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Smiles Search of ChemSpider

Created: 2008-02-27 16:21:30 | Last updated: 2012-01-12 21:12:15

Credits: Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

Comments: 0 | Viewed: 510 times | Downloaded: 238 times

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Example PubChem, ChEBI and ChemSpider workflows

Created: 2010-07-23 11:13:09 | Last updated: 2010-07-23 11:21:05

40 items in this pack

Comments: 0 | Viewed: 109 times | Downloaded: 33 times

Download from ChemSpider using Accurate Mass (2)

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No description

Created: 2007-11-26 | Last updated: 2008-02-05

Credits: Egon Willighagen

getInchIfromMassBankPeaklist_ChemSpider_wo... (2)

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uses InChI's retrieved from a MassBank peaklist query to get compound information about those compounds via querying ChemSpider for information and displaying those results with image

Created: 2008-06-05 | Last updated: 2008-06-16

Credits: Michael Gerlich

Download from ChemSpider using Accurate Ma... (1)

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updated version of Download from ChemSpider using Accurate Mass to make use of the new ChemSpider services

Created: 2008-06-11 | Last updated: 2008-06-11

Credits: Michael Gerlich Egon Willighagen

Attributions: Download from ChemSpider using Accurate Mass

Demo of ChemSpider InChi to SMILES webserv... (1)

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Created: 2009-03-28 | Last updated: 2009-03-28

Credits: David De Roure

Search InChI in ChemSpider (1)

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This workflows queries ChemSpider for compound information and compound images. Note that a Chemspider security token is needed in order to access some of the ChemSpider services (receive one by registering at ChemSpider). Possible search terms might be InChI codes, ChemSpider identifiers or names.

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

Credits: Michael Gerlich

MassBank to KEGG (1)

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: Michael Gerlich

Resolve an InChIKey on ChemSpider (1)

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 Resolves an InChIKey on ChemSpider and opens the search results in a molecules table.

Created: 2010-06-23 | Last updated: 2010-06-23

Credits: Egon Willighagen

Generate inChi information (1)

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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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

Generate inChi (1)

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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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

Generate InChi key (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChi key to ChemSpider identifier (1)

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Returns Converts an InChIKey to a ChemSpider ID

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChi key to Inchi string (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChi key to MOL file (1)

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Returns a MOL file for a given InChi key

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChIToCSID (1)

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Convert InChI to ChemSpider ID

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChIStringToInChiKey (1)

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Converts an InChI string to an InChi key

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChIStringToMolFile (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InchiStringToSmiles (1)

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Converts an inchi string into SMILES format

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

isValidInChiKey (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

MolToInchiString (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

MolToInchiKey (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

SmilesToInchi (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

Convert chemical identifier (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

Get list of chemspider databases (1)

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

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: Peter Li

Get extended compound information (1)

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

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: Peter Li

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

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 Returns information for a given list of chemspider compound identifiers.

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: Peter Li

Get ChemSpider record in MOL format (1)

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

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: Peter Li

Get spectra information (1)

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Returns information about the spectra stored in ChemSpider

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get compound spectra information (1)

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

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get spectrum information (1)

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Returns information about a spectrum identified by its chemspider spectrum identifier

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Asynchronous chemspider simple search (1)

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Performs an asynchronous simple search on ChemSpider

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get compound information (1)

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Returns information about a given compound represented by its chemspider id

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get compound thumbnail (1)

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

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get structure synonyms (1)

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

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

chemspider identifier to MOL format (1)

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

Created: 2010-07-13

Credits: Peter Li

Asynchronous chemspider search by formula (1)

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Performs an asynchronous search on ChemSpider by molecular formula

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Simple search (1)

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Performs a lite search on ChemSpider

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

List all sources from which metabolite ide... (1)

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 List all sources from which metabolite identifiers are used, sorted by use.

Created: 2013-03-08

Credits: Egon Willighagen

Text-mining using OSCAR to obtain a list o... (1)

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This service extracts chemical names from text and obtains identifiers for these names. It outputs a HTML string that can be opened in a browser providing a table of information and links to ChemSpider.Known issues - Character limit ~3000 - Unable to produce InChIs or CSID for some names - Error sometimes encountered when a trivial and systematic name for the same compound are used - Some issues with identifiers being recognised but not able to be processedrequires access ...

Created: 2013-04-18

Credits: Michael Smith Mark Borkum

Attributions: InChIToCSID

From molecule name to SMILE and InchI usin... (2)

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Created: 2013-05-21 | Last updated: 2013-05-21

Credits: Luna De Ferrari

Clustering of Molecular Compounds with Bio... (4)

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This workflow downloads an input set of molecular compounds in SMILES format, using Chemspider service. The most frequent molecular fragments are extracted by means of MoSS tool (see http://www.borgelt.net/moss.html) , in order to obtain a set of features for each compound. Then a clustering and a visual exploration of the input dataset is performed by BioDICE service (see http://biolab.pa.icar.cnr.it/biodice.html), implementing Fast Learning Self-Organized Map (FLSOM) algorithm. Finally the ...

Created: 2013-05-29 | Last updated: 2014-01-09

Credits: Antonino Fiannaca Massimo La Rosa

Attributions: Get compound information Simple search

Find Labels in WikiPathways that are IUPAC... (1)

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This scripts parses a directory with WikiPathways GPML files. For each "label" it checks if the label contains an IUPAC name (using OPSIN), calculated the InChIKey (using JNI-InChI/CDK), and looks up a ChemSpider identifiers (using the ChemSpider web service).

Created: 2013-08-20

Credits: Egon Willighagen

Finding nodes in Anopheles gambiae pathway... (1)

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Groovy script to find Anopheles g. metabolites encoded as GPML <Label> with OPSIN and provide ChemSpider identifiers.

Created: 2014-08-24

Credits: Egon Willighagen

Attributions: Extracts metabolites from GPML pathway files downloaded from WikiPathways

Finding nodes in Homo sapiens pathways wit... (1)

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Groovy script to find Homo sapiens metabolites encoded as GPML <Label> with OPSIN and provide ChemSpider identifiers. The results are stored in a report file.

Created: 2014-09-01

Credits: Egon Willighagen

Attributions: Finding nodes in Anopheles gambiae pathways with IUPAC names

Chemical2URIs (1)

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This workflow will map a chemical name or identifier to uniform resource identifiers (URIs). First the ChemSpider web service is used to map the chemical name to a ChemSpider identifier, then the ChemSpider identifier is mapped to URIs via the Open PHACTS platform.

Created: 2015-08-18

Credits: Kristina Hettne Eelke van der Horst BioSemantics