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Items tagged with "cheminformatics" (76)

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Groups (2)

Network-member Cheminformatics

Unique name: cheminformatics
Created: Thursday 04 December 2008 @ 21:18:56 (GMT)

Workflows in the area of cheminformatics, for example, using ChemSpider or PubChem webservices, or using cheminformatics plugins like CDK-Taverna.

7 shared items   |   0 announcements

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Network-member Bioclipse

Unique name: bioclipse
Created: Monday 13 September 2010 @ 10:29:24 (GMT)

 Group around Bioclipse Scripting Language workflows.

2 shared items   |   0 announcements

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Workflows (71)

Workflow Create Ugi Library 001 (1)

Created: 04/12/08 @ 20:34:13

Credits: User Jean-Claude Bradley

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Creates a virtual library of SMILES codes for all possible combinations of Ugi products based on lists of SMILES of starting materials in a Google Spreadsheet.  Uses Rajarshi Guha's web service. Can someone create a Taverna workflow that does this?

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 88 times | Downloaded: 52 times

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Workflow /me is having Bioclipse/XMPP/RDF fun.js (1)

Created: 21/08/09 @ 15:39:04

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioclipse script that combines RDF (DBPedia), XMPP cloud services, and local CDK functionality to gain some information on Farnesol in Bioclipse.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 39 times | Downloaded: 18 times

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Workflow Visualize Molecules from DBPedia as Molecu... (3)

Created: 14/03/10 @ 20:57:58

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Downloads entries from DBPedia which have a SMILES and creates a molecule table with 2D structures of the hits found with SPARQL.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 179 times | Downloaded: 46 times

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Workflow Open PDB entries in Jmol for hits found fo... (3)

Created: 14/03/10 @ 21:26:05 | Last updated: 01/03/13 @ 14:37:58

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Queries Bio2RDF for proteins of which the title contains 'HIV', downloads them using the EMBL webservices and opens them in Bioclipse for visualization with Jmol.

Rating: 1.3 / 5 (3 ratings) | Versions: 3 | Reviews: 2 | Comments: 0 | Citations: 0

Viewed: 165 times | Downloaded: 34 times

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Workflow Download CAS numbers and save as SD file (1)

Created: 15/10/09 @ 09:05:39

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Download molecules from a REST services using the CAS registry number, create 3D coordinates and save the results as a MDL SD file.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 88 times | Downloaded: 65 times

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Workflow Determine the Maximum Common SubStructure ... (1)

Created: 23/10/09 @ 12:01:42

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

BSL script to determine the maximum common substructure (MCSS) of a list of molecules and opens this in a JChemPaint editor.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 62 times | Downloaded: 47 times

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Workflow Kabsch Alignment of Small Molecules (1)

Created: 30/10/09 @ 22:12:57

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Aligns molecules using the Kabsch alignment and visualizes the results in the Jmol viewer.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 76 times | Downloaded: 48 times

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Workflow Convert a SMILES string into a connection ... (1)

Created: 16/12/09 @ 19:52:33

Credits: User

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Bioclipse script that converts a SMILES string into a LaTeX table of the connection table of the molecule.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 24 times | Downloaded: 26 times

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Workflow Download all data sets from a OpenTox API ... (3)

Created: 01/04/10 @ 12:20:18 | Last updated: 13/11/10 @ 13:53:22

Credits: User

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Uses the OpenTox API (REST+RDF) to query all data sets, downloads them as MDL SD file, and opens the results in the Bioclipse molecules table.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 28 times | Downloaded: 20 times

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Workflow Calculate molecular mass for entries in a ... (1)

Created: 08/03/10 @ 09:46:03

Credits: User

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Simple script to demonstrate how to iterate over entries in a MDL SD file and calculate some molecular property.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 20 times | Downloaded: 20 times

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Workflow Download QSAR data sets using the OpenTox ... (1)

Created: 22/03/10 @ 11:10:25

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Bioclipse script that uses the OpenTox API 1.1 to download all QSAR data sets from a given service.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 41 times | Downloaded: 37 times

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Workflow C1 Combined Workflow (1)

Created: 03/06/10 @ 11:26:48 | Last updated: 03/06/10 @ 11:30:10

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithms M1-M5 in one workflow, yielding a sparse matrix of matches annotated by match types.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 44 times | Downloaded: 33 times

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Workflow M1 Exact Matching (1)

Created: 03/06/10 @ 11:32:02

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M1 which matches fully specified molecules on the basis of their canonical representations.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 27 times | Downloaded: 26 times

