Changes between Version 9 and Version 10 of PrePostComposePhenotype


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Timestamp:
Apr 10, 2015, 4:10:13 PM (6 years ago)
Author:
mah79
Comment:

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  • PrePostComposePhenotype

    v9 v10  
    1 Page for things that will mature into guidelines for when to pre- or post-compose phenotype terms with condition information
     1Rough guidelines for when to pre- or post-compose phenotype terms with condition information
    22
    3 Midori's initial thoughts (May 2012):
     3Most phenotypes are defined independently of any experimental conditions, since we can annotate conditions separately. There are a few exceptions, however, in which condition information is included as one of the features of a pre-composed term, usually for things that users will want to find easily, e.g. "temperature sensitive".
    44
    5  * phenotypes to pre-compose:
     5 * Always pre-compose:
    66  * any sensitive to chemical other than N or C source
    77  * any resistant to chemical other than N or C source
    88
    9  * phenotype to post-compose (i.e. capture part of phenotype as conditions at annotation time)
     9 * Always post-compose (i.e. capture conditions at annotation time, not as part of a complicated phenotype term)
    1010  * anything other than viable/inviable (or growth/no growth/death) at high temperature
    1111  * anything other than viable/inviable (or growth/no growth/death) at low temperature
     12  * presence or absence of chemicals with phenotypes other than population growth sensitivity/resistance
    1213
    13  * ones I'm not sure about, but leaving in place until/unless problems crop up [updated 2013-01-07, 2013-09-06]
     14 * Grey areas - phenotypes curators haven't felt sure about, but are leaving in place until/unless problems crop up [updated 2013-01-07, 2013-09-06]
    1415  * viable/inviable (or growth/no growth/death) on specific carbon source
    1516  * anything during starvation for a specific nutrient/limiting [stuff]
    … …  
    1819   * discussing whether to make a pre/post distinction along cell vs. population lines
    1920
    20  * Outstanding issue; no terms included yet (2013-01-07)
    21   * in vitro enzyme assays, with inhibitors (e.g. [https://sourceforge.net/tracker/?func=detail&aid=3535931&group_id=65526&atid=2096431 SF 3535931])
     21 * Other outstanding issues
     22  * in vitro enzyme assays, with inhibitors (e.g. [https://sourceforge.net/p/pombase/fission-yeast-phenotype/238/ SF #238])
     23   * no terms included yet (last updated 2013-01-07)
    2224
    23  * As of 2013-11-04, decided to use conditions for aerobic/semi-aerobic/anaerobic where FYPO term mentions carbon source.
     25 * Other decisions (archived)
     26  * As of 2013-11-04, decided to use conditions for aerobic/semi-aerobic/anaerobic where FYPO term mentions carbon source.
    2427
    25 updated 2012-06-15, 2013-01-07, 2013-09-06, 2013-11-04 mah
     28updated 2012-06-15, 2013-01-07, 2013-09-06, 2013-11-04, 2015-04-10 mah