Sleep phenotypes

[Clare72]

Phenotypes for subclasses of 'abnormal sleep' e.g. 'abnormal sleep bout duration', 'abnormal daytime sleep'

Curators to decide which classes will be most useful - may need new GO terms/new upheno patterns.

[arzuozturk]

My suggestions are (I am not sure about the name of the "total" ones):

abnormal sleep

• increased (total?) sleep
• decreased (total?) sleep
• abnormal daytime sleep
  • increased daytime sleep
  • decreased daytime sleep
• abnormal nighttime sleep
  • increased daytime sleep
  • decreased nighttime sleep
• abnormal sleep bout number
  • increased daytime sleep bout number
  • increased nighttime sleep bout number
  • decreased daytime sleep bout number
  • decreased nighttime sleep bout number
• abnormal sleep bout duration
  • increased daytime sleep bout duration
  • increased nighttime sleep bout duration
  • decreased daytime sleep bout duration
  • decreased nighttime sleep bout duration

[Clare72]

'daytime sleep' and 'nighttime sleep' require new GO terms - requested in https://github.com/geneontology/go-ontology/issues/21550

[Clare72]

bout number: this will require new patterns, which should probably use the PATO terms PATO:0050000 'rate of occurrence', PATO:0055003 'increased rate of occurrence' and PATO:0055004 'decreased rate of occurrence'

bout duration: this will require new patterns, which should probably use the PATO terms PATO:0001309 'duration', PATO:0000498 'increased duration' and PATO:0000499 'decreased duration'

'overall' increased/decreased 'total' sleep: This is a tricky one, there are 2 issues here:

1. 'nighttime sleep' will (rightly) be a subclass of 'sleep' in GO, so it would be difficult not to classify 'nighttime sleep' phenotypes as 'sleep' phenotypes (if you don't want 'increased daytime sleep' under 'increased sleep'). I am not really sure of the best way to solve this.
2. There is no good PATO term for 'increased total', currently we are using 'increased rate' for increased/decreased sleep phenotypes, but this would make 'increased bout number' a subclass of 'increased sleep' (but 'increased bout duration' would not automatically be a subclass). It would probably be good to have a PATO term for the proportion of time a process happens for (rate of occurrence x duration), we could then use this in a new pattern to represent the 'increased/decreased sleep' phenotypes, so that 'increased/decreased bout' phenotypes will not be subclasses.