Changes between Version 43 and Version 44 of CapturingGeneExpression


Ignore:
Timestamp:
Apr 22, 2013, 1:59:10 PM (9 years ago)
Author:
gomidori
Comment:

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  • CapturingGeneExpression

    v43 v44  
    3232
    3333 * Each annotation must consist of these 4 bits of data:
    34   * '''Expression type''' (mRNA or protein level)
    35   * '''Relation''' (happens_during(BP) or in_presence_of(ChEBI)
    36   * '''Level''' (present, absent, unchanged, increased, decreased, constant
    37   * '''Evidence''' (ECO:xxxxxxx)
     34  * '''Expression type''' mRNA or protein level
     35  * '''Relation''' during(BP) or in_presence_of(ChEBI)
     36  * '''Level''' present, absent, unchanged, increased, decreased, constant
     37  * '''Evidence''' ECO:xxxxxxx
    3838 
    3939 * The expression type may, if it is known, be further subdivided into:
     
    4141  * protein level -> translation or degradation
    4242
    43  * Unstressed conditions are currently paired with happens_during(vegetative growth on single-celled organism)
     43 * Unstressed conditions are currently paired with during(vegetative growth on single-celled organism)
    4444 * Unstressed conditions include growth on YE and MM unless there is a known difference between the two
    4545 * Not sure how to deal with other carbon sources? Difference could be due to glucose starvation or response to other carbon source. Lets discuss if it crops up.
     
    4747
    4848Example Artemis string:
    49 /controlled_curation="term=gene expression, RNA level; annotation_extension=happens_during(GO:xxxxxxx); qualifier=increased; evidence=ECO:xxxx; db_xref=; date=YYYYMMDD"
     49/controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:xxxxxxx); qualifier=increased; evidence=ECO:xxxx; db_xref=; date=YYYYMMDD"
    5050
    5151||'''Evidence codes used'''||