This workflow uses one or more services that
are deprecated as of 31st December 2012
(over 12 years ago), and may no longer function.
Show details...
Affected service WSDL:
- http://soap.genome.jp/KEGG.wsdl
Details:
KEGG will be moving from a WSDL/SOAP interface to REST. Details of the new REST services can be found here.
Working examples that use the new REST service can be viewed here, here and here.
Gene annotation pipeline for the Graves disease scenario
Created: 2007-10-03 18:36:09
Last updated: 2007-11-22 16:03:15
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 |
|
| 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 |
|
Beanshells (4)
| |
| Name |
Description |
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 |
|
Coordinations (2)
| |
| Controller |
Target |
| addTermToViz |
getDotFromViz |
| getDotFromViz |
destroyVizSession |
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Only the first 2 workflows that use similar services are shown. View all workflows that use these services.
Mouse Microarray Analysis
(3)
This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2.
Example ids from the Mouse430_2 affymetrix array are as follows (newline separated):
1447227_at
1440624_at
1436240_at
1454904_at
1435665_at
1418148_at
1429831_at
Created: 2007-10-03
| Last updated: 2009-12-03
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Reviews
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Matthieu
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There is a missing file in this example: uniprotandPDBxml.xml. Can you upload it?.
Thanks,
Lorena