Group: LUMC Taverna user group

News

1. 

   Magnus Palmblad shared Author Publications and Citations by Year with REST and JSON

   

   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)
2. 

   Magnus Palmblad shared Author Publications and Citations by Year

   

   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)
3. 

   Magnus Palmblad shared UniProt Protein Protein Network

   

   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)
4. 

   Magnus Palmblad shared Author to Wordcloud

   

   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)
5. 

   Magnus Palmblad shared Get ENSEMBL cross-references for UniProt IDs

   

   This small workflow uses the PICR ( http://www.ebi.ac.uk/Tools/picr/ ) WDSL Web Service to look up ENSEMBL (ENSP) cross-references for UniProt IDs. The input is a list of UniProt IDs and the output a corresponding list of ENSEMBL IDs. This instance of the workflow specifically uses the ENSEMBL_HUMAN …

   Monday 16 November 2015 13:40:48 (UTC)
6. 

   Magnus Palmblad shared Author Citation Network

   

   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)
7. 

   Magnus Palmblad shared Tavernathon partial solution 1

   Wednesday 14 October 2015 12:46:44 (UTC)
8. 

   Yassene joined the LUMC Taverna user group group

   Wednesday 14 October 2015 12:13:17 (UTC)
9. 

   Magnus Palmblad shared Create Local Citation Graph

   Wednesday 14 October 2015 12:09:19 (UTC)
10. 

    Arzu Tugce Guler, Rob Marissen, and Malas joined the LUMC Taverna user group group
11. 

    Magnus Palmblad shared Make Groups for Tutorial

    

    The workflow pairs people from two groups of equal size into the same number of pairs with one member from each group. This is done randomly, using the random.org randomization engine, which in turn is based on atmospheric radio noise.

    Monday 12 October 2015 12:56:00 (UTC)
12. 

    Magnus Palmblad shared Create Local Citation Graph

    

    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 publica …

    Sunday 11 October 2015 14:45:46 (UTC)