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Workflow M2 Similarity Matching (1)

Created: 03/06/10 @ 11:33:36

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M2 which reads molecules from two sources and produces clusters of highly similar molecules.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 31 times | Downloaded: 35 times

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Workflow M3 Non-stereo Matching (1)

Created: 03/06/10 @ 11:35:03

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M3 which strips stereochemical information from molecules, performs exact matching, and restores stereochemistry.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 20 times | Downloaded: 30 times

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Workflow M4 Tautomer Matching (1)

Created: 03/06/10 @ 11:38:27

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M4 which generates canonical tautomers prior to matching, matches, then restores original structures.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 18 times | Downloaded: 21 times

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Workflow M5 Charge Matching (1)

Created: 03/06/10 @ 11:39:28

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. This workflow implements matching algorithm M5 which ionises molecules at pH 7 prior to matching, restores original structures.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 32 times | Downloaded: 23 times

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Workflow Generate inChi (1)

Created: 09/07/10 @ 10:06:35 | Last updated: 09/07/10 @ 10:08:37

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Generates an inChi string for a given chemical represented by its SMILES string, SDF or MOL file using the inchi web service provided by ChemSpider

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 29 times | Downloaded: 20 times

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Workflow Generate inChi information (1)

Created: 09/07/10 @ 10:22:29 | Last updated: 09/07/10 @ 10:23:47

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Uses the GenerateInchiInfo web service operation from ChemSpider to generate information relating to the InChi string for a given chemical compound

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 18 times | Downloaded: 24 times

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Workflow Generate InChi key (1)

Created: 09/07/10 @ 10:45:09 | Last updated: 09/07/10 @ 10:45:11

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Generates an inchi key for a given compound using the inchi web service provided by ChemSpider

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 20 times | Downloaded: 18 times

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Workflow InChi key to ChemSpider identifier (1)

Created: 09/07/10 @ 10:54:07 | Last updated: 09/07/10 @ 10:54:08

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns Converts an InChIKey to a ChemSpider ID

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 18 times | Downloaded: 17 times

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Workflow InChi key to Inchi string (1)

Created: 09/07/10 @ 10:58:54 | Last updated: 09/07/10 @ 11:00:16

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Converts an InChI key to an InChI string using the ChemSpider Inchi web service.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 11 times | Downloaded: 11 times

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Workflow InChi key to MOL file (1)

Created: 09/07/10 @ 11:05:11 | Last updated: 09/07/10 @ 11:05:13

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns a MOL file for a given InChi key

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 21 times | Downloaded: 25 times

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Workflow InChIToCSID (1)

Created: 09/07/10 @ 11:09:29 | Last updated: 09/07/10 @ 11:09:31

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Convert InChI to ChemSpider ID

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 10 times | Downloaded: 13 times

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Workflow InChIStringToInChiKey (1)

Created: 09/07/10 @ 11:12:58 | Last updated: 09/07/10 @ 11:23:55

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Converts an InChI string to an InChi key

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 8 times | Downloaded: 12 times

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Workflow InChIStringToMolFile (1)

Created: 09/07/10 @ 11:21:23 | Last updated: 09/07/10 @ 11:23:05

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Converts an InChI string into a MOL file using the Inchi ChemSpider web service

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 11 times | Downloaded: 11 times

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Workflow InchiStringToSmiles (1)

Created: 09/07/10 @ 11:38:59 | Last updated: 09/07/10 @ 11:39:01

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Converts an inchi string into SMILES format

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 15 times | Downloaded: 12 times

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Workflow isValidInChiKey (1)

Created: 09/07/10 @ 11:55:56 | Last updated: 09/07/10 @ 11:55:58

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Checks that specified argument is valid InChIKey. Works for v1.02b InChIKey only.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 12 times | Downloaded: 15 times

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Workflow MolToInchiString (1)

Created: 09/07/10 @ 12:01:45 | Last updated: 09/07/10 @ 12:01:47

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Converts a MOL file to InChI. Result is v1.02s InChI.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 9 times | Downloaded: 8 times

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Workflow MolToInchiKey (1)

Created: 09/07/10 @ 12:10:00 | Last updated: 09/07/10 @ 12:10:02

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Converts a MOL file to an InChIKey. Result is v1.02s InChIKey.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 11 times | Downloaded: 14 times

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Workflow SmilesToInchi (1)

Created: 09/07/10 @ 15:37:08 | Last updated: 09/07/10 @ 15:37:10

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Convert SMILES to InChI. Result is v1.02s InChI.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 10 times | Downloaded: 8 times

