pubmedAbstract

Description

Get the text of a journal article's abstract from PubMed.

Usage

  pubmedAbstract(pmid, split=TRUE)

Arguments

Value

A single character string, or a vector of strings split on the embedded newline characters.

Author(s)

Paul Shannon

See Also

RefNet, providerClasses, interactions, addStandardNames

Examples

  pubmedAbstract("22959076")

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(RefNet)
Loading required package: IRanges
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: PSICQUIC
Loading required package: biomaRt
Loading required package: httr
Loading required package: plyr

Attaching package: 'plyr'

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

Loading required package: AnnotationHub
Loading required package: RCurl
Loading required package: bitops
Loading required package: shiny
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RefNet/pubmedAbstract.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pubmedAbstract
> ### Title: pubmedAbstract
> ### Aliases: pubmedAbstract
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   pubmedAbstract("22959076")
 [1] ""                                                                                    
 [2] "1. Cell. 2012 Sep 14;150(6):1274-86. doi: 10.1016/j.cell.2012.04.040. Epub 2012 Sep "
 [3] "5."                                                                                  
 [4] ""                                                                                    
 [5] "Circuitry and dynamics of human transcription factor regulatory networks."           
 [6] ""                                                                                    
 [7] "Neph S(1), Stergachis AB, Reynolds A, Sandstrom R, Borenstein E,"                    
 [8] "Stamatoyannopoulos JA."                                                              
 [9] ""                                                                                    
[10] "Author information: "                                                                
[11] "(1)Department of Genome Sciences, University of Washington, Seattle, WA 98195,"      
[12] "USA."                                                                                
[13] ""                                                                                    
[14] "The combinatorial cross-regulation of hundreds of sequence-specific transcription"   
[15] "factors (TFs) defines a regulatory network that underlies cellular identity and"     
[16] "function. Here we use genome-wide maps of in vivo DNaseI footprints to assemble"     
[17] "an extensive core human regulatory network comprising connections among 475"         
[18] "sequence-specific TFs and to analyze the dynamics of these connections across 41 "   
[19] "diverse cell and tissue types. We find that human TF networks are highly cell"       
[20] "selective and are driven by cohorts of factors that include regulators with"         
[21] "previously unrecognized roles in control of cellular identity. Moreover, we"         
[22] "identify many widely expressed factors that impact transcriptional regulatory"       
[23] "networks in a cell-selective manner. Strikingly, in spite of their inherent"         
[24] "diversity, all cell-type regulatory networks independently converge on a common"     
[25] "architecture that closely resembles the topology of living neuronal networks."       
[26] "Together, our results provide an extensive description of the circuitry,"            
[27] "dynamics, and organizing principles of the human TF regulatory network."             
[28] ""                                                                                    
[29] "Copyright <U+00A9> 2012 Elsevier Inc. All rights reserved."                          
[30] ""                                                                                    
[31] "DOI: 10.1016/j.cell.2012.04.040 "                                                    
[32] "PMCID: PMC3679407"                                                                   
[33] "PMID: 22959076  [PubMed - indexed for MEDLINE]"                                      
[34] ""                                                                                    
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>