All content

Search filter terms
Filter by category
Filter by type
Filter by tag
Filter by user
Filter by licence
Filter by group
Filter by wsdl
Results per page:
Sort by:
Showing 17 results. Use the filters on the left and the search box below to refine the results.
Category: Workflow Group: Bibliometrics and Scientometrics

Workflow Author Citation Network (1)

Thumb
Map citation/reference network for one author using Europe PMC Web services. This workflow was created during the Tavernathon exercise held at the LUMC on October 14, 2015 and is intended to show the integration of several Web services, XPath XML parsing and use of the igraph package in R. Although the workflow is functional, the information in PubMed is incomplete, resulting in the workflow producing a subset of the correct citation graph.

Created: 2015-10-20

Credits: User Magnus Palmblad

Workflow Create Local Citation Graph (1)

Thumb
This workflow demonstrates how to build a local citation/reference graph for a single pubilcation in PubMed. The id input is the PubMed id (pmid) for any publication in the PubMed or PMC Europe. The workflow then queries the PMC Europe Web services to get the citations and references for this publication. Two XPath parsers are used to extract the citation and reference ids, which are then combined and passed on to an Rshell that draws a Sugiyama style layered graph using the igraph package. T...

Created: 2015-10-11

Credits: User Magnus Palmblad

Workflow Author Publications and Citations by Year (2)

Thumb
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: User Magnus Palmblad

Workflow Visualize Geographical Bias between PubMed... (3)

Thumb
This workflow analyzes the scientific output, as documented by PubMed, geographically. The workflow takes as input the PubMed data in XML and the ISO 3166-1 and ISO 3166-3 country lists. The XML files can contain any subset from two specific PubMed searches. for example for two different journals in the same field. The XPath components extract author affiliations, and feed these to a series of Beanshell components that match these with countries in the ISO standard. This data is then fed to ...

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

Credits: User Magnus Palmblad User Arzu Tugce Guler

Workflow Get article titles from Europe PMC for sin... (2)

Thumb
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: User Magnus Palmblad

Workflow connect to WoS Web services lite concept (1)

Thumb
This workflow is a concept for how Taverna could connect to the Thomson Reuters Web of Science (WoS) Web services lite. However, at this moment (2015-01-20), the authentication generate a session ID, but the other services (here search and closeSession) do not have an input port for this session ID. According to the documentation, this is required. The error message from the Web service also show this is missing. This workflow is "work in progress", but may nevertheless be of interest to an...

Created: 2015-08-19

Credits: User Magnus Palmblad User Yassene User Arzu Tugce Guler

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

Thumb
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: User Magnus Palmblad User Arzu Tugce Guler

Results per page:
Sort by: