drseb/phenopposites

Project to generate phenotype opposite_of relationships and investigate the effect on ontology-based algorithms

phenopposites's Issues

combustible,noncombustible

There are lots of antonyms that do not seem to apply to human phenotypes.
I would suggest removing the following unless they exist somewhere in the HPO definitions.

asynchronous,synchronous
active,inactive
difficult,easy
quick,slow
huge,tiny
more,less
never,always
old,young
down,up
coiled,uncoiled
auxotrophic,prototrophic
invariant,variant
conspicuous,inconspicuous
good,bad
insensitive,sensitive
oriented,disoriented
crowded,uncrowded
continuous,discontinuous
lethal,viable
balanced,unbalanced
coordinated,uncoordinated
permeable,impermeable
porous,non-porous
consistent,inconsistent
susceptibility,resistance
susceptible,insusceptible
concentrated,unconcentrated
damaged,undamaged
elastic,inelastic
structured,unstructured
aerobic,anaerobic
magnetic,non-magnetic
hydrophobic,hydrophilic
front,back
differentiated,undifferentiated
active,inactive
minimal,maximal
minimally,maximally
distributed,undistributed
serrated,unserrated
adequate,inadequate
responsive,unresponsive
soluble,insoluble
inflated,uninflated
interrupted,uninterrupted
complete,incomplete
sufficient,insufficient
drinkable,undrinkable
stratified,unstratified
discriminate,indiscriminate
contiguous,discontiguous
ornamented,unornamented
polar,nonpolar
efficient,inefficient
organized,disorganized
potable,non-potable
modified,unmodified
fragile,non-fragile
discriminate,indiscriminate
functional,non-functional
adhesive,non-adhesive
phosphorylated,dephosphorylated
compatible,incompatible
flexible,inflexible
resinous,non-resinous
contractile,non-contractile
condensed,decondensed
necessary,unnecessary
branched,unbranched
divided,undivided
edible,inedible
lumenized,unlumenized
aromatic,non-aromatic
transparent,non-transparent
micro,macro

fasciculated,defasciculated

THis is not really an antonym, see https://en.wiktionary.org/wiki/defasciculation

frequent,infrequent

While these may be considered antonyms in some contexts, the data they are referring to are not necessarily antonyms. For instance, frequent would be 70% and infrequent could be 5%. These are different but not really miore of an antonym than 70% vs 0% or 70% vs 40%.

cleft,joint

This is not a pair of opposites
Similarl;y

insomnia, narcolepsy
indifference, difference
modified direction and unmodified direction

Not antonyms/opposites

These pairs appear to be synonyms

unilateral,monolateral
unidirectional,monodirectional
unipotent,monopotent

Not opposite phenotypes

In the following cases, there might be a normal phenotype (i.e., not in the HPO) and an abnormal phenotype characterized by these pairs. For instance, a respiratory cilium is MOTILE (mobile) and the abnormal phenotype is NOT MOTILE (immobile). But these are not opposites in the sense of the rest of the paper.

mobile,immobile
localised,unlocalised
localised,mislocalised
functional,disfunctional (not misspeling, it should be dys...)