Map between PubMed Identifiers and TAIR Identifiers

Description

org.At.tairPMID2TAIR is an R object that provides mappings between PubMed identifiers and TAIR identifiers.

Details

Each PubMed identifier is mapped to a named vector of TAIR identifiers. The name represents the PubMed identifier and the vector contains all TAIR identifiers that are represented by that PubMed identifier. The length of the vector may be one or longer, depending on how many TAIR 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: Tair ftp://ftp.arabidopsis.org/home/tair/User_Requests/Locus_Published_20130305.txt With a date stamp from the source of: 2015-Apr07

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:
# Convert the object to a list
xx <- as.list(org.At.tairPMID2TAIR)
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() && 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")
    }
}

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.tairPMID2TAIR.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.At.tairPMID2TAIR
> ### Title: Map between PubMed Identifiers and TAIR Identifiers
> ### Aliases: org.At.tairPMID2TAIR
> ### 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:
> # Convert the object to a list
> xx <- as.list(org.At.tairPMID2TAIR)
> 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() && 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")
+ #    }
+ }
Error: could not find function "pubmed"
Execution halted