Maps between Manufacturer Identifiers and PubMed Identifiers

Description

indacPMID is an R object that provides mappings between manufacturer identifiers and PubMed identifiers. indacPMID2PROBE is an R object that provides mappings between PubMed identifiers and manufacturer identifiers.

Details

When indacPMID is viewed as a list 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.

When indacPMID2PROBE is viewed as a list each PubMed identifier is mapped to a named vector of manufacturer identifiers. The name represents the PubMed identifier and the vector contains all manufacturer identifiers that are represented by that PubMed identifier. The length of the vector may be one or longer, depending on how many manufacturer identifiers 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 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: 2015-Sep27

References

http://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 <- indacPMID
# 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){
    # 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")
    }
}

# Now convert the reverse map object indacPMID2PROBE to a list
xx <- as.list(indacPMID2PROBE)
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")
    }
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(indac.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: org.Dm.eg.db


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/indac.db/indacPMID.Rd_%03d_medium.png", width=480, height=480)
> ### Name: indacPMID
> ### Title: Maps between Manufacturer Identifiers and PubMed Identifiers
> ### Aliases: indacPMID indacPMID2PROBE
> ### Keywords: datasets
> 
> ### ** 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 <- indacPMID
> # 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){
+     # 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)){
Error: unexpected '&&' in:
"#    if(interactive() && !is.null(xx[[1]]) && !is.na(xx[[1]])
       &&"
Execution halted