myExperiment.org - Workflows - Gene annotation pipeline for the Graves disease scenario (Katy Wolstencroft) [Taverna 1 Workflow]

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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Gene_annotation_pipeline_for_the_graves_disease_scenario_19721

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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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http://www.myexperiment.org/workflows/28/download?version=2
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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
getMedlineIds	soaplabwsdl	For cross-referencing between databanks
getPathwayDiagrams	local
mark_pathway_by_objects	arbitrarywsdl
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.
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

Outputs (12)

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

Links (38)

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