Workflows in this Topic

Retrieve SNPs from regions around known genes (1)

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Given a list of Gene IDs this workflow will query against the Ensembl human genome data to fetch the genomic region for each gene, extend that region by 1000bp in each direction and use this set of ranges, one per gene, to build a query against dbSNP to return the SNP identifier and location information (chromosome name, strand and position)

Created: 2007-11-07

Download from ChemSpider using Accurate Mass (2)

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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

getUPIForSequence workflow (2)

Given a sequence retrieve the UPI (UniProt Archive (UniParc)) identifier.

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

Credits: Franck Tanoh

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

Identification of differential genes using... (1)

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This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data which are then analysed by the LIMMA Bioconductor package in an R script. This produces a list of significant differentially expressed genes which is then analysed using the Go Term Finder tool to generate a PDF report of the common GO terms associated with the genes. A CSV file containing the list of sign...

Created: 2008-07-02 | Last updated: 2008-07-02

Credits: Peter Li

unnested_qtl_pathway_3.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

unnested_qtl_pathway_2.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

geneId_to_pathway.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

blast_simplifier.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

add_ncbi_to_string.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Gi_to_pathway.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

parse_swiss.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

geneHunt.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

ensembl_gene_info.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

parse_gene_info.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

ensembl_genes_to_go_terms.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

parse_uniprot_2.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

gene_ontology_analysis_2.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

gene_ontology_analysis.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

complete_2_text_mining.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

sub_gene_info_to_uniprot.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

complete_3.1.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

extract_uniprot_embl_gi.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

maxdBrowse_geneHunt.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Probeset_id_2_Swissport_id.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

text_mining.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

complete_2.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

remove_nulls.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

linking.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

lister.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Ensembl_id_2_Swissport_id.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

parse_uniprot.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

complete.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

complete_deleted.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

maxdBrowse.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

remove_duplicates_full.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

remove_duplicates.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

complete_test.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

qtl_analysis.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

uniprot_search.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

interpro_scan.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

interpro_url.xml (1)

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An example of how a more complex workflow can federate multiple resources to perform data mining. In this case a single input data item in the form of a probe set identifier is cross referenced to data sets in multiple locations to answer a kind of 'show me everything about this data' question.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

parse_sequence.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

swiss_and_name_seq.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

swiss_and_name.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

expression_values.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

parse_gene_name.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

metabolic_pathway.xml (1)

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A list of Kegg entires are supplied to the Kegg database which then retrieves the associated metabolic pathways for each entry supplied. e.g. Ids takes in a value of 351, whilst abbr takes in a value of hsa. Thus hsa:351 corresponds to neurodegenerative disorders and alzheimers disease pathways. [fisherp@cs.man.ac.uk]

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

ACC_to_GI.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Ensembl_genes_to_swiss_id.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

string_complete.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

gene_info_to_gene_name.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

SUB_genes_info_names.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

bind-idsearch.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

bind-text.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

genes_from_probesets.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

probeset_in_qtl.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

database_and_genes.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

protein_protein_interactions.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

gene_by_species.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

blast_GO.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

BlastComparer.xml (1)

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Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers. N.B. this workflow does not function correctly as it is designed for use with NCBI blast scripts. Some errors may occur. Please use two blast text file inputs for a secure result output.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

stringList.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

maxdBrowse_strings.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

getgenesbyspecies.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

gene_ontology_diagram.xml (1)

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This workflow builds up a subgraph of the Gene Ontology (http://www.geneontology.org) to show the context for a supplied term or terms. It shows this context by colouring all ancestors of the term, all children and all siblings. By default, ancestors of the supplied term or terms are coloured orange, siblings purple and direct children teal. Other terms appear in the default wheat colour.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

affy_ids.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

example.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

metabolic.xml (1)

