org.Sc.sgdPMID {org.Sc.sgd.db} | R Documentation

## Map between ORF Identifiers and PubMed Identifiers

### Description

org.Sc.sgdPMID is an R object that provides mappings between ORF identifiers and PubMed identifiers.

### Details

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-Sep06

### References

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

### Examples

            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")
            }
        }

[Package org.Sc.sgd.db version 2.2.6 Index]