GeneIlluminator_GetClusters

Created: 2008-02-27 00:46:22 Last updated: 2008-03-03 22:11:17

Download Workflow

Example workflow demonstrating how to use GeneIlluminator_GetClusters, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service provides GI_Clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. Provides also gene symbol aliases associated to the input gene symbol.

(Use GeneIlluminator_GetGraph for a graphical representation of the clusters or GeneIlluminator_Disambiguate to get the most likely cluster for a certain species of interest in addition to the clusters.)

Visit http://www.bioinformatics.nl/gi/ for more info about GeneIlluminator.

GeneIlluminator services use a secure connection over HTTPS. To make this work you *must* import our SSL certificates in your local Java keystores. More information can be found on https://www.bioinformatics.nl/phenolink/home/

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/150/download?version=2
[ More Info Expand ]

Workflow Components

Inputs (1)

Name	Description
GeneSymbol	Your potentially ambiguous gene symbol of interest or one of it's aliases.

Processors (2)

Name	Type	Description
GeneIlluminator_GetClusters	biomobywsdl	Synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service provides GI_Clusters describing which different genes sharing the same symbol exist in different parts of the tree of life. Provides also gene symbol aliases associated to the input gene symbol. Have a look at the GeneIlluminator_GetGraph service for a graphical representation of this data.
Object	biomobyobject	an object

Beanshells (0)

Outputs (1)

Name	Description
Clusters	BioMoby collection (list) of objects describing clusters of gene symbols that were mentioned in databases / literature in the same "context". Each cluster has: 1. One or more genes with a gene symbol. All genes and their symbols listed for the same cluster are aliases. These gene symbols might be ambiguous. 2. One or more fuctional descriptions. These are the terms that describe the context where the gene symbol was mentioned and that were used for the clustering. 3. One or more clades, identified by IDs from the NCBI Taxonomy. These clades are the last common ancestors (LCAs) of those parts of the tree of life where the gene symbols for this cluster are mentioned in the context of the functional descriptions for this cluster.

Links (3)

Source	Sink
GeneSymbol	Object:id
GeneIlluminator_GetClusters:GI_Cluster(Collection - 'gi_clusters')	Clusters
Object:mobyData	GeneIlluminator_GetClusters:Object(gene_symbol)

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Pieter Neerincx

Information License

All versions of this Workflow are licensed under:

Information Version 2 (latest) (of 2)

Information Credits (2)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (4)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

2772 viewings

2362 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

GeneIlluminator_GetClusters

Created by Pieter Neerincx on Wednesday 27 February 2008 00:46:22 (UTC)
GeneIlluminator_GetClusters

Created by Pieter Neerincx on Wednesday 27 February 2008 00:46:22 (UTC)

Last edited by Pieter Neerincx on Monday 03 March 2008 22:11:17 (UTC)

Revision comment:

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 (0)

There are no workflows in myExperiment that use similar services to this Workflow.