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Workflow Convert chemical identifier (1)

Created: 09/07/10 @ 15:45:53 | Last updated: 09/07/10 @ 15:46:31

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Converts a chemical compound identifier from one format to another using the open babel web service provided by ChemSpider

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 28 times | Downloaded: 14 times

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Workflow Get list of chemspider databases (1)

Created: 12/07/10 @ 09:53:38 | Last updated: 12/07/10 @ 09:53:40

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns a list of databases catalogedReturns a list of databases cataloged by ChemSpider

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 13 times | Downloaded: 15 times

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Workflow Get extended compound information (1)

Created: 12/07/10 @ 10:06:37 | Last updated: 12/07/10 @ 10:06:39

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns information from chemspider for a given chemical represented by its chemspider identifier

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 23 times | Downloaded: 19 times

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Workflow Get extended compound information for a li... (1)

Created: 12/07/10 @ 10:33:31 | Last updated: 12/07/10 @ 10:34:11

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Returns information for a given list of chemspider compound identifiers.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 19 times | Downloaded: 13 times

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Workflow Get ChemSpider record in MOL format (1)

Created: 12/07/10 @ 10:47:44 | Last updated: 12/07/10 @ 10:47:46

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns ChemSpider record in MOL format or empty string in case of failure.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 23 times | Downloaded: 13 times

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Workflow Get spectra information (1)

Created: 13/07/10 @ 09:32:27 | Last updated: 13/07/10 @ 09:32:28

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns information about the spectra stored in ChemSpider

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 24 times | Downloaded: 14 times

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Workflow Get compound spectra information (1)

Created: 13/07/10 @ 09:42:03 | Last updated: 13/07/10 @ 09:42:04

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns information about spectra stored in ChemSpider for a given compound represented by its chemspider identifier

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 15 times | Downloaded: 13 times

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Workflow Get spectrum information (1)

Created: 13/07/10 @ 09:48:50 | Last updated: 13/07/10 @ 09:48:51

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns information about a spectrum identified by its chemspider spectrum identifier

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 18 times | Downloaded: 8 times

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Workflow Asynchronous chemspider simple search (1)

Created: 13/07/10 @ 11:08:34 | Last updated: 13/07/10 @ 11:08:35

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Performs an asynchronous simple search on ChemSpider

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 23 times | Downloaded: 12 times

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Workflow Get compound information (1)

Created: 13/07/10 @ 11:17:08 | Last updated: 13/07/10 @ 11:17:09

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns information about a given compound represented by its chemspider id

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 15 times | Downloaded: 12 times

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Workflow Get compound thumbnail (1)

Created: 13/07/10 @ 11:29:03 | Last updated: 13/07/10 @ 11:29:04

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns a small image of the 2D structure of given chemical compound represented by its chemspider identifier

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 26 times | Downloaded: 10 times

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Workflow Get structure synonyms (1)

Created: 13/07/10 @ 11:38:56 | Last updated: 13/07/10 @ 11:38:57

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns synonyms for a given compound represented by a MOL fileReturns synonyms for a given compound

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 25 times | Downloaded: 13 times

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Workflow chemspider identifier to MOL format (1)

Created: 13/07/10 @ 13:52:02

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns the MOL file for a given compound represented by its chemspider identifier

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 36 times | Downloaded: 21 times

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Workflow getLiteEntity (1)

Created: 13/07/10 @ 14:14:52 | Last updated: 13/07/10 @ 14:14:53

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieves a list of "lite" entities containing only the ChEBI ASCII name and ChEBI identifier. The input parameters are a search string and a search category. If the search category is null then it will search under all fields. The search string accepts the wildcard character "*" and also unicode characters. You can get maximum results upto 5000 entries at a time.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 12 times | Downloaded: 10 times

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Workflow Asynchronous chemspider search by formula (1)

Created: 13/07/10 @ 14:15:41 | Last updated: 13/07/10 @ 14:16:17

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Performs an asynchronous search on ChemSpider by molecular formula

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 32 times | Downloaded: 14 times

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Workflow Get complete chebi entity (1)

Created: 13/07/10 @ 14:38:12 | Last updated: 13/07/10 @ 14:38:13

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns informations for a given compound represented by its chebi identifier

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 10 times | Downloaded: 11 times

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Workflow Get complete entity by list (1)

Created: 13/07/10 @ 14:44:02 | Last updated: 13/07/10 @ 14:47:57

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns information from the chebi database for a list of chebi identifiers

