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PubChem substructure search

Created: 2010-07-16 10:31:51      Last updated: 2010-07-16 10:52:28

Performs a substucture search in PubChem. This workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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http://myexperiment.org/workflows/1434/download?version=1
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Information Workflow Components

Information Authors (3)
Information Titles (1)
Information Descriptions (3)
Information Dependencies (0)
Inputs (0)
Processors (15)
Beanshells (1)
Outputs (2)
Datalinks (16)
Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

254?size=60x60 Cn Peter Li

Information License

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Information Version 1 (earliest) (of 2)

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Information Statistics

3970 viewings

1762 downloads

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Version History

In chronological order:

  1. smiles-substructure-idlist

    Created by Peter Li on Friday 16 July 2010 10:31:51 (UTC)

    Last edited by Peter Li on Friday 16 July 2010 10:33:40 (UTC)

  2. PubChem substructure search

    Created by Peter Li on Friday 16 July 2010 10:35:48 (UTC)

    Last edited by Peter Li on Friday 16 July 2010 10:52:28 (UTC)

    Revision comment:

    Placed calls to the PubChem web service in nested workflows. Simplified the polling of PubChem by removing beanshell script and using the looping functionality in Taverna 2. Replaced string constants with workflow input ports.



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Taverna 1
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Avatar De Michael Gerlich

Workflow Download Entries from PubChem (1)

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Given a list of identifiers (e.g. CID) and their appropriate type (eID_CID - note that these differ slightly from the original identifier name -> CID <-> eID_CID), this workflow queries PubChem via PUG to retrieve a download URL for the resulting XML file containing the results. Adding support for downloading this XML file and writing it to filesystem is planned.

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

Credits: User Michael Gerlich

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Avatar De Michael Gerlich

Workflow MassBank to KEGG (1)

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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)

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

Credits: User Michael Gerlich

Funded by: BioVeL, EPSRC, JISC, Microsoft

Affiliates: myGrid, Taverna, BioCatalogue
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