Workflows

Tuiuiu asynchronous workflow (1)

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Tuiuiu removes from a sequence or from a set of sequences areas as large as possible that do not contain researched repeats. Tuiuiu is used as a preliminary step before applying a multiple local aligner tool. Modeling and algorithmic details are provided in the following paper. Please, cite this paper if you use Tuiuiu. P. Peterlongo, G. Sacomoto, A. Pereira do Lago, N. Pisanti, M.-F. Sagot Lossless filter for multiple repeats with bounded edit distance BMC Algorithms for Mole...

Created: 2009-06-29 | Last updated: 2009-06-29

Credits: http://osallou.myopenid.com/ GenOUEST Platform

Tuiuiu synchronous workflow (1)

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Tuiuiu removes from a sequence or from a set of sequences areas as large as possible that do not contain researched repeats. Tuiuiu is used as a preliminary step before applying a multiple local aligner tool. Modeling and algorithmic details are provided in the following paper. Please, cite this paper if you use Tuiuiu. P. Peterlongo, G. Sacomoto, A. Pereira do Lago, N. Pisanti, M.-F. Sagot Lossless filter for multiple repeats with bounded edit distance BMC Algorithms for Mole...

Created: 2009-06-29 | Last updated: 2009-06-29

Credits: http://osallou.myopenid.com/ GenOUEST Platform

searchPublications_and_MapAffil (1)

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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 by the MapAffil Web server to get latitude and longitudes. The coordinates are then concatenated together with the publication year, to produce a single list of publication years, latitudes and ...

Created: 2017-04-19

Credits: Magnus Palmblad

profilePublications_over_time (1)

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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.

Created: 2017-04-19

Credits: Magnus Palmblad

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

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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 work of a single author. Then, we getCitations to extract the year of all articles citing the work of this author. The pubYear fields is extracted from the raw Web service results and fed to an Rshel...

Created: 2015-12-04

Credits: Magnus Palmblad

SImple Europe PMC Search (1)

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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.

Created: 2015-12-04

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

Author Citation Network (1)

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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 results may be a subset of the correct citation graph.

Created: 2015-12-04 | Last updated: 2015-12-04

Credits: Magnus Palmblad Yassene

Author to Wordcloud (3)

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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_wordcloud also applies text mining operations (transformation to lower case, removing punctuation, stripping whitespace and removing English stopwords) using the R package tm.

Created: 2015-12-02 | Last updated: 2015-12-07

Credits: Magnus Palmblad

Get ENSEMBL cross-references for UniProt IDs (1)

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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 database and taxonID 9606 (Homo sapiens).

Created: 2015-11-16

Credits: Magnus Palmblad