Changes between Version 9 and Version 10 of PrePostComposePhenotype
- Timestamp:
- Apr 10, 2015, 4:10:13 PM (6 years ago)
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PrePostComposePhenotype
v9 v10 1 Page for things that will mature intoguidelines for when to pre- or post-compose phenotype terms with condition information1 Rough guidelines for when to pre- or post-compose phenotype terms with condition information 2 2 3 M idori's initial thoughts (May 2012):3 Most 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". 4 4 5 * phenotypes topre-compose:5 * Always pre-compose: 6 6 * any sensitive to chemical other than N or C source 7 7 * any resistant to chemical other than N or C source 8 8 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) 10 10 * anything other than viable/inviable (or growth/no growth/death) at high temperature 11 11 * 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 12 13 13 * ones I'm not sure about, butleaving 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] 14 15 * viable/inviable (or growth/no growth/death) on specific carbon source 15 16 * anything during starvation for a specific nutrient/limiting [stuff] … … 18 19 * discussing whether to make a pre/post distinction along cell vs. population lines 19 20 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) 22 24 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. 24 27 25 updated 2012-06-15, 2013-01-07, 2013-09-06, 2013-11-04 mah28 updated 2012-06-15, 2013-01-07, 2013-09-06, 2013-11-04, 2015-04-10 mah