Sim_Jiang_1997

Sim_Jiang_1997(
  dag,
  terms,
  IC_method = "IC_annotation",
  norm_method = "max",
  verbose = simona_opt$verbose
)

Methods

First semantic distance between term a and b via MICA term c is defined as:

D(a, b) = IC(a) + IC(b) - 2*IC(c)

Then there are several normalization method to change the distance to similarity and to scale it into the range of [0, 1].

max: 1 - D(a, b)/2/IC_max
Couto: min(1, D(a, b)/IC_max)
Lin: 1 - D(a, b)/(IC(a) + IC(b)) which is the same as the Sim_Lin_1998 method
Garla: 1 - log(D(a, b) + 1)/log(2*IC_max + 1)
log-Lin: 1 - log(D(a, b) + 1)/log(IC(a) + IC(b) + 1)
Rada: 1/(1 + D(a, b))

There is a parameter norm_method which takes value in "max", "Couto", "Lin", "Carla", "log-Lin", "Rada":

term_sim(dag, terms, method = "Sim_Jiang_1997",
    control = list(norm_method = "Lin"))