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 19 times | Downloaded: 13 times

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Workflow Get ontology parents (1)

Created: 13/07/10 @ 14:48:37 | Last updated: 13/07/10 @ 14:48:38

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieves the ontology parents of an entity including the relationship type, using the ChEBI identifier.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 10 times | Downloaded: 12 times

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Workflow Get ontology children (1)

Created: 13/07/10 @ 14:51:32 | Last updated: 13/07/10 @ 14:51:33

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieves the ontology children of an entity including the relationship type, using the ChEBI identifier.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 10 times | Downloaded: 12 times

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Workflow Search structures in ChEBI database (1)

Created: 13/07/10 @ 15:08:20 | Last updated: 13/07/10 @ 15:10:10

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Does a substructure, similarity or identity search using a structure in the Chebi database

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 26 times | Downloaded: 18 times

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Workflow Simple search (1)

Created: 13/07/10 @ 15:18:44 | Last updated: 13/07/10 @ 15:18:45

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Performs a lite search on ChemSpider

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 129 times | Downloaded: 13 times

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Workflow file-similarity-entrez-url (2)

Created: 16/07/10 @ 09:34:45 | Last updated: 16/07/10 @ 09:43:39

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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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Workflow smiles-identity-idlist (1)

Created: 16/07/10 @ 09:50:50 | Last updated: 16/07/10 @ 09:53:16

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Searches for similar structures in PubChem to an input SMILES string. This workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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Workflow smiles-identity-idlist (2)

Created: 16/07/10 @ 10:20:48 | Last updated: 16/07/10 @ 10:25:06

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Performs a search in Pubchem for compounds similar to an input compound represented in SMILES notation. This workflow is based on the original smiles-identity-idlist workflow written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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Workflow PubChem substructure search (2)

Created: 16/07/10 @ 10:31:51 | Last updated: 16/07/10 @ 10:52:28

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Search PubChem Compound for structures containing the one given by the structure key input, based on a user-selected level of chemical identity: connectivity only, match isotopes and/or stereo, etc. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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Workflow download (2)

Created: 16/07/10 @ 10:41:38 | Last updated: 16/07/10 @ 10:53:32

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Given a list key, prepare for download a file containing those records in the selected format. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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Workflow Predict chemical solubility in solvents (2)

Created: 04/08/10 @ 11:42:55 | Last updated: 04/08/10 @ 11:43:30

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Predicts solubility in molar units for a given chemical compound represented as a SMILES string in a given solvent. Uses a beanshell script to enable the user to select the solvent from a list.

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Workflow Predict Abraham descriptors (1)

Created: 05/08/10 @ 16:26:19 | Last updated: 05/08/10 @ 16:26:20

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Predicts descriptor values using a model derived from a linear regression analysis of the Open Notebook Science solubility data and literature values. The workflow returns all the Abraham descriptors E, S, A, B and V in a HTML file.Predicts descriptor values using a model derived from a linear regression analysis of the Open Notebook Science solubility data and literature values

Rating: 4.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Generate CombiUgi library (1)

Created: 10/08/10 @ 12:15:37 | Last updated: 10/08/10 @ 12:16:00

Credits: User Peter Li User Romney

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Generates a CombiUgi library using data from a Goolgle spreadsheet containing smiles strings of compounds to undergo virtual Ugi reactions

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Workflow Visualize the boiling point data from the ... (1)

Created: 10/08/10 @ 16:32:51 | Last updated: 10/08/10 @ 16:32:54

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Downloads the RDF data from a HTML page, extracts the boiling point data, calculates atom counts from SMILES representations, and opens the data in a matrix editor, ready to be visualized in a scatter plot.

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Workflow Calculate molecular descriptors with OpenT... (1)

Created: 30/10/10 @ 17:03:27 | Last updated: 30/10/10 @ 17:03:31

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Queries an OpenTox ontology server for available molecular descriptor, picks one, and calculates the descriptor value for a few molecules.

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Workflow Run OpenTox models on local data. (1)

Created: 13/11/10 @ 14:09:43 | Last updated: 13/11/10 @ 14:09:45

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Runs a remote OpenTox model to predict properties for local data which is uploaded on the fly.

