Get_homologous_from_NCBI_homoloGene_using_one_UniProt_accessionproteinAccession00
A UniProt protein Accession
2011-10-14 14:00:23.210 BST
P99999
2011-10-14 14:00:27.114 BST
taxonomyAcc00
9606
2011-10-14 14:04:10.351 BST
Specie where to find homologous. Use a taxonomy accession. Input "all" if you would like to find homologous in all the species.
2011-10-14 14:04:03.823 BST
homologousEBI_PICR__find_cross_references_for_protein_accessionsonlyActive0taxonId0searchDatabases1Protein_accessions0mapping_table00net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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false
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REFSEQ
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string
0
'text/plain'
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true
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newline
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetProteinRefSeqAccstring0mappedProtein00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
string
0
'text/plain'
java.lang.String
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0
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org.embl.ebi.escience.scuflworkers.java.SplitByRegex
UserNameHere
2011-10-14 14:40:26.434 BST
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeEBI_PICR__find_cross_references_for_protein_accessions_2searchDatabases1onlyActive0Protein_accessions0taxonId0mapping_table00net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
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SWISSPROT,TREMBL
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false
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expression_2_2string0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeselectSecondColumnstring0mappedProtein00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
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2011-10-14 13:04:58.700 BST
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeEBI_PICR__find_cross_references_for_protein_accessionsonlyActiveEBI_PICR__find_cross_references_for_protein_accessionstaxonIdEBI_PICR__find_cross_references_for_protein_accessionssearchDatabasesEBI_PICR__find_cross_references_for_protein_accessionsProtein_accessionsSplit_string_into_string_list_by_regular_expression_2stringSplit_string_into_string_list_by_regular_expression_2regexgetProteinRefSeqAccstringfilterOutBlankResultslist1Get_homologous_from_NCBI_homoloGenespecieGet_homologous_from_NCBI_homoloGeneproteinAccsBeanshelllist1Beanshell_2list1EBI_PICR__find_cross_references_for_protein_accessions_2searchDatabasesEBI_PICR__find_cross_references_for_protein_accessions_2onlyActiveEBI_PICR__find_cross_references_for_protein_accessions_2Protein_accessionsEBI_PICR__find_cross_references_for_protein_accessions_2taxonIdSplit_string_into_string_list_by_regular_expressionregexSplit_string_into_string_list_by_regular_expressionstringSplit_string_into_string_list_by_regular_expression_2_2stringSplit_string_into_string_list_by_regular_expression_2_2regexselectSecondColumnstringBeanshell_2_2list1Merge_String_List_to_a_String_3stringlistMerge_String_List_to_a_String_3seperatorhomologous
4fd8b9fc-d7a7-4ebd-91fe-f1a738c7efcc
2011-10-14 14:39:11.182 BST
4867750e-1131-48c4-939d-cc5c006614f3
2011-10-14 16:49:04.642 BST
80b5f958-7a32-49e3-9980-5ea85e7ff976
2011-10-14 15:26:26.809 BST
Get homologous from NCBI homoloGene for one UniProt protein accession. Use PICR to convert UniProt to RefSeq, get homologous from homoloGene and convert RefSeq results to UniProt. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README
2011-10-14 17:24:25.31 BST
493eab4b-3a46-40c5-9e5e-d9d4203c2d67
2011-10-14 14:33:30.533 BST
cf87c41f-dd01-417c-a08a-9cf46dc3c74a
2011-10-14 16:10:37.86 BST
78c7b00f-076e-4c88-9578-27eeb0a4f561
2011-10-14 16:20:47.293 BST
e57f848e-817d-4157-8c64-3aca9d9f73ec
2011-10-14 14:48:15.73 BST
Rafael C. Jimenez
2011-10-14 14:27:42.905 BST
43181f7c-e99f-465e-ad98-2008fdba556c
2011-10-14 17:24:35.204 BST
eec627f7-d6ea-4763-85b8-14dce216bfc1
2011-10-14 14:28:39.827 BST
b5531852-afa4-48f8-9746-01712c3c2e9f
2011-10-14 16:15:26.396 BST
cca47e7f-6ad0-4deb-af3c-c36dcd27d4d5
2011-10-14 15:07:53.482 BST
a901f614-2745-412b-8c34-2cffea964d1d
2011-10-14 14:40:44.743 BST
Get homologous from NCBI homoloGene using one UniProt accession
2011-10-14 17:22:02.820 BST
a6311218-6f7d-4263-b9f2-855d427e2f98
2011-10-14 15:27:50.387 BST
cd47862c-9fee-42a0-bdc7-52d4d4434521
2011-10-14 14:06:04.514 BST
1a9eda0d-a327-4d8d-95c2-d28a64651e07
