file-similarity-entrez-url

Created: 2010-07-16 09:34:45 Last updated: 2010-07-16 09:43:39

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Performs a 2D structure similarity search on the PubChem database. This workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (0)

Processors (20)

Name	Type	Description
SimilaritySearch2D_in_simOptions	xmlsplitter
InputStructureBase64_out	xmlsplitter
InputStructureBase64	wsdl	Wsdl http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl Wsdl Operation InputStructureBase64
SimilaritySearch2D_out	xmlsplitter
format	stringconstant	Value eFormat_SDF
InputStructureBase64_in	xmlsplitter
SimilaritySearch2D	wsdl	Wsdl http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl Wsdl Operation SimilaritySearch2D
GetEntrezKey	wsdl	Wsdl http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl Wsdl Operation GetEntrezKey
GetEntrezUrl_in_EntrezKey	xmlsplitter
SimilaritySearch2D_in	xmlsplitter
FileName	stringconstant	Value E:\Users\thiessen\Downloads\aspirin.sdf
GetEntrezUrl_out	xmlsplitter
GetEntrezKey_out_EntrezKey	xmlsplitter
threshold	stringconstant	Value 95
GetEntrezUrl	wsdl	Wsdl http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl Wsdl Operation GetEntrezUrl
GetEntrezKey_in	xmlsplitter
GetEntrezKey_out	xmlsplitter
GetEntrezUrl_in	xmlsplitter
Status_Check	workflow
file_to_base64	workflow

Beanshells (2)

Name	Description	Inputs	Outputs
CheckForSuccess		status	success
File_to_byte_array		filename	bytes

Outputs (2)

Name	Description
URL
Success

Datalinks (23)

Source	Sink
threshold:value	SimilaritySearch2D_in_simOptions:threshold
InputStructureBase64:parameters	InputStructureBase64_out:input
InputStructureBase64_in:output	InputStructureBase64:parameters
SimilaritySearch2D:parameters	SimilaritySearch2D_out:input
format:value	InputStructureBase64_in:format
file_to_base64:Base64String	InputStructureBase64_in:structure
SimilaritySearch2D_in:output	SimilaritySearch2D:parameters
GetEntrezKey_in:output	GetEntrezKey:parameters
GetEntrezKey_out_EntrezKey:db	GetEntrezUrl_in_EntrezKey:db
GetEntrezKey_out_EntrezKey:key	GetEntrezUrl_in_EntrezKey:key
GetEntrezKey_out_EntrezKey:webenv	GetEntrezUrl_in_EntrezKey:webenv
SimilaritySearch2D_in_simOptions:output	SimilaritySearch2D_in:simOptions
InputStructureBase64_out:StrKey	SimilaritySearch2D_in:StrKey
GetEntrezUrl:parameters	GetEntrezUrl_out:input
GetEntrezKey_out:EntrezKey	GetEntrezKey_out_EntrezKey:input
GetEntrezUrl_in:output	GetEntrezUrl:parameters
Status_Check:KeyOut	GetEntrezKey_in:ListKey
GetEntrezKey:parameters	GetEntrezKey_out:input
GetEntrezUrl_in_EntrezKey:output	GetEntrezUrl_in:EntrezKey
SimilaritySearch2D_out:ListKey	Status_Check:KeyIn
FileName:value	file_to_base64:FileName
GetEntrezUrl_out:url	URL
Status_Check:Success	Success

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Peter Li

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 2)

Information Credits (1)

(People/Groups)

Peter Li

Information Attributions (0)

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None

Information Tags (2)

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Information Shared with Groups (0)

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Information Featured In Packs (1)

Example PubChem, ChEBI and ChemSpider workflows

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Information Attributed By (0)

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Information Favourited By (0)

No one

Information Statistics

3980 viewings

1690 downloads

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Citations (0)

None

Version History

In chronological order:

file-similarity-entrez-url

Created by Peter Li on Friday 16 July 2010 09:34:45 (UTC)

Last edited by Peter Li on Friday 16 July 2010 09:38:26 (UTC)
file-similarity-entrez-url

Created by Peter Li on Friday 16 July 2010 09:40:15 (UTC)

Last edited by Peter Li on Friday 16 July 2010 09:43:39 (UTC)

Revision comment:

Simplified the workflow by nesting calls to the pubchem web service in sub-workflows. Also replaced string constants with workflow input ports.

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file-similarity-entrez-url

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Other workflows that use similar services (7)