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Viewed: 24 times | Downloaded: 11 times

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Workflow QSPR Model Discovery -- workflow structure... (2)

Created: 18/01/11 @ 18:13:17 | Last updated: 18/01/11 @ 18:24:36

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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replicates the structure of the QSPR model discovery workflow. Ref.: replicates the structure of the QSPR model discovery workflow. Ref.: http://www.openqsar.com/

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Workflow RDKit-pains (3)

Created: 07/02/11 @ 02:05:36 | Last updated: 08/08/11 @ 11:11:40

Credits: User sauberns

Attributions: Workflow Indigo-pains

License: Creative Commons Attribution 3.0 Unported License

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 If you like this workflow, please reference our paper doi:10.1002/minf.201100076, and check the related workflow Indigo-pains. Implementation of the PAINS filters[1] using the RDKit (1.0.0.0000763) nodes in KNIME (2.3.1). Original PAINS filters were published in SLN format. This workflow contains the SMARTS form of the filters published by the Guha group[2]. Also distributed with a 10k reference structure set from WEHI[1] which is used by default as input if no other file is chosen. T...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow Extract chemical structures from a Beilste... (1)

Created: 12/05/11 @ 07:54:39 | Last updated: 12/05/11 @ 07:54:41

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Uses the Oscar4 text mining tool to extract chemical structures from a Beilstein Journal of Organic Chemistry paper and visualizes them in the molecules table. Jericho is used to extract text from the paper's HTML page.

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

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

Credits: User Kalai User Michael Gerlich

Attributions: Workflow Download Entries from PubChem

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.  

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Workflow Indigo-pains (1)

Created: 07/06/11 @ 00:39:29 | Last updated: 08/08/11 @ 11:08:04

Credits: User sauberns

Attributions: Workflow RDKit-pains

License: Creative Commons Attribution 3.0 Unported License

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If you like this workflow, please reference our paper doi:10.1002/minf.201100076. Implementation of the PAINS filters[1] using the Indigo (1.0.0.0000951) nodes in KNIME (2.3.4). Original PAINS filters were published in SLN format. This workflow contains the SMARTS form of the filters published by the Guha group[2]. Also distributed with a 10k reference structure set from WEHI[1] which is used by default as input if no other file is chosen. The Indigo nodes require installation of the...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow RDKit-pains-parallel (1)

Created: 13/10/11 @ 02:33:12 | Last updated: 10/08/12 @ 04:56:57

Credits: User sauberns

Attributions: Workflow RDKit-pains

License: Creative Commons Attribution 3.0 Unported License

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 If you like this workflow, please reference our paper doi:10.1002/minf.201100076, and check the related workflow Indigo-pains. Implementation of the PAINS filters[1] using the RDKit (2.0.0.1088) nodes in KNIME (2.5.0). Parallel processing nodes added to take advantage of mutil-core processors. Original PAINS filters were published in SLN format. This workflow contains the SMARTS form of the filters published by the Guha group[2]. Also distributed with a 10k reference structure ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 43 times | Downloaded: 15 times

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Workflow RDKit-bioisosteres (1)

Created: 18/01/12 @ 03:42:13 | Last updated: 18/01/12 @ 22:42:28

Credits: User sauberns

Attributions: Workflow RDKit-pains

License: Creative Commons Attribution 3.0 Unported License

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Implementation of a simple bioisostere replacement workflow using the RDKit (2.0.0) nodes in KNIME (2.5.1). Includes short list of classical bioisostere replacements (not exhaustive), selectable by the functional group to be transformed. We added this control to the workflow as our own internal list of bioisostere replacements generated huge libraries for each structure fed into the workflow. The bioisostere replacement list is stored in a tab separated text file, so can be replaced...

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Packs (3)

Pack useful_for_sysmo


Created: 17/12/08 @ 12:31:48 | Last updated: 10/06/09 @ 09:43:20

These workflows have been collected as potentially useful protocols for the sysmo consortium

0 items in this pack

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Pack Mapping Metabolites for Metabolic Network Reconstruc...


Created: 03/06/10 @ 11:43:43 | Last updated: 03/06/10 @ 11:47:16

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. These problems include finding identical structures across sources, which is trivial, but also structures that differ due to idiosyncrasies of the sources or annotators. This includes charge differences, varying stereochemistry, tautomers, and so forth. Workflows in this pack allow sets of ...

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Pack Example PubChem, ChEBI and ChemSpider workflows


Created: 23/07/10 @ 11:13:09 | Last updated: 23/07/10 @ 11:21:05

This pack contains example pipelines showing how the PubChem, ChEBI and ChemSpider web services can be called from Taverna workflows. Descriptions of the operations found in the PubChem, ChEBI and ChemSpider web services are available at http://www.taverna.org.uk/introduction/related-projects/chemtaverna/chemistry-web-services. 

0 items in this pack

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