Changes between Version 55 and Version 56 of PhenotypeConditions


Ignore:
Timestamp:
Dec 6, 2012, 12:08:26 PM (8 years ago)
Author:
antonialock
Comment:

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  • PhenotypeConditions

    v55 v56  
    1 Experimental conditions for phenotype annotation extensions - original set collected here; Antonia and Midori have converted to OBO file.
    2 
    3 Phenotype conditions ontology (PCO) in !PomBase subversion repository: http://pombase.svn.sourceforge.net/viewvc/pombase/phenotype_ontology/pco.obo
    4 
    5 Request additions or changes via the [https://sourceforge.net/tracker/?group_id=65526&atid=2096431 FYPO tracker]
    6 
    7 Current syntax: condition=PCO:nnnnnnn  [[BR]]
    8 note: should change to has_condition per Chris Mungall's recommendation, i.e. has_condition=PCO:nnnnnnn
    9 
    10 also see relations [wiki:ListOfRelations on wiki] and in [http://pombase.svn.sourceforge.net/viewvc/pombase/phenotype_ontology/supplemental_files/fypo_extension_relations.obo FYPO svn]
    11 
    12  == older page content ==
    13 
    14 '''Warning: some of this is now out of date (as of 2012-04-10)'''
    15 
    16 Syntax in use approx late 2011 - early 2012: condition=condition [[BR]]
    17 E.g. condition=at high temperature [[BR]]
    18 [[BR]]
    19 
    20 ''Legacy syntax --> annotation_extension=condition(in_minimal_media)''
    21 
    22 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....)
    23 
    24 ||condition||synonyms||definition||example||
    25 ||at high temperature ||at_high_temperature||Cultures are grown at temperatures >32 degrees C||||
    26 ||at normal temperature||at_normal_temperature||Cultures are grown at temperatures 25-32 degrees C||||
    27 ||low temperature||at_low_temperature||Cultures are grown at temperatures <25 degrees C||||
    28 ||overexpression||-||gene product is overexpressed||||
    29 ||knockdown||-||the expression of the gene product is artificially lowered||||
    30 ||in rich media||in_rich_media||Cultures are grown in rich media such as YE||||
    31 ||in high [glucose]||in_high_[glucose]||Cells are grown in 'minimal media' where the concentration of glucose is increased.||||
    32 ||in minimal media||in_minimal_media||Cultures are grown in minimal media||||
    33 ||in glycerol carbon source||in_glycerol_carbon_source||Cultures are grown with glycerol as the carbon source||||
    34 ||nitrogen starvation||nitrogen_starvation||Cultures are starved of nitrogen||||
    35 ||xenobiotic substrate||in_vitro||an artificial (not normally found in pombe or nature) substrate was used||
    36 ||in absence of adenine||-||Limited adenine||
    37 ||in absence of sugar||-||Limited sugar||
    38 ||in absence of P factor||-||In presence of P-factor pheromone||
    39 [[BR]]
    40 ||in presence of 3',5'-cyclic AMP||-||In presence of 3',5'-cyclic AMP||
    41 ||in presence of sugar||-||In presence of sugar||
    42 ||in presence of sorbitol||-||In presence of sorbitol||
    43 ||in presence of vanadate||-||In presence of vanadate||
    44 ||in presence of P factor||-||In presence of P-factor pheromone||
    45 ||in presence of TBC||in_presence_of_TBC||-||||
    46 ||in presence of tacrolimus||-||In presence of tacrolimus||
    47 ||in presence of KCl||-||In presence of potassium chloride||
    48 ||in presence of Cl ions||in presence of Cd||in presence of chloride ions||
    49 ||in presence of Cd ions||-||In presence of cadmium ions||
    50 ||in presence of Ca ions||-||In presence of calcium ions||
    51 ||in presence of Cu ions||-||In presence of copper ions||
    52 ||in presence of Pb ions||-||In presence of lead ions||
    53 ||in presence of Bi ions||-||In presence of bismuth ions||
    54 ||in presence of Mg ions||-||In presence of magnesium ions||
    55 ||in presence of palmitic acid||-||In presence of palmitic acid||
    56 ||in presence of myristic acid||-||In presence of myristic acid||
    57 ||in presence of pentadecanoic acid||-||In presence of pentadecanoic acid||
    58 ||in presence of margaric acid||-||In presence of margaric acid||
    59 ||in presence of stearic acid||-||In presence of stearic acid||
    60 ||in presence of petroselinic acid||-||In presence of petroselinic acid||
    61 ||in presence of oleic acid||-||In presence of oleic acid||
    62 ||in presence of vaccenic acid||-||In presence of vaccenic acid||
    63 ||in presence of linoleic acid||-||In presence of linoleic acid||
    64 ||in presence of linolenic acid||-||In presence of linolenic acid||
    65 ||in presence of arachidic acid||-||In presence of arachidic acid||
    66 ||in presence of melissic acid||-||In presence of melissic acid||
    67 
    68 [[BR]]
    69 
    70 ||deprecated terms||definition||condition to use instead||
    71 ||nitrogen_limitation||||nitrogen_starvation||
    72 ||in vitro||in vitro 'artificial' experiment (using, for instance, artificial substrates)||use eco49 instead||
    73 ||plasmid_expression_repressed||chromosomal copy deleted and gene is instead expressed from a repressible plasmid||knockdown||
    74 
    75 
    76 note: [[BR]]
    77 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)