Workflows

Author Publications and Citations by Year ... (1)

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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 work of a single author. Then, we "getCitations" to extract the year of all articles citing the work of this author. A conditional JSONPath is here used to only look up citing articles for cited work...

Created: 2016-05-09

Credits: Magnus Palmblad

Author Publications and Citations by Year ... (2)

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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 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...

Created: 2016-05-09 | Last updated: 2016-05-09

Credits: Magnus Palmblad

UniProt Protein Protein Network (1)

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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 up the second degree connections, i.e. proteins co-occuring with proteins co-occuring with the protein given as input, but not with this protein itself. The output is a (1) Pajek graph file, a GM...

Created: 2015-12-04

Credits: Magnus Palmblad Yassene

Create Local Citation Graph (1)

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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: Magnus Palmblad

Author Publications and Citations by Year (2)

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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...

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

Credits: Magnus Palmblad

Visualize Geographical Bias between PubMed... (3)

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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 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: Magnus Palmblad Arzu Tugce Guler