Group: Bibliometrics and Scientometrics

Overview

This is a myExperiment group for people interested in building Taverna workflows for bibliometrics, scientometrics and related topics.

Created at: Friday 09 January 2015 15:12:56 (UTC)

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    Magnus Palmblad shared searchPublications_and_MapAffil
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    This is a workflow for spatiotemporal analysis of literature indexed in PubMed. The workflow takes an arbitrary Europe PMC search query, calls the Europe PMC Web service searchPublications and extracts the publication year and PubMed ID from the results. The first author affiliation is then geoparsed …
    Wednesday 19 April 2017 09:31:23 (UTC)
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    Magnus Palmblad shared profilePublications_over_time
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    This workflow takes a list of arbitrary Europe PMC search queries and generates the corresponding profiles of the number of matching publications per publication year.
    Wednesday 19 April 2017 09:30:17 (UTC)
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    Magnus Palmblad shared Author Publications and Citations by Year with REST and JSON
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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 REST calls are made. First, we "searchPublications" to retrieve the bibliographic records for all published w …
    Monday 09 May 2016 11:33:35 (UTC)
  4. 3655?size=48x48
    Magnus Palmblad shared Author Publications and Citations by Year
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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 REST calls are made. First, we "searchPublications" to retrieve the bibliographic records for all published w …
    Monday 09 May 2016 08:56:51 (UTC)
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    Magnus Palmblad shared Example results from the UniProt Protein Protein Network workflow
    Example results from the UniProt Protein Protein Network workflow ( http://www.myexperiment.org/workflows/4778.html ) on Apolipoprotein A-I (P02647). The purpose of the igraph graph is to check that the workflow ran OK. For further exploration and visualization of the network, one of the output files …
    Friday 04 December 2015 14:50:06 (UTC)
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    Magnus Palmblad shared Author Publications and Citations by Year with 2D Histogram
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    This 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 wo …
    Friday 04 December 2015 12:39:59 (UTC)
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    Magnus Palmblad shared Connecting to Europe PMC
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    This very simple workflow connects to Europe PMC using the searchPublications Web Service.
    Friday 04 December 2015 12:28:38 (UTC)
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    Magnus Palmblad shared SImple Europe PMC Search
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    This very simple workflow searches Europe PMC using the searchPublications Web Service and a conditional XPath to retrieve the article titles for all cited work matching the search query.
    Friday 04 December 2015 12:24:12 (UTC)
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    Magnus Palmblad shared UniProt Protein Protein Network
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    This workflow uses the Europe PMC Web Services searchPublications and getDatabaseLinks to reconstruct a protein-protein network based on co-occurence in the scientific literature, arbitrary filtered by a PubMed query, e.g. the word "complex" appearing in the title or abstract. The workflow also looks …
    Friday 04 December 2015 12:12:49 (UTC)
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    Magnus Palmblad shared Author Citation Network
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    Map citation/reference network for one author using Europe PMC Web services. This workflow 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. This means the re …
    Friday 04 December 2015 12:01:51 (UTC)
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    Magnus Palmblad shared Author to Wordcloud
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    This small workflow demonstrates how to connect to and use Europe PMC ( http://europepmc.org/RestfulWebService ). The workflow searches the publications of an author, extracts the abstracts, counts the word frequencies and plot a wordcloud using the R package of the same name. The Rshell plot_wordclo …
    Wednesday 02 December 2015 18:00:16 (UTC)
  12. 3655?size=48x48
    Magnus Palmblad shared Author Citation Network
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    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 t …
    Tuesday 20 October 2015 10:10:36 (UTC)

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Workflow

Workflow compare_pubmed_results_geographically (1)

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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 file can contain any subset from a specific PubMed search. 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 an Rshell using the rworldmap R package to map the affiliation ...

Created: 2015-05-05 | Last updated: 2015-05-05

Credits: User Magnus Palmblad User Arzu Tugce Guler Network-member Bibliometrics and Scientometrics

Attributions: Blob ISO 3166-1 and ISO 3166-3 Blob Former countries


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Non-Information Resource URI: https://www.myexperiment.org/groups/1278


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