getInchIfromMassBankPeaklist_ChemSpider_workflow_withImage

Created: 2008-06-05 16:00:38 Last updated: 2008-06-16 11:40:46

Download Workflow

workflow that queries MassBank DB with peaklist of m/z and intensity values and retrieves SMILES codes for results

after that, it converts these SMILES into ChemSpider's own identifier CSID and queries ChemSpider to get extended compound info according to SMILES/CSID

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/223/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (2)

Name	Description
PeakList	peaklist containing pairwise(!) values for m/z and intensity as well as single tolerance values for both example for 2 peaks and tolerance values set: <?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">153.0</moby:Float> </moby:ElementFloat> <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: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_mz"> <moby:Value>0.2</moby:Value> </moby:Parameter> <moby:Parameter moby:articleName="tolerance_int"> <moby:Value>500</moby:Value> </moby:Parameter> </moby:mobyData> </moby:mobyContent> </moby:MOBY>
SecurityToken	security token needed for invoking ChemSpider services get your own through registering at http://www.chemspider.com

Name

Description

PeakList

peaklist containing pairwise(!) values for m/z and intensity as well as single tolerance values for both example for 2 peaks and tolerance values set: <?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">153.0</moby:Float> </moby:ElementFloat> <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: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_mz"> <moby:Value>0.2</moby:Value> </moby:Parameter> <moby:Parameter moby:articleName="tolerance_int"> <moby:Value>500</moby:Value> </moby:Parameter> </moby:mobyData> </moby:mobyContent> </moby:MOBY>

SecurityToken

security token needed for invoking ChemSpider services get your own through registering at http://www.chemspider.com

Processors (11)

Name	Type	Description
parametersXML2	local	takes converted results of SimpleSearch (CSID) and SecurityToken as input for GetExtendedCompoundInfoArray service from ChemSpider
parametersXML3	local	takes xml results of GetExtendedCompoundInfoArray service and prepares them for workflow output
parametersXML5	local	takes image results of GetCompoundThumbnail service and prepares them for workflow output
parametersXML	local	prepares text output of MassBank query and security token for ChemSpider to get involved in SimpleSearch service
parametersXML4	local	takes converted results of SimpleSearch (CSID) and SecurityToken as input for GetCompoundThumbnail service from ChemSpider
parametersXML1	local	takes xml results of SimpleSearch service and prepares them for further use in following services
SimpleSearch	arbitrarywsdl	Try to find whatever is entered. Return the list of found IDs. 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.
GetExtendedCompoundInfoArray	arbitrarywsdl	Get array of extended record details by an array of CSIDs. Security token is required to get access to this service.
MassBank_Query_PeakList	biomobywsdl	queries MassBank DB with peaklist containing m/z, intensity and tolerance values and retrieves found records/SMILES
Parse_Moby_Data_ArrayString	biomobyparser	Processor to parse the datatype ArrayString

Beanshells (0)

Outputs (2)

Name	Description
CompoundImage	contains images of resulting compounds
CompoundInfo	contains chemical information about compounds resulting from MassBank and ChemSpider query

Links (18)

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

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Michael Gerlich

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 2)

Information Credits (1)

(People/Groups)

Michael Gerlich

Information Attributions (0)

(Workflows/Files)

None

Information Tags (8)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (1)

useful_for_sysmo

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

3316 viewings

2665 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

get compound information from ChemSpider using MassBank query

Created by Michael Gerlich on Thursday 05 June 2008 16:00:38 (UTC)

Last edited by Michael Gerlich on Thursday 05 June 2008 16:03:52 (UTC)
getInchIfromMassBankPeaklist_ChemSpider_workflow_withImage

Created by Michael Gerlich on Thursday 05 June 2008 16:00:38 (UTC)

Last edited by Michael Gerlich on Monday 16 June 2008 11:40:46 (UTC)

Revision comment:

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

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (17)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Uploader

Michael Gerlich

Search InChI in ChemSpider (1)

Download

This workflows queries ChemSpider for compound information and compound images. Note that a Chemspider security token is needed in order to access some of the ChemSpider services (receive one by registering at ChemSpider). Possible search terms might be InChI codes, ChemSpider identifiers or names.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

Taverna 2

Uploader

Peter Li

Asynchronous chemspider search by formula (1)

Download

Performs an asynchronous search on ChemSpider by molecular formula

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li