Workflows

Get complete chebi entity (1)

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Returns informations for a given compound represented by its chebi identifier

Created: 2010-07-13 | Last updated: 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

getLiteEntity (1)

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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.

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

Spreadsheed Data Import Example (1)

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date. The source data is from http://data.gov.uk/

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

Credits: David Withers

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

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

Spreadsheet Import Example (1)

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date. The source data is from http://data.gov.uk/

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

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

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 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

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 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 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 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 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 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

Tag Metadata (2)

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

Credits: David De Roure

Similar Workflows (1)

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Created: 2010-07-09

Credits: David De Roure David R Newman Danius Michaelides

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

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

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

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

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

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

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

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

InChIToCSID (1)

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Convert InChI to ChemSpider ID

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

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 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

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

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

EBI_InterProScan for Taverna 2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2010-07-08 | Last updated: 2010-07-08

Credits: Benb

EBI_InterProScan for Taverna 2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2010-07-08 | Last updated: 2010-07-08

Credits: Benb

Who is Dr Labrie according to Pubmed publi... (2)

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To use this wokflow you need to import services from To use this wokflow you need to import services from http://proxy.bio2rdf.org/bio2rdf/services.txt you can explore the loaded data at http://proxy.bio2rdf.org/fct

Created: 2010-07-08 | Last updated: 2010-07-08

Credits: Francois Belleau

AlitoraKDAInputModule test workflow (1)

 This workflow calls the AlitoraKDAInputModule service from the test GenePattern server.

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

Credits: Peter Li

Pivoting with Consideration of Example Wei... (1)

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This process shows how the Pivoting operator can also consider example weights encoded by a special attribute with the role 'weight'. The first operators only create a demo data set for this purpose, the actual pivoting is performed by the last operator only. I recommend to place a breakpoint before the Pivoting and check the data (structure) in order to see how the Pivoting handles the weights.

Created: 2010-07-07

CTF - MEG Event Averager (1)

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This workflow applies parametrs in a user-specified processing.cfg file to a set of MEG data files. The datasets must be in CTF-format, such as those produced by Omega275 systems. The processing.cfg file and datasets are selected at the initialization of the workflow.  processing.cfg can be created by the data inspection tool DataEditor, and contains desired filter settings etc. This file can also be edited easily with a text editor to tweak settings. The workflow identifies all the trig...

Created: 2010-07-06 | Last updated: 2010-07-06

Credits: Lakelander

A template example workflow using U-Compar... (2)

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An example workflow using the U-Compare text mining system inside embedded. Users can easily make their own workflow with U-Compare reusing this workflow. This workflow retrieves abstract texts from Pubmed with user specified query, inputs the texts to U-Compare, interprets the output of U-Compare. You have to download and store the UIMA CPE XML descriptor file (StdinPPIExtraction-CPE-EventMine.xml) to run the default setting, which runs a event extraction text mining workflow by U-Compare. S...

Created: 2010-07-05 | Last updated: 2010-09-02

Credits: Yoshinobu Kano

Phenotype to pubmed (3)

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This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

Created: 2010-07-05 | Last updated: 2011-01-11

Credits: Paul Fisher

Gene to Pubmed (3)

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This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2010-07-05 | Last updated: 2011-01-26

Credits: Paul Fisher

Perfrom a text based search through PubMed (1)

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This workflow takes in a number of search terms in which to perform a search over the PubMed literature database. These search terms may be input as if entered in the web based version of PubMed. The output from this workflow is a list of PubMed identifiers in xml based format

Created: 2010-07-05 | Last updated: 2010-07-05

Credits: Paul Fisher

Retrieve sequence in EMBL format (1)

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This workflow retrieves a sequence associated with its features in embl format

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Franck Tanoh

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Ian Dunlop Stian Soiland-Reyes

GBSeq test (1)

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Franck Tanoh

Fetch today's xkcd comic (1)

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Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn Stian Soiland-Reyes

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn

EBI_InterProScan for Taverna 2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Alan Williams