Author Publications and Citations by Year with 2D Histogram

None

/ns1:searchPublicationsResponse/return/resultList/result[pubYear>0]/id
queryString = "auth:\"" + author_name +  "\" sort_date:y";  // generate query string

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);
/ns1:getCitationsResponse/return/request/id|/ns1:getCitationsResponse/return/citationList/citation/pubYear
/ns1:searchPublicationsResponse/return/resultList/result[pubYear>0]/pubYear
library(gplots);
png("2D_histogram.png", width=480, height=480);
A<-matrix(NA,length(citations),2);
pub<-0;
for(i in 1:length(citations)) if(citations[i]>=2100) pub<-pub+1 else A[i,]<-c(publications[pub],as.integer(citations[i]));
span<-2015-min(publications);
hist2d(A, col=c("black", heat.colors(50)), nbins=span, same.scale=F, main="PubMed Citations", las=1, xlab="Publication Year", ylab="Citation Year");
dev.off();

png("citation_report.png", width=1024, height=480);
citations_numeric<-rep(0,length(citations));
for(i in 1:length(citations)) {
	if(suppressWarnings(!is.na(as.numeric(citations[i])))) citations_numeric[i]<-as.numeric(citations[i]) else citations_numeric[i]<-NA;  
	if(citations_numeric[i]>=2100) citations_numeric[i]<-NA;
}
span<-2015-min(publications);
par(mfrow=c(1,2));
hist(publications, col="red", breaks=span, right=F, main="PubMed Publications", las=1, xlab="Year", ylab="Publications");
hist(citations_numeric, col="green", breaks=span, right=F, main="PubMed Citations", las=1, xlab="Year", ylab="Citations");
dev.off();

Name	Type	Description
searchPublications	wsdl	The searchPublications calls the Europe PMC Web service to retrieve the bibliographic information for all published work indexed in PubMed by author_name. Wsdl http://www.ebi.ac.uk/europepmc/webservices/soap?wsdl Wsdl Operation searchPublications
extract_id	xpath	Xpath Expression /ns1:searchPublicationsResponse/return/resultList/result[pubYear>0]/id
build_query	beanshell	The build_query BeanShell constructs the Europe PMC search query for a single author, sorting the results by year. Script queryString = "auth:\"" + author_name + "\" sort_date:y"; // generate query string
searchPublications_input	xmlsplitter
Flatten_List	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
getCitations	wsdl	The getCitations call fetches data for all articles citing cited work by author_name. Note that this is a different call with different input and output than searchPublications. Input is a list of pmid. Wsdl http://www.ebi.ac.uk/europepmc/webservices/soap?wsdl Wsdl Operation getCitations
getCitations_input	xmlsplitter
PubMed_and_MEDLINE	stringconstant	Value MED
citing_articles_to_retrieve	stringconstant	Value 100
extract_citation_pubYear	xpath	Xpath Expression /ns1:getCitationsResponse/return/request/id\|/ns1:getCitationsResponse/return/citationList/citation/pubYear
articles_to_retrieve	stringconstant	Value 1000
resultType_lite	stringconstant	Value lite
offSet_zero	stringconstant	Value 0
extract_pubYear	xpath	Xpath Expression /ns1:searchPublicationsResponse/return/resultList/result[pubYear>0]/pubYear
make_2D_histogram	rshell	This Rshell takes as input (flattened) lists of years for the publications and citations of author_name and outputs two histograms, one for the publications and one for the citations, per year. Script library(gplots); png("2D_histogram.png", width=480, height=480); A<-matrix(NA,length(citations),2); pub<-0; for(i in 1:length(citations)) if(citations[i]>=2100) pub<-pub+1 else A[i,]<-c(publications[pub],as.integer(citations[i])); span<-2015-min(publications); hist2d(A, col=c("black", heat.colors(50)), nbins=span, same.scale=F, main="PubMed Citations", las=1, xlab="Publication Year", ylab="Citation Year"); dev.off(); R Server localhost:6311
generate_citation_report	rshell	This Rshell takes as input (flattened) lists of years for the publications and citations of author_name and outputs a heatmap of the publications and citations over time. Script png("citation_report.png", width=1024, height=480); citations_numeric<-rep(0,length(citations)); for(i in 1:length(citations)) { if(suppressWarnings(!is.na(as.numeric(citations[i])))) citations_numeric[i]<-as.numeric(citations[i]) else citations_numeric[i]<-NA; if(citations_numeric[i]>=2100) citations_numeric[i]<-NA; } span<-2015-min(publications); par(mfrow=c(1,2)); hist(publications, col="red", breaks=span, right=F, main="PubMed Publications", las=1, xlab="Year", ylab="Publications"); hist(citations_numeric, col="green", breaks=span, right=F, main="PubMed Citations", las=1, xlab="Year", ylab="Citations"); dev.off(); R Server localhost:6311

Name	Description
2D_histogram
citation_report

Source	Sink
searchPublications_input:output	searchPublications:parameters
searchPublications:parameters	extract_id:xml_text
author_name	build_query:author_name
build_query:queryString	searchPublications_input:queryString
offSet_zero:value	searchPublications_input:offSet
articles_to_retrieve:value	searchPublications_input:pageSize
resultType_lite:value	searchPublications_input:resultType
extract_citation_pubYear:nodelist	Flatten_List:inputlist
getCitations_input:output	getCitations:parameters
PubMed_and_MEDLINE:value	getCitations_input:source
citing_articles_to_retrieve:value	getCitations_input:pageSize
extract_id:nodelist	getCitations_input:id
getCitations:parameters	extract_citation_pubYear:xml_text
searchPublications:parameters	extract_pubYear:xml_text
extract_pubYear:nodelist	make_2D_histogram:publications
Flatten_List:outputlist	make_2D_histogram:citations
Flatten_List:outputlist	generate_citation_report:citations
extract_pubYear:nodelist	generate_citation_report:publications
make_2D_histogram:2D_histogram	2D_histogram
generate_citation_report:citation_report	citation_report

Author Publications and Citations by Year with 2D Histogram

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Wsdl

Wsdl Operation

Xpath Expression

Script

Script

Wsdl

Wsdl Operation

Value

Value

Xpath Expression

Value

Value

Value

Xpath Expression

Script

R Server

Script

R Server

Reviews (0)

Comments (0)

Other workflows that use similar services (15)