FunctionalClusterDavid

Created: 2014-09-05 07:43:48

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This workflow takes a list of Entrez Gene IDs as input and submits them to the DAVID REST API for functional clustering using OG annotaiton, biological pathways and disease associations. Used for analysing a set of genes (i.e. those differentially expressed for a particular disease condition).

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Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
ids

Processors (5)

Name	Type	Description
REST_Service	rest
Text_constant	stringconstant	Value GOTERM_BP_FAT,GOTERM_CC_FAT,GOTERM_MF_FAT,INTERPRO,PIR_SUPERFAMILY,SMART,BBID, BIOCARTA,KEGG_PATHWAY,COG_ONTOLOGY,SP_PIR_KEYWORDS,UP_SEQ_FEATURE,GENETIC_ASSOCIATION_DB_DISEASE, OMIM_DISEASE
Open_web_browser_at_a_URL	localworker	Script import java.awt.Desktop; import java.net.URI; if ((url == void) \|\| (url == null)) { throw new RuntimeException("Url must be specified"); } URI uri = null; uri = new URI(url); Desktop.getDesktop().browse(uri);
Merge_String_List_to_a_String	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
seperator_value	stringconstant	Value ,

Beanshells (0)

Outputs (3)

Name	Description
responseBody
status
actualURL

Datalinks (8)

Source	Sink
Text_constant:value	REST_Service:annot
Merge_String_List_to_a_String:concatenated	REST_Service:ids
REST_Service:actualURL	Open_web_browser_at_a_URL:url
seperator_value:value	Merge_String_List_to_a_String:seperator
ids	Merge_String_List_to_a_String:stringlist
REST_Service:responseBody	responseBody
REST_Service:status	status
REST_Service:actualURL	actualURL

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Information Workflow Type

Taverna 2

Information Uploader

Katy Wolstencroft

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Katy Wolstencroft

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Information Attributed By (1)

(Workflows/Files)

SNP identification and evaluation for Diabetes Type II genes & GO annotation and functional clustering

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Information Statistics

1564 viewings

1141 downloads

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Citations (0)

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Version History

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FunctionalClusterDavid

Created by Katy Wolstencroft on Friday 05 September 2014 07:43:47 (UTC)

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Magnus Palmblad

Hi Kate,

Is this service still working? I get a "peer not authenticated" error when trying to run this, and have problem connecting using the simple URL API in a browser as well (for some examples, it works, but for most things not).

The DAVID team claims to have a WSDL service that is more advanced, but I cannot import this in Taverna or find any suggestion it is still up...

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FunctionalClusterDavid

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