Map between TAIR Identifiers and PubMed Identifiers

Description

org.At.tairPMID is an R object that provides mappings between TAIR identifiers and PubMed identifiers.

Details

Each TAIR identifier is mapped to a named vector of PubMed identifiers. The name associated with each vector corresponds to the TAIR identifier. The length of the vector may be one or greater, depending on how many PubMed identifiers a given TAIR identifier is mapped to. An NA is reported for any TAIR 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/home/tair/User_Requests/Locus_Published_20130305.txt With a date stamp from the source of: 2015-Apr07

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 <- org.At.tairPMID
# Get the tair 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 tair 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")
    }
}

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(org.At.tair.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


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/org.At.tair.db/org.At.tairPMID.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.At.tairPMID
> ### Title: Map between TAIR Identifiers and PubMed Identifiers
> ### Aliases: org.At.tairPMID
> ### 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 <- org.At.tairPMID
> # Get the tair 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 tair 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)){
Error: unexpected '&&' in:
"#    if(interactive() && !is.null(xx[[1]]) && !is.na(xx[[1]])
        &&"
Execution halted