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Download Structures from PubChem given chemical names

Workflow Entry: Download Structures from PubChem given chemical names

Created at: 24/05/11 @ 13:13:52 Last updated: 24/05/11 @ 14:19:24

Version 1 (of 1)

Version created on: 24/05/11 @ 13:13:52 by: Kalai | Revision comments Expand

Last edited on: 24/05/11 @ 14:19:24 by: Kalai

Title: Download Structures from PubChem given chemical names

Type: Taverna 2

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Description

This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search.

If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned.

The pubchem compound_ID is then used to download structures from PubChem.

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http://www.myexperiment.org/workflows/2139/download?version=1
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Workflow Components

Authors (0)

Titles (0)

Descriptions (0)

Inputs (0)

Processors (29)

Name	Type	Description
run_eSearch	wsdl
run_eSearch_request	xmlsplitter
db_value	stringconstant
Read_Text_File	localworker
Split_string_into_string_list_by_regular_expression	localworker
regex_value	stringconstant
fileurl_value	stringconstant
RetMax_value	stringconstant
Flatten_List	localworker
idType_value	stringconstant
Download_out	xmlsplitter
GetDownloadUrl_out	xmlsplitter
Format	stringconstant
GetDownloadUrl	wsdl	See the Service entry for this web service.
Download	wsdl	See the Service entry for this web service.
InputListText_out	xmlsplitter
Compression	stringconstant
GetDownloadUrl_in	xmlsplitter
Download_in	xmlsplitter
Status_Check	workflow
Echo_List	localworker
Merge_String_List_to_a_String	localworker
seperator_value	stringconstant
InputListText	wsdl	See the Service entry for this web service.
InputListText_input	xmlsplitter
Write_Text_File_2	localworker
Read_Text_File_2	localworker
outputFile_value_1	stringconstant
XPath_Service	xpath

Beanshells (1)

Name	Description	Inputs	Outputs
CheckForSuccess		status	success

Outputs (6)

Name	Description
run_eSearch_result
Flatten_List_outputlist
URL
Success
InputListText_out_ListKey
Merge_String_List_to_a_String_concatenated

Datalinks (34)

Source	Sink
run_eSearch_request:output	run_eSearch:request
db_value:value	run_eSearch_request:db
Split_string_into_string_list_by_regular_expression:split	run_eSearch_request:term
RetMax_value:value	run_eSearch_request:RetMax
fileurl_value:value	Read_Text_File:fileurl
Read_Text_File:filecontents	Split_string_into_string_list_by_regular_expression:string
regex_value:value	Split_string_into_string_list_by_regular_expression:regex
XPath_Service:nodelist	Flatten_List:inputlist
Download:parameters	Download_out:input
GetDownloadUrl:parameters	GetDownloadUrl_out:input
GetDownloadUrl_in:output	GetDownloadUrl:parameters
Download_in:output	Download:parameters
InputListText:parameters	InputListText_out:input
Status_Check:KeyOut	GetDownloadUrl_in:DownloadKey
Format:value	Download_in:eFormat
Compression:value	Download_in:eCompress
InputListText_out:ListKey	Download_in:ListKey
Download_out:DownloadKey	Status_Check:KeyIn
Flatten_List:outputlist	Echo_List:inputlist
Echo_List:outputlist	Merge_String_List_to_a_String:stringlist
seperator_value:value	Merge_String_List_to_a_String:seperator
InputListText_input:output	InputListText:parameters
idType_value:value	InputListText_input:idType
Merge_String_List_to_a_String:concatenated	InputListText_input:ids
Read_Text_File_2:filecontents	Write_Text_File_2:filecontents
outputFile_value_1:value	Write_Text_File_2:outputFile
GetDownloadUrl_out:url	Read_Text_File_2:fileurl
run_eSearch:result	XPath_Service:xml_text
run_eSearch:result	run_eSearch_result
Flatten_List:outputlist	Flatten_List_outputlist
GetDownloadUrl_out:url	URL
Status_Check:Success	Success
InputListText_out:ListKey	InputListText_out_ListKey
Merge_String_List_to_a_String:concatenated	Merge_String_List_to_a_String_concatenated

Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

Kalai

Information License

All versions of this Workflow are licensed under:

Information Credits (2)

(People/Groups)

Information Attributions (1)

(Workflows/Files)

Download Entries from PubChem

Information Tags (26)

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Information Attributed By (0)

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Information Favourited By (0)

No one

Information Statistics

130 viewings

238 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - Download Structures from PubChem given chemical names

Created on: Tuesday 24 May 2011 @ 13:13:52 (GMT)

Created by: Kalai

Last edited on: Tuesday 24 May 2011 @ 14:19:24 (GMT)

Last edited by: Kalai

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