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ListAllWikiPathways (2)

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This workflow retrieves all pathways currently in the WikiPathways database, using the WikiPathways REST API.

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

Credits: Kristina Hettne Eleni

PW2CHEBI (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 the given pathway.

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

Credits: Kristina Hettne Eleni

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Pathway analysis with WikiPathways

Created: 2015-09-01 14:24:28 | Last updated: 2015-11-16 09:58:55

8 items in this pack

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Phenotype to pubmed (1)

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This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

Created: 2015-09-01

Credits: Heiko Schoof Paul Fisher

Attributions: Phenotype to pubmed

Chemical2URIs (1)

This workflow will map a chemical name or identifier to uniform resource identifiers (URIs). First the ChemSpider web service is used to map the chemical name to a ChemSpider identifier, then the ChemSpider identifier is mapped to URIs via the Open PHACTS platform.

Created: 2015-08-20

Credits: Aylin Metzner

connect to WoS Web services lite concept (1)

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This workflow is a concept for how Taverna could connect to the Thomson Reuters Web of Science (WoS) Web services lite. However, at this moment (2015-01-20), the authentication generate a session ID, but the other services (here search and closeSession) do not have an input port for this session ID. According to the documentation, this is required. The error message from the Web service also show this is missing. This workflow is "work in progress", but may nevertheless be of interest to an...

Created: 2015-08-19

Credits: Magnus Palmblad Yassene Arzu Tugce Guler

Online PubMed author search and geographic... (2)

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This workflow retrieves bibliographic data for a single author using the PMC Europe RESTful Web service and visualizes the geographic distribution of this author's and their co-authors' geographic distribution using the rworldmap package. This is version 2.0 of this workflow, incorporating changes to the Web service allowing up to 1,000 records to be retrieved at once, using the pageSize parameter.

Created: 2015-08-19 | Last updated: 2015-09-07

Credits: Magnus Palmblad Arzu Tugce Guler

Chemical2URIs (1)

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This workflow will map a chemical name or identifier to uniform resource identifiers (URIs). First the ChemSpider web service is used to map the chemical name to a ChemSpider identifier, then the ChemSpider identifier is mapped to URIs via the Open PHACTS platform.

Created: 2015-08-18

Credits: Kristina Hettne Eelke van der Horst BioSemantics

Get properties of drugs for genes by Entre... (3)

Given a Entrez gene_id the workflow extracts features of its protein (e.g. function, cellular localization and name) and properties of specific drugs for this protein (including activity, PSA, RO5, Smiles and molweight). This workflow uses 3 different services of OpenPHACTS (Target Pharmacology, Compound Information, Target Information).

Created: 2015-07-24 | Last updated: 2015-07-28

Credits: Katerina Nosikova Marco Roos Eleni Eelke van der Horst Elizaveta Besedina

SNP identification and evaluation for Diab... (1)

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This workflow gathers SNP information for a gene set of Diabetes Type II phenotype using BioMart queries. Furthermore, GO Terms and functional annotation clustering are defined for this gene set using FunctionalClusterDavid workflow. 

Created: 2015-06-23

Credits: Nikolaos Bismpikos Katy Wolstencroft

Attributions: FunctionalClusterDavid