2011-10-14 16:39:43.205 BST
4d1abfa0-0973-490e-b353-69841637d508
2011-10-14 15:33:11.815 BST
4ff9f5d6-d1c9-4dfd-8661-488b01ab7e87
2011-10-14 15:01:04.85 BST
855d9a0a-3174-4217-9a2a-72fc5138285c
2011-10-14 17:20:31.989 BST
72f8cfd9-485d-407d-bbaa-2c6ba3694a41
2011-10-14 17:09:56.963 BST
54ba8db2-3d58-492c-9317-00a2112382e1
2011-10-14 16:04:12.922 BST
466bf68d-73e3-4ea2-a50a-c6d55546b81e
2011-10-14 14:35:17.922 BST
493eab4b-3a46-40c5-9e5e-d9d4203c2d67
2011-10-14 14:37:46.761 BST
ff6a37f5-70e2-44ed-acda-b8ab331fb83d
2011-10-14 14:38:10.21 BST
1592daa0-7937-4373-8a90-cf287c0d8a77
2011-10-14 15:36:45.693 BST
ec0ee587-bb5c-4c4d-9a6c-6252fbf4da9e
2011-10-14 15:31:19.707 BST
19201ff3-4330-4af0-9851-ec1203531542
2011-10-14 15:13:18.638 BST
EBI_PICR__find_cross_references_for_protein_accessionsProtein_accessions00
Input a list (comma-separated values) of protein accessions
2011-05-29 13:03:08.70 BST
ENSP00000307786,ENSP00000369497
2011-05-29 13:01:48.270 BST
searchDatabases11
SWISSPROT
2011-05-18 08:48:33.320 BST
Which databases do you want the cross-references for? You can add more than one. You can get a list of databases available in PICR using the method "getMappedDatabaseNames" from the same PICR service or looking at this document http://www.ebi.ac.uk/Tools/picr/WSDLDocumentation.do
2011-05-18 08:48:28.762 BST
onlyActive00
Do you just want accession that are active (no-deprecated)? … write down "true" or "false". If you do not specify this parameter the workflow will not work.
2011-05-18 08:47:24.674 BST
true
2011-05-18 08:47:28.100 BST
taxonId00
Create a new value and leave it empty if you do not want to filter by specie. Chose a Taxa Id if you want to limit by specie … http://www.uniprot.org/taxonomy/?query=*
2011-05-18 08:47:05.919 BST
9606
2011-05-18 08:47:10.722 BST
mapping_tablegetUPIForAccessionparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://www.ebi.ac.uk/Tools/picr/service?wsdl
getUPIForAccession
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetUPIForAccession_inputsearchDatabases1onlyActive0taxonId0accession0output00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
accession
0
'text/plain'
false
ac_version
0
'text/plain'
false
searchDatabases
1
l('text/plain')
false
taxonId
0
'text/plain'
false
onlyActive
0
'text/plain'
false
output
0
'text/xml'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getUPIForAccession" name="parameters" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}getUPIForAccession"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="accession" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}>getUPIForAccession>accession" /><s:basetype optional="false" unbounded="false" typename="string" name="ac_version" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}>getUPIForAccession>ac_version" /><s:arraytype optional="false" unbounded="true" wrapped="false" typename="string" name="searchDatabases" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}>getUPIForAccession>searchDatabases"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:basetype optional="false" unbounded="false" typename="string" name="taxonId" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}>getUPIForAccession>taxonId" /><s:basetype optional="false" unbounded="false" typename="boolean" name="onlyActive" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}>getUPIForAccession>onlyActive" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetUPIForAccession_outputinput0getUPIForAccessionReturn11net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
input
0
'text/xml'
java.lang.String
false
getUPIForAccessionReturn
1
l('text/xml')
1
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getUPIForAccessionResponse" name="parameters" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}getUPIForAccessionResponse"><s:elements><s:arraytype optional="false" unbounded="true" wrapped="false" typename="UPEntry" name="getUPIForAccessionReturn" qname="{http://www.ebi.ac.uk/picr/AccessionMappingService}>getUPIForAccessionResponse>getUPIForAccessionReturn"><s:elementtype><s:complextype optional="false" unbounded="false" typename="UPEntry" name="" qname="{http://model.picr.ebi.ac.uk}UPEntry"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="CRC64" qname="{http://model.picr.ebi.ac.uk}UPEntry>CRC64" /><s:basetype optional="false" unbounded="false" typename="string" name="UPI" qname="{http://model.picr.ebi.ac.uk}UPEntry>UPI" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="CrossReference" name="identicalCrossReferences" qname="{http://model.picr.ebi.ac.uk}UPEntry>identicalCrossReferences"><s:elementtype><s:complextype