Dear all, I think it's better to post here, instead on r-help. It's about MedlineR package in R; I receive the following error message when using "getAmatrix" (co-occurance matrix between terms in PubMed) command: Error in xmlTreeParse(file = query, isURL = T) : error in creating parser for http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&re ttype=count&term=GLB1+AND+ARSA Error in xmlRoot(result.xml) : no applicable method for "xmlRoot" Andrej

Hi Morten, On 30 Nov 2005, morten.mattingsdal at student.uib.no wrote: > Hei Andrej Yes.. Ive seen this error before.. dont know the nature > of the error though... maybe because newer R/XML versions.. anyway I > got it working with the following code: Since it looks like you have a fix, have you communicated with the package's maintainer? + seth

Hi Andrej Yes.. its a common error in MedLineR.. May be because of newer R/XML packages.. I got it working again though :)).. (dont remeber what i did).. The authour of MedLineR seems absent from support at bioinformatics.org.......... try this code.. it workes with: R 2.2.0 XML 0.97-8 ###################################################################### ### # # # Basic textminer in R/CRAN. Count co-occuring terms in MedLine/PubMed # # # # Adopted from MedLineR # # # ###################################################################### ### library(XML) options("serviceUrl.entrez" = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/") countApair<- function ( term1, term2, termAdditional="", baseUrl=getOption("serviceUrl.entrez") ) { # QC: make sure the baseUrl is all right. if (is.null (baseUrl)) { stop ("Need to define the URL of the Pubmed service!") } query<- paste (baseUrl, "esearch.fcgi?", "db=pubmed&", # replace pubmed with db of interest (omim,snp,unigene ++) "rettype=count&", "term=", term1, "+AND+", term2, termAdditional, sep="") result.xml<- try (xmlTreeParse(file=query, isURL=T)) count<- as.numeric(xmlValue (xmlRoot (result.xml) [["Count"]])) return (count) } pauseBetweenQueries<- function ( sleep.peak=15, # pause (in seconds) during peak hours sleep.offpeak=3 # pause (in seconds) during off-peak ) { result.date<- unlist (strsplit( date(), split=" ")) hour<- as.numeric(unlist (strsplit (result.date[4], split=':'))[1]) if ( (result.date[1]=="Sat") | (result.date[1]=="Sun") | (hour > 21) | (hour<5) ) {off.peak<-T} else {off.peak<-F} if (off.peak) { print("--Off hours at NCBI (faster)--") Sys.sleep (sleep.offpeak) } else { print("--Its peaktime at NCBI (slower)--") Sys.sleep (sleep.peak) } } termList=c("alcohol","benefit","gene","chromosome","income","norway") # Define your searchterms n.terms<- length (termList) matrix (0, ncol=n.terms, nrow=n.terms) n.terms<- length (termList) result.matrix<-matrix (0, ncol=n.terms, nrow=n.terms) for (i in 1:n.terms){ result.matrix[i,i]<- countApair ( term1=termList[i], term2=termList[i]) pauseBetweenQueries() } for (i in 1:(n.terms-1)){ if (result.matrix [i,i]==0) {next} for (j in (i+1):n.terms) { n.counts <-countApair ( term1=termList[i], term2=termList[j]) pauseBetweenQueries() result.matrix[i,j]<- n.counts result.matrix[j,i]<- n.counts } } row.names(result.matrix)<-termList colnames(result.matrix)<-termList result.matrix dotchart(result.matrix,cex=0.7) #END good luck morten >Dear all, > >I think it's better to post here, instead on r-help. It's about MedlineR >package in R; I receive the following error message when using >"getAmatrix" (co-occurance matrix between terms in PubMed) command: > >Error in xmlTreeParse(file = query, isURL = T) : > error in creating parser for >http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&r ettype=count&term=GLB1+AND+ARSA >Error in xmlRoot(result.xml) : no applicable method for "xmlRoot" > >Andrej > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > >

Hei Andrej Yes.. Ive seen this error before.. dont know the nature of the error though... maybe because newer R/XML versions.. anyway I got it working with the following code: ###################################################################### ### # # # Basic textminer in R/CRAN. Count co-occuring terms in MedLine/PubMed # # # # Adopted from MedLineR # # # ###################################################################### ### library(XML) options("serviceUrl.entrez" = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/") countApair<- function ( term1, term2, termAdditional="", baseUrl=getOption("serviceUrl.entrez") ) { # QC: make sure the baseUrl is all right. if (is.null (baseUrl)) { stop ("Need to define the URL of the Pubmed service!") } query<- paste (baseUrl, "esearch.fcgi?", "db=pubmed&", # replace pubmed with db of interest (omim,snp,unigene ++) "rettype=count&", "term=", term1, "+AND+", term2, termAdditional, sep="") result.xml<- try (xmlTreeParse(file=query, isURL=T)) count<- as.numeric(xmlValue (xmlRoot (result.xml) [["Count"]])) return (count) } pauseBetweenQueries<- function ( sleep.peak=15, # pause (in seconds) during peak hours sleep.offpeak=3 # pause (in seconds) during off-peak ) { result.date<- unlist (strsplit( date(), split=" ")) hour<- as.numeric(unlist (strsplit (result.date[4], split=':'))[1]) if ( (result.date[1]=="Sat") | (result.date[1]=="Sun") | (hour > 21) | (hour<5) ) {off.peak<-T} else {off.peak<-F} if (off.peak) { print("--Off hours at NCBI (faster)--") Sys.sleep (sleep.offpeak) } else { print("--Its peaktime at NCBI (slower)--") Sys.sleep (sleep.peak) } } termList=c("alcohol","benefit","gene","chromosome","income","norway") # Define your searchterms n.terms<- length (termList) matrix (0, ncol=n.terms, nrow=n.terms) n.terms<- length (termList) result.matrix<-matrix (0, ncol=n.terms, nrow=n.terms) for (i in 1:n.terms){ result.matrix[i,i]<- countApair ( term1=termList[i], term2=termList[i]) pauseBetweenQueries() } for (i in 1:(n.terms-1)){ if (result.matrix [i,i]==0) {next} for (j in (i+1):n.terms) { n.counts <-countApair ( term1=termList[i], term2=termList[j]) pauseBetweenQueries() result.matrix[i,j]<- n.counts result.matrix[j,i]<- n.counts } } row.names(result.matrix)<-termList colnames(result.matrix)<-termList result.matrix dotchart(result.matrix,cex=0.7) #END good luck :) morten >Dear all, > >I think it's better to post here, instead on r-help. It's about MedlineR >package in R; I receive the following error message when using >"getAmatrix" (co-occurance matrix between terms in PubMed) command: > >Error in xmlTreeParse(file = query, isURL = T) : > error in creating parser for >http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&r ettype=count&term=GLB1+AND+ARSA >Error in xmlRoot(result.xml) : no applicable method for "xmlRoot" > >Andrej > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > >