About | Mailing List | Publications

Give us Feedback |

Invite

Home
»
Workflows
»
gene_ontology_diagram.xml

Workflow Entry: gene_ontology_diagram.xml

Created at: 12/07/08 @ 10:39:09 Last updated: 12/07/08 @ 10:39:32

Version 1 (of 1)

Version created on: 12/07/08 @ 10:39:09 by: Antoon Goderis | Revision comments Expand

Last edited on: 12/07/08 @ 10:39:32 by: Antoon Goderis

Title: gene_ontology_diagram.xml

Type: Taverna 1

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

Description

This workflow builds up a subgraph of the Gene Ontology (http://www.geneontology.org) to show the context for a supplied term or terms. It shows this context by colouring all ancestors of the term, all children and all siblings. By default, ancestors of the supplied term or terms are coloured orange, siblings purple and direct children teal. Other terms appear in the default wheat colour.

Download

Download Workflow File/Package (SCUFL)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Launch in Taverna

Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/317/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (1)

Name	Description
termID	The term for which to display context within the Gene Ontology. An example is the term for vision, GO:0007601

Processors (15)

Name	Type	Description
childColour	stringconstant
getChildren	arbitrarywsdl
getresults	arbitrarywsdl
getAncestry	arbitrarywsdl
markAncestors	arbitrarywsdl
getParents	arbitrarywsdl
add	arbitrarywsdl
colourChildren	arbitrarywsdl
colourInputTerm	arbitrarywsdl
addImmediateChildren	arbitrarywsdl
finish	arbitrarywsdl
create	arbitrarywsdl
getImmediateChildren	arbitrarywsdl
inputTermColour	stringconstant
ancestorColour	stringconstant

Beanshells (0)

Outputs (1)

Name	Description
graphical	A text file containing the dot coded representation of the GO subgraph generated by this workflow. To see the graph you'll have to run it through the 'dot' tool, part of AT&T's graphviz package.

Links (20)

Source	Sink
termID	getParents:geneOntologyID
ancestorColour:value	markAncestors:colour
create:createSessionReturn	add:sessionID
create:createSessionReturn	finish:sessionID
create:createSessionReturn	getresults:sessionID
getChildren:getChildrenReturn	add:geneOntologyID
getParents:getParentsReturn	getChildren:geneOntologyID
termID	getAncestry:geneOntologyID
create:createSessionReturn	markAncestors:sessionID
getAncestry:getAncestorsReturn	markAncestors:geneOntologyID
termID	getImmediateChildren:geneOntologyID
childColour:value	colourChildren:colour
create:createSessionReturn	addImmediateChildren:sessionID
create:createSessionReturn	colourChildren:sessionID
getImmediateChildren:getChildrenReturn	addImmediateChildren:geneOntologyID
getImmediateChildren:getChildrenReturn	colourChildren:geneOntologyID
inputTermColour:value	colourInputTerm:colour
termID	colourInputTerm:geneOntologyID
create:createSessionReturn	colourInputTerm:sessionID
getresults:getDotReturn	graphical

Coordinations (6)

Controller	Target
getresults	finish
add	markAncestors
addImmediateChildren	colourChildren
colourChildren	getresults
markAncestors	colourInputTerm
colourInputTerm	getresults

Information Workflow Type

Taverna 1

Information Original Uploader

Antoon Goderis

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Paul Fisher

Information Attributions (0)

(Workflows/Files)

None

Information Tags (1)

Original Uploader tags

benchmarks

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (1)

Paul Fisher workflows for benchmarks PR and CA2

Log in to add to one of your Packs

Information Ratings (0)

Current:

0.0 / 5

(0 ratings)

Log in to rate and see breakdown of ratings

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

289 viewings

703 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - gene_ontology_diagram.xml

Created on: Saturday 12 July 2008 @ 10:39:09 (GMT)

Created by: Antoon Goderis

Last edited on: Saturday 12 July 2008 @ 10:39:32 (GMT)

Last edited by: Antoon Goderis

Revision comments:

None

This Workflow only has one version.

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (3)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Original Uploader

Katy Wolstencroft

Gene annotation pipeline for the Graves disease scenario (v2)

Created: 03/10/07 @ 18:36:09 | Last updated: 22/11/07 @ 16:03:15

Credits: Katy Wolstencroft Peter Li

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This is a revised workflow for the Graves disease scenario gene annotation pipeline used in the myGrid project. The workflow had to be re-written due to the loss of the services invoked in the original workflow.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 594 times | Downloaded: 205 times

Tags (6):

View

Download (v2)

Taverna 1

Original Uploader

Antoon Goderis

metabolic.xml (v1)

Created: 12/07/08 @ 10:42:42 | Last updated: 12/07/08 @ 10:42:56

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

An example of how a more complex workflow can federate multiple resources to perform data mining. In this case a single input data item in the form of a probe set identifier is cross referenced to data sets in multiple locations to answer a kind of 'show me everything about this data' question.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 39 times | Downloaded: 34 times

Tags (1):