optional="false" unbounded="false" typename="CrossReference" name="" qname="{http://model.picr.ebi.ac.uk}CrossReference"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="accession" qname="{http://model.picr.ebi.ac.uk}CrossReference>accession" /><s:basetype optional="false" unbounded="false" typename="string" name="accessionVersion" qname="{http://model.picr.ebi.ac.uk}CrossReference>accessionVersion" /><s:basetype optional="false" unbounded="false" typename="string" name="databaseDescription" qname="{http://model.picr.ebi.ac.uk}CrossReference>databaseDescription" /><s:basetype optional="false" unbounded="false" typename="string" name="databaseName" qname="{http://model.picr.ebi.ac.uk}CrossReference>databaseName" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="dateAdded" qname="{http://model.picr.ebi.ac.uk}CrossReference>dateAdded" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="dateDeleted" qname="{http://model.picr.ebi.ac.uk}CrossReference>dateDeleted" /><s:basetype optional="false" unbounded="false" typename="boolean" name="deleted" qname="{http://model.picr.ebi.ac.uk}CrossReference>deleted" /><s:basetype optional="false" unbounded="false" typename="string" name="gi" qname="{http://model.picr.ebi.ac.uk}CrossReference>gi" /><s:basetype optional="false" unbounded="false" typename="string" name="taxonId" qname="{http://model.picr.ebi.ac.uk}CrossReference>taxonId" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="CrossReference" name="logicalCrossReferences" qname="{http://model.picr.ebi.ac.uk}UPEntry>logicalCrossReferences"><s:elementtype><s:complextype id="{http://model.picr.ebi.ac.uk}CrossReference" optional="false" unbounded="false" typename="CrossReference" name="" /></s:elementtype></s:arraytype><s:basetype optional="false" unbounded="false" typename="string" name="sequence" qname="{http://model.picr.ebi.ac.uk}UPEntry>sequence" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="timestamp" qname="{http://model.picr.ebi.ac.uk}UPEntry>timestamp" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetUPIForAccession_getUPIForAccessionReturninput0identicalCrossReferences11net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
input
0
'text/xml'
java.lang.String
false
CRC64
0
'text/plain'
0
UPI
0
'text/plain'
0
identicalCrossReferences
1
l('text/xml')
1
logicalCrossReferences
1
l('text/xml')
1
sequence
0
'text/plain'
0
timestamp
0
'text/plain'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="UPEntry" name="" qname="{http://model.picr.ebi.ac.uk}UPEntry"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="CRC64" qname="{http://model.picr.ebi.ac.uk}UPEntry>CRC64" /><s:basetype optional="false" unbounded="false" typename="string" name="UPI" qname="{http://model.picr.ebi.ac.uk}UPEntry>UPI" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="CrossReference" name="identicalCrossReferences" qname="{http://model.picr.ebi.ac.uk}UPEntry>identicalCrossReferences"><s:elementtype><s:complextype optional="false" unbounded="false" typename="CrossReference" name="" qname="{http://model.picr.ebi.ac.uk}CrossReference"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="accession" qname="{http://model.picr.ebi.ac.uk}CrossReference>accession" /><s:basetype optional="false" unbounded="false" typename="string" name="accessionVersion" qname="{http://model.picr.ebi.ac.uk}CrossReference>accessionVersion" /><s:basetype optional="false" unbounded="false" typename="string" name="databaseDescription" qname="{http://model.picr.ebi.ac.uk}CrossReference>databaseDescription" /><s:basetype optional="false" unbounded="false" typename="string" name="databaseName" qname="{http://model.picr.ebi.ac.uk}CrossReference>databaseName" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="dateAdded" qname="{http://model.picr.ebi.ac.uk}CrossReference>dateAdded" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="dateDeleted" qname="{http://model.picr.ebi.ac.uk}CrossReference>dateDeleted" /><s:basetype optional="false" unbounded="false" typename="boolean" name="deleted" qname="{http://model.picr.ebi.ac.uk}CrossReference>deleted" /><s:basetype optional="false" unbounded="false" typename="string" name="gi" qname="{http://model.picr.ebi.ac.uk}CrossReference>gi" /><s:basetype