agPMID2PROBE               package:ag               R Documentation

_M_a_p _b_e_t_w_e_e_n _P_u_b_M_e_d _I_d_e_n_t_i_f_i_e_r_s _a_n_d _M_a_n_u_f_a_c_t_u_r_e_r _I_d_e_n_t_i_f_i_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     agPMID2PROBE is an R environment that provides mappings between
     PubMed identifiers and manufacturer identifiers.

_D_e_t_a_i_l_s:

     Each PubMed identifier is mapped to a named vector of manufacturer
     identifiers. The name represents the PubMed identifier and the
     vector contains all manufacturer identifiers that are represented
     by that PubMed identifier. The length of the vector may be one or
     longer, depending on how many manufacturer identifiers are mapped
     to a given 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: <URL:
     ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_AG
     _array_elements-2006-07-14.txt> Tair: <URL:
     ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes>
     Tair: <URL:
     ftp://ftp.arabidopsis.org/home/tair/User_Requests/LocusPublished.0
     8012006.txt> Built: N/A 

     Package built Wed Sep  6 11:22:37 2006

_E_x_a_m_p_l_e_s:

         # Convert the environment to a list
         xx <- as.list(agPMID2PROBE)
         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() && require(annotate)){
                 # Gets article information as XML files for a PubMed id
                 xmls <- pubmed(names(xx)[1], disp = "data")
                 # Views article information using a browser
                 pubmed(names(xx)[1], disp = "browser")
             }
         }

