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Tag: bioinformatics

Wsdl: http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl

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Taverna 1

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Michael Gerlich

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: Michael Gerlich

Taverna 2

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Kalai

Download Structures from PubChem given che... (1)

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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.

Created: 2011-05-24 | Last updated: 2011-05-24

Credits: Kalai Michael Gerlich

Attributions: Download Entries from PubChem

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