Find pathways in which two genes co-occur (in WikiPathways)

Created: 2013-06-28 13:45:23 Last updated: 2013-06-28 14:14:23

Download Workflow

This workflow finds all pathways in which two gene symbols co-occur.

This workflow was created as an exercise for the "Managing and Integrating Information in the Life Sciences course 2013" at the LUMC, which is organized by the Netherlands Bioinformatics Center (NBIC).

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/3636/download?version=1
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (2)

Name	Description
Gene_1	The first gene name.
Gene_2	The second gene name.

Processors (3)

Name	Type	Description
WikiPathways_REST_Sparql_query	rest	SPARQL query to WikiPathways.
Extract_pathway_titles	xpath	Xpath Expression /default:sparql/default:results/default:result/default:binding/default:literal
Extract_pathway_URIs	xpath	Xpath Expression /default:sparql/default:results/default:result/default:binding/default:uri

Beanshells (0)

Outputs (2)

Name	Description
pathway_titles	List of pathway titles.
pathway_uris	List of pathway URIs.

Datalinks (6)

Source	Sink
Gene_1	WikiPathways_REST_Sparql_query:gene1
Gene_2	WikiPathways_REST_Sparql_query:gene2
WikiPathways_REST_Sparql_query:responseBody	Extract_pathway_titles:xml_text
WikiPathways_REST_Sparql_query:responseBody	Extract_pathway_URIs:xml_text
Extract_pathway_titles:nodelist	pathway_titles
Extract_pathway_URIs:nodelist	pathway_uris