Get ENSEMBL cross-references for UniProt IDs

Created: 2015-11-16 13:40:48

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This small workflow uses the PICR (http://www.ebi.ac.uk/Tools/picr/) WDSL Web Service to look up ENSEMBL (ENSP) cross-references for UniProt IDs. The input is a list of UniProt IDs and the output a corresponding list of ENSEMBL IDs. This instance of the workflow specifically uses the ENSEMBL_HUMAN database and taxonID 9606 (Homo sapiens).

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Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
UniProtID_list	A list of UniProt identifiers

Processors (8)

Name	Type	Description
getUPIForAccession	wsdl	Wsdl http://www.ebi.ac.uk/Tools/picr/service?wsdl Wsdl Operation getUPIForAccession
getUPIForAccession_input	xmlsplitter
getUPIForAccession_output	xmlsplitter
taxonID	stringconstant	Value 9606
onlyActive	stringconstant	Value TRUE
searchDB	stringconstant	Value ENSEMBL_HUMAN
extract_accession	xpath	Xpath Expression /ns2:getUPIForAccessionReturn/default:identicalCrossReferences/default:accession
Flatten_List	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);

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Outputs (1)

Name	Description
ENSP_ID_list

Datalinks (9)

Source	Sink
getUPIForAccession_input:output	getUPIForAccession:parameters
UniProtID_list	getUPIForAccession_input:accession
taxonID:value	getUPIForAccession_input:taxonId
searchDB:value	getUPIForAccession_input:searchDatabases
onlyActive:value	getUPIForAccession_input:onlyActive
getUPIForAccession:parameters	getUPIForAccession_output:input
getUPIForAccession_output:getUPIForAccessionReturn	extract_accession:xml_text
extract_accession:firstNode	Flatten_List:inputlist
Flatten_List:outputlist	ENSP_ID_list

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Information Workflow Type

Taverna 2

Information Uploader

Magnus Palmblad

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Magnus Palmblad

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1641 viewings

969 downloads

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Magnus Palmblad	Monday 16 November 2015 13:50:41 (UTC)
	As a comment - the PICR Web service currently (2015-11-16) does not work fully with the XML output splitters in Taverna.

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Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status.

Created: 2011-05-18 | Last updated: 2011-05-29

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Get ENSEMBL cross-references for UniProt IDs

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Comments (1)

Other workflows that use similar services (9)