Get a list of proteins annotated with an Ontology term and use these proteins to query BioModels

Created: 2012-08-22 08:05:33 Last updated: 2013-07-10 13:58:29

Download Workflow

A service to look for models in BioModels using an Ontology Id as input. First the workflow will look in QuickGO for UniProt accessions annotated with the provided Ontology Id. Then it will look for models using the list of proteins. If one of the input protein is found in one model the workflow will provide the BioModels Id, the SBML and a link to the BioModels database. Please use taverna 2.4 or above.

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/3113/download?version=3
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (2)

Name	Description
TaxonomyId	Taxonomy ID used to describe Species. Search for a taxonomy ID in "www.uniprot.org/browse/taxonomy". Set a value with empty content to search for all the species.
GeneOntologyId	Gene Ontology Id

Processors (4)

Name	Type	Description
Get_a_list_of_proteins_from_a_Gene_Ontology__GO__term	workflow
header_value	stringconstant	Value true
Get_models_from_BioM	workflow
Parse_QuickGO__proteinList__file_format_2	workflow

Beanshells (2)

Name	Description	Inputs	Outputs
processQuickGoProteinListFormat		quickGoProteinListFormat header	idList synonymList typeList taxonList nameList symbolList dbList test
GetBiomodelsUrl		BiomodelsId	BiomodelsUrl

Outputs (4)

Name	Description
proteinListFromGO
BioModelsIds
SBML
BioModelsUrl

Datalinks (9)

Source	Sink
TaxonomyId	Get_a_list_of_proteins_from_a_Gene_Ontology__GO__term:TaxonomyId
GeneOntologyId	Get_a_list_of_proteins_from_a_Gene_Ontology__GO__term:GeneOntologyId
Parse_QuickGO__proteinList__file_format_2:idList	Get_models_from_BioM:UniProtId
header_value:value	Parse_QuickGO__proteinList__file_format_2:header
Get_a_list_of_proteins_from_a_Gene_Ontology__GO__term:listOfProteins	Parse_QuickGO__proteinList__file_format_2:quickGoProteinListFormat
Parse_QuickGO__proteinList__file_format_2:idList	proteinListFromGO
Get_models_from_BioM:BioModelsIds	BioModelsIds
Get_models_from_BioM:SBML	SBML
Get_models_from_BioM:BioModelsUrl	BioModelsUrl

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Rafael C. Jimenez

Information License

All versions of this Workflow are licensed under:

Information Version 3 (latest) (of 3)

Information Credits (1)

(People/Groups)

Rafael C. Jimenez

Information Attributions (0)

(Workflows/Files)

None

Information Tags (2)

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

2323 viewings

1161 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Get a list of proteins annotated with an Ontology term and use these proteins to query BioModels

Created by Rafael C. Jimenez on Wednesday 22 August 2012 08:05:32 (UTC)

Last edited by Rafael C. Jimenez on Wednesday 22 August 2012 08:05:57 (UTC)
Get a list of proteins annotated with an Ontology term and use these proteins to query BioModels

Created by Rafael C. Jimenez on Friday 24 August 2012 02:45:18 (UTC)
Get a list of proteins annotated with an Ontology term and use these proteins to query BioModels

Created by Rafael C. Jimenez on Wednesday 10 July 2013 13:58:29 (UTC)

Revision comment:

Make it work in windows using the new workflow to parse quickgo

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 2

Uploader

Rafael C. Jimenez

Find Biological Models by GO. (1)

Download

Find Biological Models (Ids and Names) from Biomodels querying by Gene Ontology terms.

Created: 2011-05-29 | Last updated: 2011-05-29

Credits: Rafael C. Jimenez

Taverna 2

Uploader

Rafael C. Jimenez

Get models from BioModels including the in... (3)

Download

A service to look for models in BioModels using a UniProt accession as input. If the input protein is found in one model the workflow will provide the BioModels Id, the SBML and a link to the BioModels database. Please use taverna 2.4 or above.

Created: 2012-08-22 | Last updated: 2012-08-24

Credits: Rafael C. Jimenez

Get a list of proteins annotated with an Ontology term and use these proteins to query BioModels

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Value

Reviews (0)

Comments (0)

Other workflows that use similar services (3)