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 PubChem. The input structure has to be in the form of a SDF file. The original SDF-based similarity search workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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http://myexperiment.org/workflows/1431/download?version=2
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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (3)

Name	Description
sdf	A chemical compound in SDF format
threshold	Parameter to define cut off for similarity
format	Format of input chemical structure

Processors (6)

Name	Type	Description
checkStatus	workflow
getEntrezUrl	workflow
encode	localworker	Script import org.apache.commons.codec.binary.Base64; base64 = new String(Base64.encodeBase64(bytes));
getEntrezKey	workflow
doSimilaritySearch2D	workflow
createInputStructureBase64	workflow

Beanshells (0)

Outputs (2)

Name	Description
URL
Success

Datalinks (12)

Source	Sink
doSimilaritySearch2D:listKey	checkStatus:KeyIn
getEntrezKey:webenv	getEntrezUrl:webenv
getEntrezKey:key	getEntrezUrl:key
getEntrezKey:db	getEntrezUrl:db
sdf	encode:bytes
doSimilaritySearch2D:listKey	getEntrezKey:listKey
createInputStructureBase64:strKey	doSimilaritySearch2D:strKey
threshold	doSimilaritySearch2D:threshold
encode:base64	createInputStructureBase64:structure
format	createInputStructureBase64:format
getEntrezUrl:url	URL
checkStatus:status	Success

Coordinations (1)

Controller	Target
checkStatus	getEntrezKey

Information Workflow Type

Taverna 2

Information Uploader

Peter Li

Information License

All versions of this Workflow are licensed under:

Information Version 2 (latest) (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)

None

Information Featured In Packs (1)

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Information Attributed By (0)

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None

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)