agPMID                 package:ag.db                 R Documentation

_M_a_p _b_e_t_w_e_e_n _M_a_n_u_f_a_c_t_u_r_e_r _I_d_e_n_t_i_f_i_e_r_s _a_n_d _P_u_b_M_e_d _I_d_e_n_t_i_f_i_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     agPMID is an R object that provides mappings between manufacturer
     identifiers and PubMed identifiers.

_D_e_t_a_i_l_s:

     Each manufacturer identifier is mapped to a named vector of PubMed
     identifiers. The name associated with each vector corresponds to
     the manufacturer identifier. The length of the vector may be one
     or greater, depending on how many PubMed identifiers a given
     manufacturer identifier is mapped to. An 'NA' is reported for any
     manufacturer identifier that cannot be mapped to a PubMed
     identifier.

     Titles, abstracts, and possibly full texts of articles can be
     obtained from PubMed by providing a valid PubMed identifier. The
     pubmed function of annotate can also be used for the same purpose.

     Mappings were based on data provided by: Tair (
     ftp://ftp.arabidopsis.org/User_Requests/LocusPublished.08022007.txt
     ) on 2007-Aug2

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed>

_E_x_a_m_p_l_e_s:

             x <- agPMID
             # Get the probe identifiers that are mapped to any PubMed ID
             mapped_probes <- mappedkeys(x)
             # Convert to a list
             xx <- as.list(x[mapped_probes])
         if(length(xx) > 0){
             # The probe identifiers for the first two elements of XX
             xx[1:2]
             # Get the first one
             xx[[1]]
             if(interactive() && !is.null(xx[[1]]) && !is.na(xx[[1]])
                && require(annotate)){
                 # Gets article information as XML files
                 xmls <- pubmed(xx[[1]], disp = "data")
                 # Views article information using a browser
                 pubmed(xx[[1]], disp = "browser")
             }
         }

