Workflow Entry: getInchIfromMassBankPeaklist_ChemSpider_workflow_withImage

Created at: 05/06/08 @ 16:00:39 Last updated: 16/06/08 @ 11:40:46

Version 2 (latest) (of 2)

Version created on: 05/06/08 @ 16:00:38 by: Michael Gerlich | Revision comments Expand

Last edited on: 16/06/08 @ 11:40:46 by: Michael Gerlich

Title: getInchIfromMassBankPeaklist_ChemSpider_workflow_withImage

Type: Taverna 1

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Getinchifrommassbankpeaklist_chemspider_workflow_withimage_5588_2

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Description

uses InChI’s retrieved from a MassBank peaklist query to get compound information about those compounds via querying ChemSpider for information and displaying those results with image

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Option 1:

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Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

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http://www.myexperiment.org/workflows/223/download?version=2
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Workflow Components

Inputs (2)

Name	Description
PeakList	xml input for Biomoby service - complete peaklist with m/z, intensity and tolerance values of both example: <?xml version="1.0" encoding="UTF-8"?> <moby:MOBY xmlns:moby="http://www.biomoby.org/moby"> <moby:mobyContent> <moby:mobyData moby:queryID="sip_1_"> <moby:Simple moby:articleName="mz"> <moby:ArrayFloat moby:id="" moby:namespace=""> <moby:ElementFloat moby:id="" moby:namespace="" moby:articleName="Element"> <moby:Float moby:id="" moby:namespace="" moby:articleName="Value">273.0</moby:Float> </moby:ElementFloat> <moby:ElementFloat moby:id="" moby:namespace="" moby:articleName="Element"> <moby:Float moby:id="" moby:namespace="" moby:articleName="Value">153.0</moby:Float> </moby:ElementFloat> </moby:ArrayFloat> </moby:Simple> <moby:Simple moby:articleName="int"> <moby:ArrayFloat moby:id="" moby:namespace=""> <moby:ElementFloat moby:id="" moby:namespace="" moby:articleName="Element"> <moby:Float moby:id="" moby:namespace="" moby:articleName="Value">10000.0</moby:Float> </moby:ElementFloat> <moby:ElementFloat moby:id="" moby:namespace="" moby:articleName="Element"> <moby:Float moby:id="" moby:namespace="" moby:articleName="Value">10000.0</moby:Float> </moby:ElementFloat> </moby:ArrayFloat> </moby:Simple> <moby:Parameter moby:articleName="tolerance_int"> <moby:Value>500</moby:Value> </moby:Parameter> <moby:Parameter moby:articleName="tolerance_mz"> <moby:Value>0.3</moby:Value> </moby:Parameter> </moby:mobyData> </moby:mobyContent> </moby:MOBY>
SecurityToken	security token which is required to access ChemSpider services get your own by registering at http://www.chemspider.com

Name

Description

PeakList

xml input for Biomoby service - complete peaklist with m/z, intensity and tolerance values of both example: <?xml version="1.0" encoding="UTF-8"?> <moby:MOBY xmlns:moby="http://www.biomoby.org/moby"> <moby:mobyContent> <moby:mobyData moby:queryID="sip_1_"> <moby:Simple moby:articleName="mz"> <moby:ArrayFloat moby:id="" moby:namespace=""> <moby:ElementFloat moby:id="" moby:namespace="" moby:articleName="Element"> <moby:Float moby:id="" moby:namespace="" moby:articleName="Value">273.0</moby:Float> </moby:ElementFloat> <moby:ElementFloat moby:id="" moby:namespace="" moby:articleName="Element"> <moby:Float moby:id="" moby:namespace="" moby:articleName="Value">153.0</moby:Float> </moby:ElementFloat> </moby:ArrayFloat> </moby:Simple> <moby:Simple moby:articleName="int"> <moby:ArrayFloat moby:id="" moby:namespace=""> <moby:ElementFloat moby:id="" moby:namespace="" moby:articleName="Element"> <moby:Float moby:id="" moby:namespace="" moby:articleName="Value">10000.0</moby:Float> </moby:ElementFloat> <moby:ElementFloat moby:id="" moby:namespace="" moby:articleName="Element"> <moby:Float moby:id="" moby:namespace="" moby:articleName="Value">10000.0</moby:Float> </moby:ElementFloat> </moby:ArrayFloat> </moby:Simple> <moby:Parameter moby:articleName="tolerance_int"> <moby:Value>500</moby:Value> </moby:Parameter> <moby:Parameter moby:articleName="tolerance_mz"> <moby:Value>0.3</moby:Value> </moby:Parameter> </moby:mobyData> </moby:mobyContent> </moby:MOBY>

SecurityToken

security token which is required to access ChemSpider services get your own by registering at http://www.chemspider.com

Processors (11)

Name	Type	Description
parametersXML1	local
parametersXML4	local
parametersXML3	local
parametersXML5	local
parametersXML	local
parametersXML2	local
GetExtendedCompoundInfoArray	arbitrarywsdl	Get array of extended record details by an array of CSIDs. Security token is required to get access to this service.
GetCompoundThumbnail	arbitrarywsdl	Get compound thumbnail in PNG format. Security token is required to get access to this service.
SimpleSearch	arbitrarywsdl	Try to find whatever is entered. Return the list of found IDs. Security token is required to get access to this service.
getInChIfromMassBankPeaklist	biomobywsdl	retrieval of InChI's according to peaklist query in MassBank DB - later use of InChI's for further compound information from other databases
Parse_Moby_Data_ArrayString	biomobyparser	Processor to parse the datatype ArrayString

Outputs (2)

Name	Description
CompoundInfo	displays the resulting information about the found compounds
CompoundImage	displays an image for each found compound displaying chemical structure

Links (18)

Sink	Source
getInChIfromMassBankPeaklist:ArrayFloat(int)	PeakList
getInChIfromMassBankPeaklist:ArrayFloat(mz)	PeakList
getInChIfromMassBankPeaklist:input	PeakList
parametersXML2:token	SecurityToken
parametersXML:token	SecurityToken
parametersXML3:input	GetExtendedCompoundInfoArray:parameters
parametersXML4:token	SecurityToken
parametersXML5:input	GetCompoundThumbnail:parameters
parametersXML:query	Parse_Moby_Data_ArrayString:result_'Element'_'Value'
parametersXML1:input	SimpleSearch:parameters
Parse_Moby_Data_ArrayString:mobyData('ArrayString')	getInChIfromMassBankPeaklist:ArrayString(result)
parametersXML2:CSIDs	parametersXML1:SimpleSearchResult
parametersXML4:id	parametersXML1:SimpleSearchResult
GetExtendedCompoundInfoArray:parameters	parametersXML2:output
CompoundInfo	parametersXML3:GetExtendedCompoundInfoArrayResult
GetCompoundThumbnail:parameters	parametersXML4:output
CompoundImage	parametersXML5:GetCompoundThumbnailResult
SimpleSearch:parameters	parametersXML:output