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An example of how a more complex workflow can federate multiple resources to perform data mining. In this case a single input data item in the form of a probe set identifier is cross referenced to data sets in multiple locations to answer a kind of 'show me everything about this data' question.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

interpro_scan_3.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

interpro_scan_2.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

genomic_sequence.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

linking3.xml (1)

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This workflow links between a specified EMBL accesion number to corresponding identifiers in the MEDLINE database.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

protein2dna.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

blast_to_fasta.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

blast.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

DDBJ_BLAST.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

AffyidToGeneAnnotationnoGOIDandPepstats.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Peter Li

simple_xcms_pipeline (1)

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A (very) simple demo pipeline that takes an experiment ID, gets the data from the (currently in beta) metware metabolomics datawarehouse and runs XCMS.

Created: 2008-07-14 | Last updated: 2008-07-14

Credits: Markf

bfind (1)

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Used for searching entries by keywords. User needs to specify a database from those which are supported by DBGET system before keywords. List of databases available at : http://www.genome.jp/dbget/ Example of input parameter: gb E-cadherin human

Created: 2008-09-29 | Last updated: 2008-09-29

Credits: Franck Tanoh

bget (1)

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Retrieve database entries specified by a list of entry_id. Number of entry_id retrieves at a time is restricted up to 100 Example of input: eco:b0002 hin:tRNA-Cys-1

Created: 2008-09-29

Credits: Franck Tanoh

get_best_best_neighbors_by_gene (1)

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Search the best-best neighbor of a gene in all organisms. Example of input: gene_id: eco:b0002 offset: 1 limit: 10

Created: 2008-10-02

Credits: Franck Tanoh

get_compounds_by_pathway (1)

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Retrieves all compounds on the specified pathway Example of input: path:eco00020

Created: 2008-10-07

Credits: Franck Tanoh

get_compounds_by_reaction (1)

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Retrieve all compounds which have a link to a given reaction_id Example on input: rn:R00100

Created: 2008-10-07

Credits: Franck Tanoh

Monitoring the formation of an imine (1)

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Created: 2008-10-21

Credits: Danius Michaelides UsefulChem

To monitor the reaction of the imine forme... (1)

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Created: 2008-10-21

Credits: Danius Michaelides UsefulChem

Isolating the "demethylated" product of th... (1)

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Created: 2008-10-21

Credits: Danius Michaelides UsefulChem

Isolating the free amines of Ugi products ... (1)

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Created: 2008-10-21 | Last updated: 2008-10-21

Credits: Danius Michaelides UsefulChem

Ugi Reactions in Eppendorf tubes (1)

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Created: 2008-10-21

Credits: Danius Michaelides UsefulChem

XSL Transform (1)

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This WF downloads a web page and converts the content from HTML to XSL.

Created: 2008-10-21

Credits: Trident

Make 28 CPUh load on the Grid (1)

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This workflow makes 28 CPU hours load on a Grid. Therefore it calls 100 times (represented by 100 input tokens) the program "makeload", which makes 1000 Seconds load each. The processing is done recurrent, so you can use this workflow to benchmark the speedup of your Grid environment, or just to heat up your computer center... This workflow also serves as an example of a typical parameter study modeled with GWorkflowDL. Of cause this workflow can only be invoked with a X509 certif...

Created: 2008-11-25 | Last updated: 2008-12-17

Credits: Andreas Hoheisel

Create Ugi Library 001 (1)

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Created: 2008-12-04

Credits: Jean-Claude Bradley

Run XMPP cloud services. (2)

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Basic workflow indicating how a XMPP service can be called with XML input and output. Source code for the activity is available from: github.com/egonw/xws-taverna/tree/master That page explains you how to install the plugin you must install on top of Taverna 2.0. The workflow will not work otherwise.

Created: 2009-04-25 | Last updated: 2010-03-22

Credits: Egon Willighagen

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

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

Retrieve Pathways and Compound information... (1)

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Given a KEGG compound identifier (e.g. cpd:C00905), this workflow queries KEGG DB for pathways and compound information for each of these compounds. As the KEGG pathway service tries to find pathways which contain all input compounds, the input list is split up to circumvent this behaviour and to search for only one compound in a pathway at a time. Compounds identified in pathways are marked as red in the resulting pathway image.

