Workflow Entry: Gene annotation pipeline for the Graves disease scenario

Created at: 03/10/07 @ 18:36:09 Last updated: 22/11/07 @ 16:03:15

Version 2 (latest) (of 2)

Version created on: 03/10/07 @ 18:36:09 by: Katy Wolstencroft | Revision comments Expand

Last edited on: 22/11/07 @ 16:03:15 by: Katy Wolstencroft

Title: Gene annotation pipeline for the Graves disease scenario

Type: Taverna 1

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Description

This is a revised workflow for the Graves disease scenario gene annotation pipeline used in the myGrid project. The workflow had to be re-written due to the loss of the services invoked in the original workflow.

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Workflow Components

Inputs (0)

Processors (26)

Name	Type	Description
ProbeSetId	stringconstant
removePrefix	beanshell
cleanGoIds	beanshell
cleanInterproIds	beanshell
splitString	local
createVizSession	arbitrarywsdl
destroyVizSession	arbitrarywsdl
getInterProIds	arbitrarywsdl
getEmblId	arbitrarywsdl
getSwissProtId	arbitrarywsdl
getMolFuncGoIds	arbitrarywsdl
getDotFromViz	arbitrarywsdl
addTermToViz	arbitrarywsdl
getEC	arbitrarywsdl
cleanEcNumbers	beanshell
getPathwaysByECNumbers	arbitrarywsdl	See the Service entry for this web service.
getMedlineIds	soaplabwsdl	For cross-referencing between databanks
getPathwayDiagrams	local
mark_pathway_by_objects	arbitrarywsdl	See the Service entry for this web service.
DDBJ_Blastn	arbitrarywsdl	This call to a Blastn service at the DDBJ is to check that the target sequence of the probe set is specific to the gene whose mRNA expression that the probe sequences have been designed to measure. See the Service entry for this web service.
getTargetSequence	arbitrarywsdl
ebi_uniprot	soaplabwsdl	The UniProt Knowledgebase is a central database of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
ebi_medline2007	soaplabwsdl	MEDLINE is the NLM's premier bibliographic database covering the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences. MEDLINE contains bibliographic citations and author abstracts from more than 4,000 biomedical journals published in the United States and 70 other countries. The file contains over 12 million citations dating back to the mid-1960's. Coverage is worldwide, but most records are from English-language sources or have English abstracts.
ebi_embl	soaplabwsdl	The European Bioinformatics Institute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the Swiss-Prot Protein Sequence database, in collaboration with Amos Bairoch of the University of Geneva. Over fifty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists are available. The EBI network services include database searching and sequence similarity searching facilities.
calcMeltTemp	soaplabwsdl	Calculates DNA RNA/DNA melting temperature
UniprotAndPdb	workflow	UniprotAndPDB

Beanshells (4)

Name	Inputs	Outputs
removePrefix	str prefix	id
cleanGoIds	inputStr	goIds
cleanInterproIds	inputStr	interproIds
cleanEcNumbers	inputStr	ecNumbers

Outputs (12)

Name	Description
swissprot
embl
medlineIds
medline
interproIds
goDiagram
ecNumbers
pathways
meltTemp
targetSequence
blastReport
PDBStructure

Links (38)

Source	Sink
ProbeSetId:value	getEC:probeSetId
ProbeSetId:value	getEmblId:probeSetId
ProbeSetId:value	getInterProIds:probeSetId
ProbeSetId:value	getMolFuncGoIds:probeSetId
ProbeSetId:value	getSwissProtId:probeSetId
ProbeSetId:value	getTargetSequence:probeSetId
cleanEcNumbers:ecNumbers	getPathwaysByECNumbers:enzyme_id_list
cleanEcNumbers:ecNumbers	mark_pathway_by_objects:object_id_list
cleanGoIds:goIds	addTermToViz:geneOntologyID
createVizSession:createSessionReturn	addTermToViz:sessionID
createVizSession:createSessionReturn	destroyVizSession:sessionID
createVizSession:createSessionReturn	getDotFromViz:sessionID
ebi_embl:result	calcMeltTemp:sequence_direct_data
getEC:getECReturn	cleanEcNumbers:inputStr
getEmblId:getRepresentativePublicIdReturn	ebi_embl:searchterm
getEmblId:getRepresentativePublicIdReturn	getMedlineIds:searchterm
getInterProIds:getInterProReturn	cleanInterproIds:inputStr
getMedlineIds:result	removePrefix:str
DDBJ_Blastn:Result	blastReport
UniprotAndPdb:pdbFlatFile	PDBStructure
getMolFuncGoIds:getGeneOntologyMolecularFunctionReturn	cleanGoIds:inputStr
mark_pathway_by_objects:return	getPathwayDiagrams:url
removePrefix:id	ebi_medline2007:searchterm
splitString:split	UniprotAndPdb:ids
splitString:split	ebi_uniprot:searchterm
calcMeltTemp:outfile	meltTemp
cleanEcNumbers:ecNumbers	ecNumbers
cleanInterproIds:interproIds	interproIds
ebi_embl:result	embl
ebi_medline2007:result	medline
ebi_uniprot:result	swissprot
getDotFromViz:getDotReturn	goDiagram
getMedlineIds:result	medlineIds
getPathwayDiagrams:image	pathways
getPathwaysByECNumbers:return	mark_pathway_by_objects:pathway_id
getSwissProtId:getSwissProtReturn	splitString:string
getTargetSequence:getTargetSequenceReturn	DDBJ_Blastn:query
getTargetSequence:getTargetSequenceReturn	targetSequence