Find PRIDE experiments by GO

Created: 2011-05-29 19:07:59 Last updated: 2011-05-29 19:08:01

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Find PRIDE experiments in Human with related information like Cell Type and Tissue location filtering results by Gene Ontology terms. This is an example of how to use the PRIDE Biomart service in Taverna. Many other options are possible by modifying the filters and attributes of this service.

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Option 1:

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http://www.myexperiment.org/workflows/2154/download?version=1
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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
GO_name	Use a Gene Ontology (GO) term name. To find GO terms 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
pride	biomart
species_filter	stringconstant	Value Homo sapiens (Human)

Beanshells (0)

Outputs (3)

Name	Description
BrendaTissueID	Find more about the ontology terms presented in this output browsing OLS ... http://www.ebi.ac.uk/ontology-lookup/
cellType	Find more about the ontology terms presented in this output browsing OLS ... http://www.ebi.ac.uk/ontology-lookup/
experimentID	You can browse PRIDE experiments in the PRIDE web interface or through PRIDE inspector (recommended). Attach the PRIDE accession number at the end of this URL: http://www.ebi.ac.uk/pride/q.do?accession=

Datalinks (5)

Source	Sink
GO_name	pride:pride.go_filter_filter
species_filter:value	pride:pride.species_filter_filter
pride:pride.bto_ac	BrendaTissueID
pride:pride.celltype	cellType
pride:pride.experiment_ac	experimentID