Author Publications and Citations by Year with REST
Created: 2016-05-09 08:56:51
Last updated: 2016-05-09 11:32:53
This small workflow demonstrates how to connect to and use Europe PMC (http://europepmc.org/RestfulWebService) to count the number of publications and citations per year for one author. Two REST calls are made. First, we searchPublications to retrieve the bibliographic records for all published work of a single author. Then, we getCitations to extract the year of all articles citing the work of this author. A conditional XPath is here used to only look up citing articles for cited work, i.e. records with result[citedByCount>0]. The pubYear fields is extracted from the raw Web Service results and fed to an Rshell that produces two histograms as output, one for publications and one for citations, very similar to the "Citation Report" in the Thomson Reuters Web of Science. This is a REST equivalent of the SOAP workflow www.myexperiment.org/workflows/4720.html.
It is possible to add output splitters for both Web service calls. This adds two components in the workflow, but simplifies the XPath expressions.
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Authors (1)
Titles (1)
| Author Publications and Citations by Year |
Descriptions (1)
| This small workflow demonstrates how to connect to and use Europe PMC (http://europepmc.org/RestfulWebService) to count the number of publications and citations per year for one author. Two REST calls are made. First, we searchPublications to retrieve the bibliographic records for all published work of a single author. Then, we getCitations to extract the year of all articles citing the work of this author. A conditional XPath is here used to only look up citing articles for cited work, i.e. records with result[citedByCount>0]. The pubYear fields is extracted from the raw Web Service results and fed to an Rshell that produces two histograms as output, one for publications and one for citations, very similar to the "Citation Report" in the Thomson Reuters Web of Science. This is a REST equivalent of the SOAP workflow www.myexperiment.org/workflows/4720.html.
It is possible to add output splitters for both Web service calls. This adds two components in the workflow, but simplifies the XPath expressions.
|
Dependencies (0)
Inputs (1)
| Name |
Description |
| author_name |
The name of an author
|
Processors (13)
| Name |
Type |
Description |
| extract_id_for_cited_work |
xpath |
Xpath Expression/responseWrapper/resultList/result[citedByCount>0]/id |
| build_query |
beanshell |
The build_query BeanShell constructs the Europe PMC search query for a single author, sorting the results by year. ScriptqueryString = "auth:\"" + author_name + "\" sort_date:y"; // generate query string
|
| Flatten_List |
localworker |
Scriptflatten(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); |
| PubMed_and_MEDLINE |
stringconstant |
ValueMED |
| citing_articles_to_retrieve |
stringconstant |
Value100 |
| extract_pubYear_for_citing_articles |
xpath |
Xpath Expression/responseWrapper/citationList/citation/pubYear |
| articles_to_retrieve |
stringconstant |
Value1000 |
| resultType_lite |
stringconstant |
Valuelite |
| offSet_zero |
stringconstant |
Value0 |
| draw_chart |
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. Scriptpng("chart.png", width=1024, height=480);
span<-max(publications, citations)-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, col="green", breaks=span, right=F, main="PubMed Citations", las=1, xlab="Year", ylab="Citations");
dev.off();
R Serverlocalhost:6311 |
| searchPublications |
rest |
|
| extract_pubYear_for_all_work |
xpath |
Xpath Expression/responseWrapper/resultList/result/pubYear |
| getCitations |
rest |
|
Beanshells (1)
| Name |
Description |
Inputs |
Outputs |
| build_query |
The build_query BeanShell constructs the Europe PMC search query for a single author, sorting the results by year. |
author_name
|
queryString
|
Datalinks (15)
| Source |
Sink |
| searchPublications:responseBody |
extract_id_for_cited_work:xml_text |
| author_name |
build_query:author_name |
| extract_pubYear_for_citing_articles:nodelist |
Flatten_List:inputlist |
| getCitations:responseBody |
extract_pubYear_for_citing_articles:xml_text |
| Flatten_List:outputlist |
draw_chart:citations |
| extract_pubYear_for_all_work:nodelist |
draw_chart:publications |
| build_query:queryString |
searchPublications:queryString |
| offSet_zero:value |
searchPublications:offSet |
| articles_to_retrieve:value |
searchPublications:pageSize |
| resultType_lite:value |
searchPublications:resultType |
| searchPublications:responseBody |
extract_pubYear_for_all_work:xml_text |
| extract_id_for_cited_work:nodelist |
getCitations:id |
| citing_articles_to_retrieve:value |
getCitations:pageSize |
| PubMed_and_MEDLINE:value |
getCitations:source |
| draw_chart:chart |
chart |
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