn
note: should change to has_condition per Chris Mungall's recommendation, i.e. has_condition=PCO:nnnnnnn

also see relations on wiki? and in FYPO svn

older page content

Warning: some of this is now out of date (as of 2012-04-10)

Syntax in use approx late 2011 - early 2012: condition=condition
E.g. condition=at high temperature

Legacy syntax --> annotation_extension=condition(in_minimal_media)

Note, I have made the names with underscores synonyms (these can be treated as exact during parsing, in the ontology we will use phrases without underscores 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
xenobiotic substratein_vitroan artificial (not normally found in pombe or nature) substrate was used
in absence of adenine-Limited adenine
in absence of sugar-Limited sugar
in absence of P factor-In presence of P-factor pheromone


in presence of 3',5'-cyclic AMP-In presence of 3',5'-cyclic AMP
in presence of sugar-In presence of sugar
in presence of sorbitol-In presence of sorbitol
in presence of vanadate-In presence of vanadate
in presence of P factor-In presence of P-factor pheromone
in presence of TBCin_presence_of_TBC-
in presence of tacrolimus-In presence of tacrolimus
in presence of KCl-In presence of potassium chloride
in presence of Cl ionsin presence of Cdin presence of chloride ions
in presence of Cd ions-In presence of cadmium ions
in presence of Ca ions-In presence of calcium ions
in presence of Cu ions-In presence of copper ions
in presence of Pb ions-In presence of lead ions
in presence of Bi ions-In presence of bismuth ions
in presence of Mg ions-In presence of magnesium ions
in presence of palmitic acid-In presence of palmitic acid
in presence of myristic acid-In presence of myristic acid
in presence of pentadecanoic acid-In presence of pentadecanoic acid
in presence of margaric acid-In presence of margaric acid
in presence of stearic acid-In presence of stearic acid
in presence of petroselinic acid-In presence of petroselinic acid
in presence of oleic acid-In presence of oleic acid
in presence of vaccenic acid-In presence of vaccenic acid
in presence of linoleic acid-In presence of linoleic acid
in presence of linolenic acid-In presence of linolenic acid
in presence of arachidic acid-In presence of arachidic acid
in presence of melissic acid-In presence of melissic acid


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)