Author Publications and Citations by Year

Created: 2015-09-14 16:33:19 Last updated: 2015-09-17 16:44:54

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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 Web service 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.

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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Inputs (1)

Name	Description
author_name	The name of an author

Processors (15)

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_pmid_for_cited_work	xpath	Xpath Expression /ns1:searchPublicationsResponse/return/resultList/result[citedByCount>0]/pmid
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_pubYear_for_citing_articles	xpath	Xpath Expression /ns1:getCitationsResponse/return/citationList/citation/pubYear
articles_to_retrieve	stringconstant	Value 1000
resultType_lite	stringconstant	Value lite
offSet_zero	stringconstant	Value 0
extract_pubYear_for_all_work	xpath	Xpath Expression /ns1:searchPublicationsResponse/return/resultList/result/pubYear
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. Script png("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 Server localhost:6311

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

Outputs (1)

Name	Description
chart

Datalinks (17)

Source	Sink
searchPublications_input:output	searchPublications:parameters
searchPublications:parameters	extract_pmid_for_cited_work: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_pubYear_for_citing_articles: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_pmid_for_cited_work:nodelist	getCitations_input:id
getCitations:parameters	extract_pubYear_for_citing_articles:xml_text
searchPublications:parameters	extract_pubYear_for_all_work:xml_text
extract_pubYear_for_all_work:nodelist	draw_chart:publications
Flatten_List:outputlist	draw_chart:citations
draw_chart:chart	chart

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Information Workflow Type

Taverna 2

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Magnus Palmblad

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Magnus Palmblad

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Version History

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Author Publications and Citations by Year

Created by Magnus Palmblad on Monday 14 September 2015 16:33:15 (UTC)
Author Publications and Citations by Year

Created by Magnus Palmblad on Thursday 17 September 2015 16:44:54 (UTC)

Revision comment:

Changed pmid to id in XPaths, as this is the key attribute.

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Magnus Palmblad

As the Europe PMC Web service is being developed further, this workflow may become obsolete, as in broken or suboptimal. I will try to keep it up-to-date, but feel free to make a comment if you experience problems with it or have suggestions!

-Magnus

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Created: 2015-08-19 | Last updated: 2015-09-07

Credits: Magnus Palmblad Arzu Tugce Guler

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This small workflow demonstrates how to connect to the new (August 2015) version of Europe PMC (http://europepmc.org/RestfulWebService). Changes from previous versions include the addition of a pageSize parameter, allowing the client to request up to 1,000 records at once. If this would still not be sufficient, the offSet paremeter can be used to retrieve data in chunks of 1,000 records and the Flatten List service used to concatenate the results.

Created: 2015-09-07 | Last updated: 2015-09-10

Credits: Magnus Palmblad

Author Publications and Citations by Year

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Xpath Expression

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