Review lethal phenotype patterns

[matentzn]

We should review the lethal phenotype patterns and add them to uPheno if we believe the way they are are the way to go!

[Clare72]

looks like this will need 8 patterns:

some die -> mortality rate = 5-100% (relative to control rate)
partially lethal - majority live -> 5-50%
majority die -> 50-100%
all die -> 98-100%

each of these needs a 'before stage' version and a 'during stage' version

[Clare72]

Example 'during stage' definition:
'has part' some
(('inheres in' some
('population of Drosophila' and ('has member' some
('multicellular organism' and (has_age some (substage_of some 'prepupal stage')))) and ('has member' only
('multicellular organism' and (has_age some (substage_of some 'prepupal stage')))))) and ('has increased age-specific mortality rate' some xsd:short[>= "50"^^xsd:short]))

We can probably change 'population of Drosophila' to 'population of organisms' (PCO:0000001) to allow use in upheno.
And change 'multicellular organism' to 'organism' for wider use.

has_age is an FBcv relationship, and substage_of is from FBdv, so would be nice to replace these with the has_stage relationship once this is added to RO:
'has part' some
('inheres in' some
('population of organisms' and ('has member' some
('organism' and has_stage some 'prepupal stage')) and ('has member' only
('organism' and has_stage some 'prepupal stage')) and ('has increased age-specific mortality rate' some xsd:short[>= "50"^^xsd:short]))
and ('has_modifier' some 'abnormal'))

'before stage' version could use
('organism' and has_stage ('life cycle stage' and precedes some 'prepupal stage'))
with 'life cycle stage' from UBERON

[Clare72]

alternatively we could overhaul the whole thing to make it more upheno-like:
'has part' some
('increased mortality rate'
and ('characteristic of' some 'population of organisms')
and ('has percentage' some xsd:short[>= "50"^^xsd:short])
and ('existence starts and ends during' some 'prepupal stage')
and ('has_modifier' some 'abnormal'))

'increased mortality rate' would be a new class (probably in PATO)
'has percentage' would be a new data property (feels like this should exist already, but I couldn't find it)

'before stage' phenotypes would use 'existence ends during'

with this general pattern, we wouldn't need to specify a percentage for the 'some die' pattern