org.Sc.sgdPMID         package:org.Sc.sgd.db         R Documentation

_M_a_p _b_e_t_w_e_e_n _O_R_F _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.Sc.sgdPMID is an R object that provides mappings between ORF
     identifiers and PubMed identifiers.

_D_e_t_a_i_l_s:

     Each ORF identifier is mapped to a named vector of PubMed
     identifiers. The name associated with each vector corresponds to
     the ORF identifier.  The length of the vector may be one or
     greater, depending on how many PubMed identifiers a given ORF
     identifier is mapped to. An 'NA' is reported for any ORF
     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: Yeast Genome (
     ftp://genome-ftp.stanford.edu/pub/yeast/data_download ) on
     2008-Mar29

_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.Sc.sgdPMID
             # Get the ORF 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 ORF 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")
             }
         }
         # Convert the object to a list
         xx <- as.list(org.Sc.sgdPMID2ORF)
         if(length(xx) > 0){
             # The ORF 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")
             }
         }