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

Credits: Michael Gerlich

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

Search InChI in NCBI eSearch (pccompound) (1)

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This workflow takes in a search term (e.g. InChI) for search in PubChem pccompound database. The result is an xml file containing summary information about the search term and also a compound image and the compound webpage fetched from Pubchem.

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

inchi to Chebi (1)

This workflow converts an inchi string to a chebi id.

Created: 2009-05-22

Credits: Paul Fisher

getSynonymsFromSBML (1)

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This service takes an SBML file (for example from the Biomodels database) and extracts synonyms for each of the SBML species in the file, using ChEBI. Service is written and maintained by Neil Swainston at the MCISB.

Created: 2009-06-09 | Last updated: 2009-06-09

Credits: Duncan Hull

getOntologyTerm (1)

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This service takes a MIRIAM compliant URI and looks up all the synonyms for that URI using ChEBI and other services. Service developed and maintained by Neil Swainston at the MCISB in Manchester.

Created: 2009-06-09 | Last updated: 2009-06-09

Credits: Duncan Hull

getTimololFromMassBank (1)

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This workflow will retrieve a peaklist from a fixed entry (Timolol) from the MassBank spectral library. Note, the API is still in alpha, as of 10.11.2009.  

Created: 2009-11-10 | Last updated: 2009-11-10

Credits: http://sneumann.pip.verisignlabs.com/

Query DBPedia for all entries with an InChI (1)

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Created: 2009-11-20

Credits: Egon Willighagen

In-silico Fragmentation of Naringenin (2)

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Created: 2010-02-08

Credits: http://sneumann.pip.verisignlabs.com/

Taverna Tutorial2 (1)

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No description

Created: 2010-02-26 | Last updated: 2010-02-26

Credits: Rodriguez

Attributions: EBI_InterProScan for Taverna 2

OpenTox Get Algorithms on TUM server (6)

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Get URIs of all available algorithms on TUM server

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

OpenTox Apply Model On Dataset (3)

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Apply a model to predict a dataset

Created: 2010-05-11 | Last updated: 2010-05-11

Calculating frequencies of gene expression... (1)

This workflow retrieves data from the MaxD microarray database and calculates the frequencies of gene expression levels using an R script

Created: 2010-03-15

Credits: Peter Li

[untitled] (1)

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No description

Created: 2010-03-16

Credits: Paul Fisher

microRNA to KEGG Pathways and Abstracts (1)

Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs

Created: 2010-03-17

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

Run MGCAT for Global Sequence Comparison (1)

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Runs the M-GCAT tool for Global Sequence Comparison. M-GCAT: http://alggen.lsi.upc.es/recerca/align/mgcat/ intro-mgcat.html

Created: 2010-03-19

Credits: Baywatch Solutions

Construction of skeleton SBML model using ... (1)

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This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given subsystem term.

Created: 2010-03-26 | Last updated: 2010-03-26

Credits: Peter Li

DPAS general query with sorted field (1)

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same as DPAS general query. Calling the DPAS sortedQuery web service. additional input: partialSorting input boolean true or false false all result entries are sorted by start measurementTime true each request is sorted by measurement time; no overall time order, but queries stay in the order they there asked.

Created: 2010-04-19 | Last updated: 2010-04-19

Credits: Anja Le Blanc

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

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

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 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 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

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

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

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

Get ontology parents (1)

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

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

Credits: Peter Li

Get ontology children (1)

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

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

Credits: Peter Li

Search structures in ChEBI database (1)

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

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

file-similarity-entrez-url (2)

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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/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

smiles-identity-idlist (1)

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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/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

smiles-identity-idlist (2)

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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/).

