Search Pubmed with R

R Project

R is a free software environment for statistical computing, data manipulation, calculation and graphical display (1,2) For those interested, the associated Bioconductor project provides many additional R packages for statistical data analysis in different life science areas, such as tools for microarray, next generation sequence and genome analysis. The R software is free and runs on all common operating systems (2-4). Facilitates the inclusion of biological metadata from literature data such as PubMed. Provides access to powerful statistical and graphical methods.
References:
1- The R Project for Statistical Computing: http://www.r-project.org/ 2- W. N. Venables, D. M. Smith and the R Development Core Team. An Introduction to RNotes on R: A Programming Environment for Data Analysis and Graphics. Version 2.14.2 (2012-02-29). 3-R & Bioconductor Manual. Author: Thomas Girke, UC. Riversidehttp://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#TOC-R-Basics 4- Bioconductor: http://www.bioconductor.org/

Install R
1- Install the latest release of R according to instructions provided in The R Project for Statistical Computing- http://www.r-project.org/ 2- Onced installed, open the R command window (R console) 3- In the R Console the > prompt in red color is where you type the commands. 4- Any text or comment in R beginning with the hash # symbol is ignored.

References 1- The R Project for Statistical Computing: http://www.r-project.org/ 2- Bioconductor: http://www.bioconductor.org/ 3-R Tutorials. W.B. King. 2010. http://ww2.coastal.edu/kingw/statistics/R-tutorials/preliminaries.html

Install packages in R
1- In the R Console type the following in the R command window to connect to Bioconductor and install packages: source("http://bioconductor.org/biocLite.R") 2- request instalation of the package type: biocLite() 3- Install packages, "RISmed" , and "tm" by typing (see next slide) : biocLite(c("RISmed", "tm")) 3- Install package "ggplot2" -type: biocLite( "ggplot2")) Package RISmed is to download content from NCBI databases. Package tm is for text mining functionalities Package ggplot2 is for data visualization
References 1- Bioconductor: http://www.bioconductor.org/ RISmed package: Stephanie Kovalchik (2013). RISmed: Download content from NCBI databases. R package version 2.1.0. http://CRAN.R-project.org/package=RISmed tm package: Ingo Feinerer and Kurt Hornik (2013). tm: Text Mining Package. R package version 0.5-8.3. http://CRAN.R-project.org/package=tm ggplot2 package: H. Wickham. ggplot2: elegant graphics for data analysis. Springer New York, 2009. http://had.co.nz/ggplot2/book also http://cran.r-project.org/web/packages/ggplot2/index.html

The R Console

Use of Packages RISmed and tm

References RISmed package: Stephanie Kovalchik (2013). RISmed: Download content from NCBI databases. R package version 2.1.0. http://CRAN.R-project.org/package=RISmed

Query pubmed titles for oncolytic virus using RISmed

Type the following in the R console: library(RISmed) onc<- EUtilsSummary("oncolytic virus[Majr]") onc # [1] "\"oncolytic viruses\"[MeSH Major Topic]" fetch.onc <- EUtilsGet(onc) fetch.onc # PubMed query: "oncolytic viruses"[MeSH Major Topic] Records: 713 onc.tit<-ArticleTitle(fetch.onc) onc.tit <-unlist(onc.tit) # export title results as text file write(onc.tit, file="title_oncolytic_virus.txt")

Query pubmed MESH topic for oncolytic virus using RISmed

# Continue to type in the R console the following: mh<-Mesh(fetch.onc) mh.per.row<- lapply(1:length(mh), function(i){ mh.df.rbind = as.data.frame(do.call(rbind, Mesh(fetch.onc)[i])) mh.per.row<-paste(mh.df.rbind$Heading, collapse= ";") }) mh.list<-unlist(mh.per.row) # The following is to export mesh results as text file write(mh.list , file="mesh_oncolytic_virus.txt")

View results in excel

# export both title and mesh results as text file to view as table with excel tit.mh<-cbind(onc.tit, mh.list) tit.mh[1:10,] # view first 10 results write.table(tit.mh, file="tit_mesh_oncolytic_virus.txt ", row.names=F, sep="\t") # !!open file in excel

Column containing titles

Column containing corresponding Mesh terms

Preparing forText Mining Analysis

Type getwd() in the R console to display the R working directory. In my case: [1] "C:/Documents and Settings/PMarqui/My Documents" Now create a new folder in the R working directory and give a name to it (for ex. OncolyticVirus) Use the new folder to place two of the recently created text files: title_oncolytic_virus.txt and mesh_oncolytic_virus.txt Start the Text Mining Analysis

Text Mining Analysis

# Type the following in the R Console library(tm) #loads the text mining package my.corpus<-Corpus(DirSource("OncolyticVirus"), readerControl=list(reader=readPlain)) # Note that "OncolyticVirus" refer to the name of the newly created folder. In my.corpus<-Corpus(DirSource(" you must use the name given to the folder containing the 2 text files my.corpus <- tm_map(my.corpus, stripWhitespace) # Removes extra
whitespace

my.corpus <- tm_map(my.corpus, gsub, pattern="[^[:alnum:][:space:]]", replacement=" ") # remove punctuation except dash
"-"

# my.corpus <- tm_map(my.corpus, removeNumbers) # Removes

numbers- optional

Text Mining Analysis

# Continue and type the following code in the R Console:

my.corpus <- tm_map(my.corpus, tolower) #Conversion to lower case letters my.corpus <- tm_map(my.corpus, removeWords, stopwords("english")) # Removes stopwords my.corpus <- tm_map(my.corpus, stemDocument) # removes suffixes from
words to get common origin Document matrix

my.corpus.matrix<-TermDocumentMatrix(my.corpus) # Creates a Termmat.my.corpus<- as.matrix(my.corpus.matrix) # Creates a matrix my.corpus.df<-as.data.frame(mat.my.corpus) # Create data frame from
matrix displaying all the terms in any of the 2 documents.

my.corpus.df[200:250,1:2] # view some of the terms copy.my.corpus.df<-my.corpus.df # make a copy of my.corpus.df

data frame for later

to keep original

Text Mining Analysis

# Continue and type the following code in the R Console:
#sort the most freq mesh term in the data frame my.corpus.df<- my.corpus.df[

order(my.corpus.df$mesh_oncolytic_virus.txt, decreasing = T),]

# assign the 50 most freq mesh term to xx

xx<- my.corpus.df[1:50,]

# view the top 5 most freq mesh term- to view you can also use "head( xx,5)" both are equivalent xx[1:5,] #sort the 50 most freq mesh term in increasing order (for plot visualization) xx<- xx[ order(xx$mesh_oncolytic_virus.txt, decreasing = FALSE),]

Text Mining Analysis

# Continue and type the following code in the R Console:
# Plot the 50 most frequent mesh terms use library ggplot2 library(ggplot2)

Terms<- rownames(xx) Mesh.count<-xx$mesh_oncolytic_virus.txt ggplot(xx) + geom_point(aes(Terms, Mesh.count ), stat = "identity", fill = "darkblue")+ coord_flip() + theme_bw() p1<-last_plot() + scale_x_discrete(limits=(Terms)) p1

Text Mining Analysis

VIEW the 50 most frequent mesh term

End of Part 1