org.EcK12.egPMID       package:org.EcK12.eg.db       R Documentation

_M_a_p _b_e_t_w_e_e_n _E_n_t_r_e_z _G_e_n_e _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:

     org.EcK12.egPMID is an R object that provides mappings between
     entrez gene identifiers and PubMed identifiers.

_D_e_t_a_i_l_s:

     Each entrez gene identifier is mapped to a named vector of PubMed
     identifiers. The name associated with each vector corresponds to
     the entrez gene identifier.  The length of the vector may be one
     or greater, depending on how many PubMed identifiers a given
     entrez gene identifier is mapped to. An 'NA' is reported for any
     entrez gene 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: Entrez Gene (
     ftp://ftp.ncbi.nlm.nih.gov/gene/DATA ) on 2008-Sep2

_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 <- org.EcK12.egPMID
             # Get the entrez gene identifiers that are mapped to any PubMed ID
             mapped_genes <- mappedkeys(x)
             # Convert to a list
             xx <- as.list(x[mapped_genes])
         if(length(xx) > 0){
             # The entrez gene 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")
             }
         }
         # For the reverse map:
         # Convert the object to a list
         xx <- as.list(org.EcK12.egPMID2EG)
         if(length(xx) > 0){
             # The entrez gene 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")
             }
         }

