Version 10 (modified by mah79, 6 years ago) (diff)


Rough guidelines for when to pre- or post-compose phenotype terms with condition information

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".

  • Always pre-compose:
    • any sensitive to chemical other than N or C source
    • any resistant to chemical other than N or C source
  • Always post-compose (i.e. capture conditions at annotation time, not as part of a complicated phenotype term)
    • anything other than viable/inviable (or growth/no growth/death) at high temperature
    • anything other than viable/inviable (or growth/no growth/death) at low temperature
    • presence or absence of chemicals with phenotypes other than population growth sensitivity/resistance
  • 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]
    • viable/inviable (or growth/no growth/death) on specific carbon source
    • anything during starvation for a specific nutrient/limiting [stuff]
    • growth at [whatever] pH, e.g. FYPO:0001157 increased cell growth rate at high pH
    • viable/inviable or population growth at high or low temperature (aka sensitive/resistant to heat/cold)
      • discussing whether to make a pre/post distinction along cell vs. population lines
  • Other outstanding issues
    • in vitro enzyme assays, with inhibitors (e.g. SF #238)
      • no terms included yet (last updated 2013-01-07)
  • Other decisions (archived)
    • As of 2013-11-04, decided to use conditions for aerobic/semi-aerobic/anaerobic where FYPO term mentions carbon source.

updated 2012-06-15, 2013-01-07, 2013-09-06, 2013-11-04, 2015-04-10 mah