agPMID {ag.db}R Documentation

Map between Manufacturer Identifiers and PubMed Identifiers

Description

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

Details

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.10042007.txt ) on 2007-Oct04

References

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

Examples

        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")
        }
    }

[Package ag.db version 2.2.0 Index]