optional="false" unbounded="false" typename="string" name="taxonId" qname="{http://model.picr.ebi.ac.uk}CrossReference>taxonId" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="CrossReference" name="logicalCrossReferences" qname="{http://model.picr.ebi.ac.uk}UPEntry>logicalCrossReferences"><s:elementtype><s:complextype id="{http://model.picr.ebi.ac.uk}CrossReference" optional="false" unbounded="false" typename="CrossReference" name="" /></s:elementtype></s:arraytype><s:basetype optional="false" unbounded="false" typename="string" name="sequence" qname="{http://model.picr.ebi.ac.uk}UPEntry>sequence" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="timestamp" qname="{http://model.picr.ebi.ac.uk}UPEntry>timestamp" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetUPIForAccessionReturn_identicalCrossReferencesinput0accession00databaseName00taxonId00accessionVersion00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
input
0
'text/xml'
java.lang.String
false
accession
0
'text/plain'
0
accessionVersion
0
'text/plain'
0
databaseDescription
0
'text/plain'
0
databaseName
0
'text/plain'
0
dateAdded
0
'text/plain'
0
dateDeleted
0
'text/plain'
0
deleted
0
'text/plain'
0
gi
0
'text/plain'
0
taxonId
0
'text/plain'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="CrossReference" name="" qname="{http://model.picr.ebi.ac.uk}CrossReference"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="accession" qname="{http://model.picr.ebi.ac.uk}CrossReference>accession" /><s:basetype optional="false" unbounded="false" typename="string" name="accessionVersion" qname="{http://model.picr.ebi.ac.uk}CrossReference>accessionVersion" /><s:basetype optional="false" unbounded="false" typename="string" name="databaseDescription" qname="{http://model.picr.ebi.ac.uk}CrossReference>databaseDescription" /><s:basetype optional="false" unbounded="false" typename="string" name="databaseName" qname="{http://model.picr.ebi.ac.uk}CrossReference>databaseName" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="dateAdded" qname="{http://model.picr.ebi.ac.uk}CrossReference>dateAdded" /><s:basetype optional="false" unbounded="false" typename="dateTime" name="dateDeleted" qname="{http://model.picr.ebi.ac.uk}CrossReference>dateDeleted" /><s:basetype optional="false" unbounded="false" typename="boolean" name="deleted" qname="{http://model.picr.ebi.ac.uk}CrossReference>deleted" /><s:basetype optional="false" unbounded="false" typename="string" name="gi" qname="{http://model.picr.ebi.ac.uk}CrossReference>gi" /><s:basetype optional="false" unbounded="false" typename="string" name="taxonId" qname="{http://model.picr.ebi.ac.uk}CrossReference>taxonId" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokebuild_mapping_tablecrossReferenceAccs3databaseNames3accessionVersions3taxonIds3originalAccs1results00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
originalAccs
1
text/plain
java.lang.String
true
crossReferenceAccs
3
text/plain
java.lang.String
true
databaseNames
3
text/plain
java.lang.String
true
taxonIds
3
text/plain
java.lang.String
true
accessionVersions
3
text/plain
java.lang.String
true
results
0
0
workflow
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_stringregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
string
0
'text/plain'
java.lang.String
true
regex
0
'text/plain'
java.lang.String
true
split
1
1
workflow
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
UserNameHere
2011-05-29 12:57:38.562 BST
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
,
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetUPIForAccessionparametersgetUPIForAccession_inputsearchDatabasesgetUPIForAccession_inputonlyActivegetUPIForAccession_inputtaxonIdgetUPIForAccession_inputaccessiongetUPIForAccession_outputinputgetUPIForAccession_getUPIForAccessionReturninputgetUPIForAccessionReturn_identicalCrossReferencesinputbuild_mapping_tablecrossReferenceAccsbuild_mapping_tabledatabaseNamesbuild_mapping_tableaccessionVersionsbuild_mapping_tabletaxonIdsbuild_mapping_tableoriginalAccssplit_stringregexsplit_stringstringmapping_table
761f8082-d028-496d-bb1c-d9690f8fb31c
2011-05-18 07:34:02.337 BST
c7604164-c633-479c-af37-210ac6c8b3ea
2011-05-18 08:16:28.999 BST
f49baecc-e9e5-4240-aca0-47c73016c58e
2011-05-18 07:48:20.20 BST
EBI PICR, find cross-references for protein accessions
2011-05-18 08:15:33.230 BST
21af884e-458f-4234-ba8b-a462ffb45f0b
2011-05-18 09:17:43.558 BST
35ef885d-1373-4d40-8597-ba5b07cbda78
2011-05-18 08:52:43.442 BST
205fea89-5fc4-4541-8c11-781b0110fd5f
2011-05-18 07:37:33.205 BST
99f35bd2-b018-4695-b0a0-b83873ac4204
2011-05-18 07:50:43.983 BST
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.
