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getInchIfromMassBankPeaklist_ChemSpider_workflow_withImage

Workflow Entry: getInchIfromMassBankPeaklist_ChemSpider_workflow_withImage

Created at: 05/06/08 @ 16:00:38 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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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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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. See the Service entry for this web service.
GetCompoundThumbnail	arbitrarywsdl	Get compound thumbnail in PNG format. Security token is required to get access to this service. See the Service entry for this web 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. See the Service entry for this web 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

Beanshells (0)

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)

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

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Michael Gerlich

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

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Michael Gerlich

Information Attributions (0)

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None

Information Tags (8)

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Information Featured In Packs (1)

useful_for_sysmo

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Information Favourited By (0)

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Information Statistics

665 viewings

917 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - get compound information from ChemSpider using MassBank query

Created on: Thursday 05 June 2008 @ 16:00:38 (GMT)

Created by: Michael Gerlich

Last edited on: Thursday 05 June 2008 @ 16:03:52 (GMT)

Last edited by: Michael Gerlich

Revision comments:

None

Latest Version:
[2] - getInchIfromMassBankPeaklist_ChemSpider_workflow_withImage

Created on: Thursday 05 June 2008 @ 16:00:38 (GMT)

Created by: Michael Gerlich

Last edited on: Monday 16 June 2008 @ 11:40:46 (GMT)

Last edited by: Michael Gerlich

Revision comments:

Biomoby service now retrieves InChI's from MassBank DB to query ChemSpider services

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Taverna 2

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Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Tags (3):

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Original Uploader

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Created: 30/03/09 @ 09:30:32 | Last updated: 30/03/09 @ 09:49:13

Credits: Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Workflow that queries MassBank DB to retrieve database identifiers (KEGG, PubChem, InChI) and continue search with them to retrieve pathways from KEGG for given compound identifier,searches PubChem via eutils and PUG, queries ChemSpider for compound information and image. Note: Usage of ChemSpider web services requires a valid security token - receive one by registering at ChemSpider (look at your profile to see your token)

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Viewed: 198 times | Downloaded: 0 times

Tags (21):