termSim                package:SemSim                R Documentation

_S_e_m_a_n_t_i_c _S_i_m_i_l_a_r_i_t_y _o_f _G_O _T_e_r_m_s

_D_e_s_c_r_i_p_t_i_o_n:

     Given two terms in the same GO subcategory, information
     content-based measures are used to estimate their semantic
     similarity or distance.

_U_s_a_g_e:

     termSim(GOID1, GOID2, measure = "Resnik", db = "UniProt")

_A_r_g_u_m_e_n_t_s:

   GOID1: Identifier of a GO term.

   GOID2: Identifier of a GO term.

 measure: One of "Resnik", "Lin", "Rel", and "Jiang" methods.

      db: Databases from which the information content of each GO term
          has been derived.

_D_e_t_a_i_l_s:

     Resnik, and Lin, and Relevance methods estimate semantic
     similarity of two GO terms, while Jiang's method calculate
     semantic distance of GO terms. The simplest measure (Resnik)
     defines the similarity as the information content of the lowest
     common ancestor of two terms, while the other three measures also
     take into accout the information content of query terms. Detailed
     description of each measure can be found in Lord, et al 2003 and
     Schlicker, et al 2006. Information content of a term is based on
     its relative frequency of occurrence in an annotation database.
     Default calculation of information content is based on all non-IEA
     annotations in UniProt. Users may specify other organism
     annotation databases for the calculation of semantic similarity.
     Options "mouse", "rat", "plant", "yeast", "fly", "worm", and
     "microbe" of argument db represent data from non-IEA annotations
     in MGI, RGD, TAIR, SGD, FB, WB, and TIGR CMR databases
     respectively.

_V_a_l_u_e:

    Sim : Value of semantic similarity or distance between two terms.

_R_e_f_e_r_e_n_c_e_s:

     Lord, P.W., Stevens, R.D., Brass, A., and Goble, C.A. (2003)
     Semantic similarity measures as tools for exploring the Gene
     Ontology. In _Pacific Symposium on Biocomputing_ 8: 601-612.
     Schlicker, A., Domingues, F.S., Rahnenfuhrer, J., and Lengauer, T.
     (2006) A new measure for functional similarity of gene products
     based on Gene Ontology. _BMC Bioinformatics_, 7(1):302.

_E_x_a_m_p_l_e_s:

     termSim("GO:0043044", "GO:0006348")
     termSim("GO:0015801", "GO:0015813", measure="Rel", db="microbe")