2011-05-18 08:13:45.883 BST
f365598f-84e9-41c5-9dac-a3d75ee5a43b
2011-05-29 12:15:12.114 BST
41be1c5e-d834-45f7-9b3c-d464dae04c54
2011-05-29 12:59:44.276 BST
9696674a-29d4-4a7c-b9b7-f994380a5ada
2011-05-29 02:57:55.703 BST
8699f6be-f587-44d2-8c86-c0e74e5232c9
2011-05-18 08:49:52.753 BST
e67869cb-4fa8-41c0-bfc9-f0d1b9b70818
2011-05-18 09:20:14.32 BST
3b3375da-905f-4f29-93b5-cd9241de9b3f
2011-05-18 07:52:21.846 BST
da8428f6-e0ee-4b6c-90fd-1c1d9c2b994f
2011-05-29 13:05:38.686 BST
a1fe0cfe-6945-4b8d-b392-0d93b75129b9
2011-05-18 08:24:35.315 BST
1da59d84-2695-447b-9191-d0d5098060e0
2011-05-29 12:58:30.517 BST
7aa06da4-2bc5-41b2-b05c-4320cbb21523
2011-05-18 09:00:46.670 BST
8ebb0413-76fc-4a12-b74a-dd70c4097f69
2011-05-18 09:16:13.262 BST
e6dd081b-ea4b-468f-b11e-d38a97396793
2011-05-18 09:24:17.357 BST
2ce11204-18ee-4628-834a-b84fb8d3ce3c
2011-05-29 12:17:37.169 BST
755870c4-e673-4bc5-88d1-ce6b5354dbb5
2011-05-18 07:38:21.962 BST
fb13dc79-dca6-4250-973d-3275d986381d
2011-05-29 03:00:42.756 BST
b958fe71-cd1e-4dab-9442-ea1c0ce7bd0f
2011-05-29 02:59:01.82 BST
Rafael C Jimenez
2011-05-18 08:46:20.213 BST
a58a95fb-b6db-4d1c-811e-2ad5f3eb1aca
2011-05-18 09:15:08.902 BST
81d2c585-f3df-4f49-8609-42facc48b85d
2011-05-18 09:28:12.188 BST
699353f1-5474-42fb-92c1-f2a1488142bb
2011-05-29 13:03:21.697 BST
Get_homologous_from_NCBI_homoloGeneproteinAccs00
A list of Refseq protein accessions to query. Use comma-separated values (CSV)
2011-10-13 18:23:03.930 BST
XP_524741.2,NP_001003746.1
2011-10-13 18:23:13.163 BST
specie00
9606
2011-10-13 18:19:44.460 BST
Specie where to find homologous. Use a taxonomy accession. Input "all" if you would like to find homologous in all the species.
2011-10-13 18:20:13.274 BST
Beanshell_listOfResultslistOfproteinAccsgetHomologousFrom_homoloGenespecie0queryAccs1homologeneUrlNCBI0listOfResults22net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
homologeneUrlNCBI
0
text/plain
java.lang.String
true
queryAccs
1
text/plain
java.lang.String
true
specie
0
text/plain
java.lang.String
true
listOfResults
2
2
workflow
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokehomologeneUrlNCBI_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/current/homologene.data
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
string
0
'text/plain'
java.lang.String
true
regex
0
'text/plain'
java.lang.String
true
split
1
l('text/plain')
1
workflow
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
,
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetHomologousFrom_homoloGenespeciegetHomologousFrom_homoloGenequeryAccsgetHomologousFrom_homoloGenehomologeneUrlNCBISplit_string_into_string_list_by_regular_expressionregexSplit_string_into_string_list_by_regular_expressionstringBeanshell_listOfResultslistOfproteinAccs
274f5ad8-0715-44fb-bd70-ffc201a89dda
2011-10-13 18:25:28.514 BST
Get homologous from NCBI homoloGene
2011-10-13 18:26:19.374 BST
bf54b0e6-6dae-4702-a625-adf7b86cca3c
2011-10-13 18:29:00.341 BST
fd5b4735-d40b-4f7a-9e96-16a86de35244
2011-10-13 18:13:22.714 BST
b62064b9-4d4c-459b-bf16-dc62f06035a3
2011-10-13 18:33:47.37 BST
Get homologous from NCBI homoloGene for a list of Refseq protein accessions. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README
2011-10-13 18:28:59.2 BST
7ccaa81c-cbce-42b8-a30e-84caf41c9a7c
2011-10-13 18:27:04.366 BST
831388bf-1e8c-4301-9903-ae37f1b6f72e
2011-10-13 18:30:45.976 BST
Rafael C. Jimenez
2011-10-13 18:23:44.729 BST