Changes between Version 34 and Version 35 of CapturingGeneExpression


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Timestamp:
Jan 8, 2013, 3:22:43 PM (9 years ago)
Author:
antonialock
Comment:

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  • CapturingGeneExpression

    v34 v35  
    3131= Qualitative Data =
    3232
    33 || expression type|| detail  || level || evidence ||
    34 || mRNA level|transcription|degradation|protein level|translation|degradation || during phase or process (S, phase, meiosis, sporulation, cellular response to X)|in_response_to(CHEBI chemical) ||increased|decreased|| ECO:... ||
     33 *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
     37  *Evidence (ECO:xxxxxxx)
     38 
     39 *The expression type may, if it is known, be further subdivided into:
     40  *RNA level -> transcription or degradation
     41  *protein level -> translation or degradation
    3542
    36  * If a gene is present in a blot under normal growth conditions I use extension during(vegetative growth of single celled organism) + qualifier=present. I then set increased/decreased during other responses (I know veg growth may not be the correct term to use - I've used it in the context of when growing in standard medium (MM or YE if a difference isn't known, if there is a difference shown I put MM=during starvation), rather than having elevated levels of some nonstandard compound in there, or starved of something, or any other arbitrarily abnormal condition)
    37  * if they don't show the level during vegetative growth use 'present' or 'absent' during a condition (nothing to compare to)
    38  * use 'unchanged' if level doesn't change during a condition
    39  * I use 'in_response_to(CHEBI chemical)' if there isn't a GO 'response to' term for the chemical
     43 *Unstressed conditions are currently paired with happens_during(vegetative growth on single-celled organism)
     44 *Unstressed conditions include growth on YE and MM unless there is a known difference between the two
     45 *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.
     46 *Use 'unchanged' if the level doesn't change during a condition compared to unstressed
    4047
     48Example Artemis string:
    4149
    42 
    43 Syntax in Artemis:
    44 
    45 /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:xxxxx),in_response_to(CHEBI:xxxxxxx); qualifier=increased/decreased/unchanged/present/absent; evidence=ECO:xxxx; db_xref=; date=YYYYMMDD"
     50/controlled_curation="term=gene expression, RNA level; annotation_extension=happens_during(GO:xxxxxxx) qualifier=increased; evidence=ECO:xxxx; db_xref=; date=YYYYMMDD"
    4651
    4752||Evidence codes used||