Maps between SomaScan SeqIds and PubMed identifiers

SomaScanPMID is an R object that provides mappings between SeqIds and PubMed identifiers.

SomaScanPMID2PROBE is an R object that provides mappings between PubMed identifiers and SeqIDs.

Details

When SomaScanPMID is viewed as a list, each SeqId is mapped to a named vector of PubMed identifiers. The name associated with each vector corresponds to the SeqId. The length of the vector may be one or greater, depending on how many PubMed identifiers a given SeqId is mapped to. An NA is reported for any SeqId that cannot be mapped to a PubMed identifier.

When SomaScanPMID2PROBE is viewed as a list, each PubMed identifier is mapped to a named vector of SeqIds. The name represents the PubMed identifier and the vector contains all SeqIds that are represented by that PubMed identifier. The length of the vector may be one or longer, depending on how many SeqIds are mapped to a given 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 the annotate package 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: 2021-Sep13

Value

A Bimap object of the ProbeAnnDbBimap class.

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 <- SomaScanPMID
# 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][1:300])
if(length(xx) > 0){
    # Get the PubMed identifiers for the first two probe identifiers
    xx[1:2]
    # Get the first one
    xx[[1]]
    if(interactive() && !is.null(xx[[1]]) && !is.na(xx[[1]]) 
    && require(annotate)){
        # Get article information as XML files
        xmls <- pubmed(xx[[1]], disp = "data")
        # View article information using a browser
        pubmed(xx[[1]], disp = "browser")
    }
}

x <- SomaScanPMID2PROBE
mapped_probes <- mappedkeys(x)
# Now convert the reverse map object SomaScanPMID2PROBE to a list
xx <- as.list(x[mapped_probes][1:300])
if(length(xx) > 0){
    # Get the probe identifiers for the first two PubMed identifiers
    xx[1:2]
    # Get the first one
    xx[[1]]
    if(interactive() && require(annotate)){
        # Get article information as XML files for a PubMed id
        xmls <- pubmed(names(xx)[1], disp = "data")
        # View article information using a browser
        pubmed(names(xx)[1], disp = "browser")
    }
}