Sim_Resnik_1999

Sim_Resnik_1999

Sim_Resnik_1999(dag, terms, norm_method = "Nmax", verbose = simona_opt$verbose)

Methods

Sim_Resnik_1999

The IC method is fixed to IC_annotation.

The original Resnik similarity is the IC of the MICA term. There are three ways to normalize the Resnik similarity into the scale of [0, 1]:

1. Nunif

sim = IC(c)/log(N)

where N is the total number of items annotated to the whole DAG, i.e. number of items annotated to the root. Then the IC of a term with only one item annotated is -log(1/N) = log(N)` which is the maximal IC value in the DAG.

1. Nmax

IC_max is the maximal IC of all terms. If there is a term with only one item annotated, Nmax is identical to the `Nunif* method.

sim = IC(c)/IC_max

1. Nunivers

The IC is normalized by the maximal IC of term a and b.

sim = IC(c)/max(IC(a), IC(b))

Paper link: doi:10.1613/jair.514 , doi:10.1186/1471-2105-9-S5-S4 , doi:10.1186/1471-2105-11-562 , doi:10.1155/2013/292063 .

The normalization method can be set with the norm_method parameter:

term_sim(dag, terms, control = list(norm_method = "Nmax"))

Possible values for the norm_method parameter are "Nunif", "Nmax", "Nunivers" and "none".