Map between Entrez Gene Identifiers and PubMed Identifiers

Description

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

Details

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 With a date stamp from the source of: 2017-Nov6

References

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

See Also

• AnnotationDb-class for use of the select() interface.

Examples

## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

## Bimap interface:
x <- org.Hs.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.Hs.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")
    }
}