Get article titles from Europe PMC for single author

Created: 2015-09-07 11:40:48 Last updated: 2015-09-10 12:22:52

Download Workflow

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.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/4717/download?version=2
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
author_name	The name of an author

Processors (8)

Name	Type	Description
searchPublications	wsdl	Wsdl http://www.ebi.ac.uk/europepmc/webservices/soap?wsdl Wsdl Operation searchPublications
searchPublications_output	xmlsplitter
extract_titles	xpath	Xpath Expression /return/resultList/result/title
build_query	beanshell	Script queryString = "auth:\"" + author_name + "\" sort_date:y";
resultType	stringconstant	Value lite
searchPublications_input	xmlsplitter
pageSize	stringconstant	Value 1000
offSet	stringconstant	Value 0

Beanshells (1)

Name	Description	Inputs	Outputs
build_query		author_name	queryString

Outputs (1)

Name	Description
titles

Datalinks (9)

Source	Sink
searchPublications_input:output	searchPublications:parameters
searchPublications:parameters	searchPublications_output:input
searchPublications_output:return	extract_titles:xml_text
author_name	build_query:author_name
offSet:value	searchPublications_input:offSet
build_query:queryString	searchPublications_input:queryString
resultType:value	searchPublications_input:resultType
pageSize:value	searchPublications_input:pageSize
extract_titles:nodelist	titles

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Magnus Palmblad

Information License

All versions of this Workflow are licensed under:

Information Version 2 (latest) (of 2)

Information Credits (1)

(People/Groups)

Magnus Palmblad

Information Attributions (0)

(Workflows/Files)

None

Information Tags (3)

Uploader tags

Log in to add Tags

Information Shared with Groups (1)

Bibliometrics and Scientometrics

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

1393 viewings

820 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Get article titles from Europe PMC for single author

Created by Magnus Palmblad on Monday 07 September 2015 11:40:46 (UTC)
Get article titles from Europe PMC for single author

Created by Magnus Palmblad on Thursday 10 September 2015 12:22:52 (UTC)

Revision comment:

In this minor update, the pageSize assignment is removed from the query string, as it is supplied as a separate parameter to the Web service.

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (15)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 2

Uploader

Magnus Palmblad

Online PubMed author search and geographic... (2)

Download

This workflow retrieves bibliographic data for a single author using the PMC Europe RESTful Web service and visualizes the geographic distribution of this author's and their co-authors' geographic distribution using the rworldmap package. This is version 2.0 of this workflow, incorporating changes to the Web service allowing up to 1,000 records to be retrieved at once, using the pageSize parameter.

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

Credits: Magnus Palmblad Arzu Tugce Guler

Taverna 2

Uploader

Magnus Palmblad

Author Publications and Citations by Year (2)

Download

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...

Created: 2015-09-14 | Last updated: 2015-09-17

Credits: Magnus Palmblad

Get article titles from Europe PMC for single author

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Wsdl

Wsdl Operation

Xpath Expression

Script

Value

Value

Value

Reviews (0)

Comments (0)

Other workflows that use similar services (15)