ontology-class           package:ontoTools           R Documentation

_C_l_a_s_s "_o_n_t_o_l_o_g_y" _w_r_a_p_s _a _r_o_o_t_e_d _D_A_G _w_i_t_h _s_o_m_e
_o_n_t_o_l_o_g_y _m_e_t_a_d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     instances of class ontology are used to represent things like Gene
     Ontology

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("ontology",
     ...)'. This simply possesses information on name and version of
     ontology.

_S_l_o_t_s:

     '_n_a_m_e': Object of class '"character"' name of ontology 

     '_v_e_r_s_i_o_n': Object of class '"character"' version tag 

     '_r_D_A_G': Object of class '"rootedDAG"' the rooted DAG representing
          the terminlogy hierarchy 

_M_e_t_h_o_d_s:

     _a_c_c_e_s_s_M_a_t 'signature(object = "ontology")': returns square matrix
          with 1 in element r,c if term corresponding to r can be
          reached from term corresponding to c

     _n_a_m_e 'signature(x = "ontology")': access name 

     _O_V_e_r_s_i_o_n 'signature(x = "ontology")':  access version

     _r_D_A_G 'signature(x = "ontology")': access the rooted DAG 

     _s_h_o_w 'signature(object = "ontology")': concise report 

_N_o_t_e:

     This class was written to deal with ontologies that are
     representable as rooted DAGs.  It is not clear that this is a good
     use of the term 'ontology', which has broader implications. 
     However this does work for Gene Ontology.

_A_u_t_h_o_r(_s):

     ~~who you are~~

_E_x_a_m_p_l_e_s:

     data(litOnto)
     print(litOnto)
     g1 <- new("rootedDAG", DAG=litOnto, root="A")
     o1 <- new("ontology", name="demo", version="0.1",
             rDAG=g1)
     # can also use
     o1b <- makeOntology( name="demo", version="0.1", 
        graph=litOnto, root="A")
     show(o1)
     print(accessMat(o1))
     print(OVersion(o1))

