Workflows

GetWikiPWByCHEBI (2)

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This workflow uses the WikiPathways Webservice/API to query for pathways containing a specific Chemical Entities of Biological Interest (ChEBI) identifier. The mapping service behind WikiPathways takes care of the identifier mapping, making sure that all relevant results are found even if they were originally reported using a different identifier scheme.

Created: 2015-09-01 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni

AllPW2CHEBI (2)

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This workflow uses the WikiPathways Webservice/API to query to retrieve all Chemical Entities of Biological Interest (ChEBI) identifers for all pathways and merge them to one, unique list.

Created: 2015-09-01 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni

REF2014 impact study summary by ID (2)

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Queries the UK REF2014 impact study API by the ID of the study, extracts the ImpactSummary element, and outputs its value as text.

Created: 2015-09-05 | Last updated: 2015-09-05

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

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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: 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

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

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2015-09-29

Credits: Thiago Soares

Loop (1)

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Example of looping over asynchronous services. The dummy beanshell scripts represents the operations of an asynchronous submit-status-results style service, such as EBI's InterProScan and NCBI Blast. createJob creates a temporary file with the content "0". Filename retuirned as a "job ID". checkStatus reads the job, and return state "RUNNING" as long as the content is less than 10, increasing the number for each call. (As no actual job is being run) getResults reads the file content, with...

Created: 2015-09-29

Credits: Thiago Soares

Merge (1)

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Created: 2015-09-29 | Last updated: 2015-09-29

Credits: Thiago Soares

Produto Lista (1)

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Created: 2015-09-29

Credits: Thiago Soares

Retry (1)

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Created: 2015-09-29

Credits: Thiago Soares

Paralelo (1)

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Created: 2015-09-29

Credits: Thiago Soares

Beanshell fibonacci (1)

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Created: 2015-09-30

Credits: igor russo

Beanshell fibonacci 2 (2)

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Created: 2015-09-30 | Last updated: 2015-09-30

Credits: igor russo

Simple test with paralel execution using b... (1)

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A simple exercise on parallel processing using BeanShell

Created: 2015-10-01 | Last updated: 2015-10-01

Credits: Ciro Barbosa

AllPW2ENS (2)

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This workflow uses the WikiPathways Webservice/API to query to retrieve all ENSEMBL identifers for all pathways and merge them into one, unique list.

Created: 2015-10-02 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni

GetWikiPWByENS (2)

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This workflow uses the WikiPathways Webservice/API to query for pathways containing a specific ENSEMBL identifier. The mapping service behind WikiPathways takes care of the identifier mapping, making sure that all relevant results are found even if they were originally reported using a different identifier scheme.

Created: 2015-10-02 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni

PW2ENS (2)

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This workflow uses the WikiPathways Webservice/API to query to retrieve all ENSEMBL identifers for the given pathway.

Created: 2015-10-02 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni

Get_Weather (1)

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Modeal based on other models already hosted at myExperiment, but with small changes (changed input from static to input type).

Created: 2015-10-06 | Last updated: 2015-10-06

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

Web Service sample in .NET (1)

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To run this sample, you should first set up a web service with the following C# code: using System; using System.Collections.Generic; using System.Linq; using System.Web; using System.Web.Services; namespace TrabsEsicnece { [WebService(Namespace = "http://trabsescience.org/")] [WebServiceBinding(ConformsTo = WsiProfiles.BasicProfile1_1)] [System.ComponentModel.ToolboxItem(false)] public class Service1 : System.Web.Services.WebService { [WebMethod] public...

Created: 2015-10-13

Submit Job Cluster (1)

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Created: 2015-10-13

Credits: Thiago Soares

Local JAR execution. (2)

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Created: 2015-10-14 | Last updated: 2015-10-14

Credits: igor russo

Remove string duplicates (1)

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Created: 2015-10-14

Credits: igor russo

Author Citation Network (1)

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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 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: Magnus Palmblad

FInd/filter idA and idB from MITAB (1)

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A workflow to filter idA and idB out of a MITAB file.

Created: 2015-11-05 | Last updated: 2015-11-05

Query PSICQUIC and filter by idA and idB (... (1)

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Queries PSICQUIC and returns idA and idB.

Created: 2015-11-05

Query for all PISCQUIC services (Name+URL) (1)

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No description

Created: 2015-11-05

Define one query and retrieve Molecular In... (1)

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Define one query and retrieve Molecular Interactions from PSICQUIC Services registered in the PSICQUIC registry.

Created: 2015-11-05

Get ontology parents (2)

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Retrieves the ontology parents of an entity including the relationship type, using the ChEBI identifier.

Created: 2015-11-16 | Last updated: 2016-04-26

Credits: Kristina Hettne

Attributions: Get ontology parents

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

getDatabaseLinks (1)

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Created: 2015-11-16 | Last updated: 2015-12-02

searchPublications (1)

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Created: 2015-11-16 | Last updated: 2015-12-02

searchPublications (1)

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Created: 2015-11-16 | Last updated: 2015-12-02

getDatabaseLinks (1)

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Created: 2015-11-16 | Last updated: 2015-12-02

single_double_flattten (1)

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Created: 2015-11-17 | Last updated: 2015-12-02

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

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

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

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

Connecting to Europe PMC (1)

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This very simple workflow connects to Europe PMC using the searchPublications Web Service.

Created: 2015-12-04

Credits: Magnus Palmblad

Search Europe PMC and get ChEBI annotations (3)

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This workflow first conducts a search and downloads the PMIDs for all publications in PubMed and PMC that match a particular query using the Europe PMC Articles API. In a second phase, the workflow fetches the ChEBI annotations for all these publications using the Europe PMC Annotations API.

Created: 2018-02-09 | Last updated: 2018-02-12

Credits: Magnus Palmblad

Get (3)

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Created: 2018-05-27 | Last updated: 2018-05-27

Demo (1)

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Created: 2019-06-25 | Last updated: 2019-06-26