\name{org.Ss.egPMID}
\alias{org.Ss.egPMID}
\alias{org.Ss.egPMID2EG}
\title{Map between Entrez Gene Identifiers and PubMed Identifiers}
\description{
   org.Ss.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 \code{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: 2025-Sep24
}

\references{
  \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed}
}

\seealso{
  \itemize{
    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
          the \code{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.Ss.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.Ss.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")
    }
}
}

\keyword{datasets}

