Workflow Entry: Find Reactome pathways and reactions by GO

Created at: 29/05/11 @ 19:09:23 Last updated: 29/05/11 @ 19:09:25

Version 1 (of 1)

Version created on: 29/05/11 @ 19:09:23 by: Rafael C. Jimenez | Revision comments Expand

Title: Find Reactome pathways and reactions by GO

Type: Taverna 2

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Description

Find Reactome pathways and reactions (names and accessions) in Human querying by a Gene Ontology term. This is an example of how to use the Reactome Biomart service in Taverna. Many other possibilities are possible by modifying the filters and attributes options of the service.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Inputs (1)

Name	Description
GO_accession	Use a GO (Gene Ontology) accession. Do not forget to leave out the GO prefix, so you do not input "GO:0006915" but "0006915" instead. To find GO accessions and browse the GO you can use Amigo ... http://amigo.geneontology.org/cgi-bin/amigo/browse.cgi ... or the OLS ... http://www.ebi.ac.uk/ontology-lookup/

Processors (2)

Name	Type	Description
pathway	biomart
species_selection	stringconstant

Beanshells (0)

Outputs (4)

Name	Description
pathway_name
stable_identifier
reaction_name
reaction_identifier

Datalinks (6)

Source	Sink
GO_accession	pathway:pathway.gobiologicalprocess_accession_filter
species_selection:value	pathway:pathway.species_selection_filter
pathway:pathway._displayname	pathway_name
pathway:pathway.stableidentifier_identifier	stable_identifier
pathway:pathway.reaction__dm__displayname	reaction_name
pathway:pathway.reaction__dm_stableidentifier_identifier	reaction_identifier