Workflow Entry: GeneIlluminator_Disambiguate

Created at: 27/02/08 @ 00:43:33 Last updated: 03/03/08 @ 22:11:52

Version 2 (latest) (of 2)

Version created on: 27/02/08 @ 00:43:33 by: Pieter Neerincx | Revision comments Expand

Last edited on: 03/03/08 @ 22:11:50 by: Pieter Neerincx

Title: GeneIlluminator_Disambiguate

Type: Taverna 1

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Description

Example workflow demonstrating how to use GeneIlluminator_Disambiguate, 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. (This is the same output as the one from the GeneIlluminator_GetClusters service.) In addition this service takes an Organism object as input and disambiguates the gene symbol in the context of that organism by assigning the gene symbol for the given organism to one of the GI_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/

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Workflow Components

Inputs (2)

Name	Description
GeneSymbol	Your potentially ambiguous gene symbol of interest or one of it's aliases.
Organism	Species in scientific latin notation. For example: Home sapiens.

Processors (4)

Name	Type	Description
GeneIlluminator_Disambiguate	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. (This is the same output as the one from the GeneIlluminator_GetClusters service.) In addition this service takes an Organism object as input and disambiguates the gene symbol in the context of that organism: GeneIlluminator_Disambiguate assigns the gene symbol for the given organism to one of the GI_Clusters.
Parse_Moby_Data_GI_ClusterAssignment	biomobyparser	Processor to parse the datatype GI_ClusterAssignment
Organism	biomobyobject	An organism object.
Object	biomobyobject	an object

Outputs (6)

Name	Description
GI_ClusterAssignment	BioMoby object that assigns a gene symbol for a certain species of interest to a GeneIlluminator Cluster with a certain probability. Hence, given the species of interest, this GeneIlluminator ClusterAssignment together with the associated GeneIlluminator Cluster describe: 1. The most likely function for your gene. 2. The aliases used for this gene. These aliases might contain ambiguous symbols. 3. Comparing the aliases with the gene symbols of the other clusters will allow you to extract unambiguous gene symbols if there are any.
GI_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.
ca_gene_symbol_id
ca_organism_id
ca_probability
ca_cluster_id

Links (11)

Sink	Source
Object:id	GeneSymbol
Parse_Moby_Data_GI_ClusterAssignment:mobyData('GI_ClusterAssignment')	GeneIlluminator_Disambiguate:GI_ClusterAssignment(gi_clusterassignment)
GeneIlluminator_Disambiguate:Object(gene_symbol)	Object:mobyData
Organism:id	Organism
GeneIlluminator_Disambiguate:Organism(organism)	Organism:mobyData
GI_Clusters	GeneIlluminator_Disambiguate:GI_Cluster(Collection - 'gi_clusters')
GI_ClusterAssignment	GeneIlluminator_Disambiguate:GI_ClusterAssignment(gi_clusterassignment)
ca_gene_symbol_id	Parse_Moby_Data_GI_ClusterAssignment:gi_clusterassignment_'gene_symbol'_id
ca_cluster_id	Parse_Moby_Data_GI_ClusterAssignment:gi_clusterassignment_'gi_cluster'_id
ca_organism_id	Parse_Moby_Data_GI_ClusterAssignment:gi_clusterassignment_'organism'_id
ca_probability	Parse_Moby_Data_GI_ClusterAssignment:gi_clusterassignment_'probability'