pubMedAbst-class          package:annotate          R Documentation

_C_l_a_s_s _p_u_b_M_e_d_A_b_s_t, _a _c_l_a_s_s _t_o _h_a_n_d_l_e _P_u_b_M_e_d _a_b_s_t_r_a_c_t_s, _a_n_d _m_e_t_h_o_d_s
_f_o_r _p_r_o_c_e_s_s_i_n_g _t_h_e_m.

_D_e_s_c_r_i_p_t_i_o_n:

     This is a class representation for PubMed abstracts.

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     ' new('pubMedAbst','
      '  authors      = ...., # Object of class vector'
      '  pmid         = ...., # Object of class character'
      '  abstText     = ...., # Object of class character'
      '  articleTitle = ...., # object of class character'
      '  journal      = ...., # Object of class character'
      '  pubDate      = ...., # Object of class character'
      '  abstUrl      = ...., # Object of class character'
      '  )'

_S_l_o_t_s:

     '_p_m_i_d': Object of class '"character"' The PubMed ID for this
          paper. 

     '_a_u_t_h_o_r_s': Object of class '"vector"' The authors of the paper. 

     '_a_b_s_t_T_e_x_t': Object of class '"character"' The contained text of
          the abstract.  

     '_a_r_t_i_c_l_e_T_i_t_l_e': Object of class '"character"' The title of the
          article the abstract pertains to. 

     '_j_o_u_r_n_a_l': Object of class '"character"' The journal the article
          was published in. 

     '_p_u_b_D_a_t_e': Object of class '"character"' The date the journal was
          published. 

     '_a_b_s_t_U_r_l': Object of class '"character"' A URL, if one is
          provided, contained in the abstract. 

_M_e_t_h_o_d_s:

     _p_m_i_d 'signature(object = "pmid")': An accessor function for 'pmid'

     _a_b_s_t_T_e_x_t 'signature(object = "pubMedAbst")': An accessor function
          for 'abstText'

     _a_b_s_t_U_r_l 'signature(object = "pubMedAbst")': An accessor function
          for 'abstUrl' 

     _a_r_t_i_c_l_e_T_i_t_l_e 'signature(object = "pubMedAbst")': An accessor
          function for 'articleTitle' 

     _a_u_t_h_o_r_s 'signature(object = "pubMedAbst")': An accessor function
          for 'authors' 

     _j_o_u_r_n_a_l 'signature(object = "pubMedAbst")': An accessor function
          for 'journal' 

     _p_u_b_D_a_t_e 'signature(object = "pubMedAbst")': An accessor function
          for 'pubDate'

_A_u_t_h_o_r(_s):

     Jeff Gentry

_S_e_e _A_l_s_o:

     'pubmed', 'genbank'

_E_x_a_m_p_l_e_s:

        x <- pubmed("9695952","8325638","8422497")
        a <- xmlRoot(x)
        numAbst <- length(xmlChildren(a))
        absts <- list()
        for (i in 1:numAbst) {
           absts[[i]] <- buildPubMedAbst(a[[i]])
        }