Created: 2010-07-16 | Last updated: 2010-07-16

PubChem substructure search (2)

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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/).

Created: 2010-07-16 | Last updated: 2010-07-16

download (2)

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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/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

Predict chemical solubility in solvents (2)

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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.

Created: 2010-08-04 | Last updated: 2010-08-04

Credits: Peter Li

Create an OpenTox API dataset and add mole... (2)

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 Bioclipse script that creates a data set  at an OpenTox API capable server, and adds molecules to it.

Created: 2010-08-04 | Last updated: 2010-11-13

Credits: Egon Willighagen

Predict Abraham descriptors (1)

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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

Created: 2010-08-05 | Last updated: 2010-08-05

Credits: Peter Li

Generate CombiUgi library (1)

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

Created: 2010-08-10 | Last updated: 2010-08-10

Credits: Peter Li Romney

gene and voice on the complete text (1)

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Created: 2011-02-05 | Last updated: 2011-02-05

Credits: Shivamuniraj0

ADR-S (2)

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  The ADR-S pathway seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are pr...

Created: 2011-03-28 | Last updated: 2011-08-09

Credits: Anna Bauer-Mehren

CGR from multiple fasta files (1)

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 The workflow generates Chaos Game Represenations (CGR) image from multiple fasta files. See http://www.g-language.org/wiki/cgr for more information about the Chaos Game Representations.

Created: 2011-04-29 | Last updated: 2011-04-29

Credits: cory (Kazuki Oshita)

External Tool: Numerically adding two valu... (1)

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The workflow is an examples for the External Tools / UseCase plugin to integrate external tools. It wraps the "bc" command line calculator. Internally, it executes the following script: if [ ! -r "$1" ]; then echo "Cannot read file indicated by first argument '$1'." ; exit -1 ; fi ; if [ ! -r "$2" ];then echo "Cannot read file indicated by second argument '$1'." ; exit -1 ; fi if [ -x /usr/bin/bc ]; then ...

Created: 2011-05-06 | Last updated: 2011-05-06

Credits: Steffen Möller

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

Get Molecular Interactions from a PSICQUIC... (3)

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Check the different iput parameter you could use for this workflow in ... http://code.google.com/p/psicquic/wiki/RestAccess Check available PSICQUIC Services in ... http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS More about PSICQUIC ... http://code.google.com/p/psicquic/

Created: 2011-07-22 | Last updated: 2013-07-10

Credits: Rafael C. Jimenez

OpenTox Upload and merge data sets (1)

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Uploads 2 data sets to OpenTox, merges them and returns the merged data set.

Created: 2011-08-08 | Last updated: 2011-08-08

Split string into string list, new line se... (1)

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Split string into string list using new line as separator. Should work in Linux, Mac and Windows.

Created: 2011-08-15 | Last updated: 2014-02-26

Credits: Rafael C. Jimenez

String input for Kepler (1)

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This Kepler workflow allows one to display multiple strings together with the use of a display actor with its input multiport.  The result is each string output on a line, but all together.

Created: 2011-09-27 | Last updated: 2011-09-27

Credits: Wdsnellg

Calculate edit distance based on words (1)

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 Calculate the word based edit distance between a scan of an OCR image and its ground truth.

Created: 2011-11-14 | Last updated: 2011-11-14

Credits: perdalum

dcraw (NoConversion, NoInterpretation, Fix... (4)

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Reads a RAW image with these parameters using dcraw and returns the image data as byte array.

Created: 2011-12-08 | Last updated: 2011-12-16

dcraw (sRGB, ColorInterpolated, FixedWhite... (2)

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Reads a RAW image with these parameters using dcraw and returns the image data as byte array.

Created: 2011-12-08 | Last updated: 2011-12-16

dcraw (sRGB, ColorInterpolated, FixedWhite... (2)

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Reads a RAW image with these parameters using dcraw and returns the image data as byte array.

Created: 2011-12-08 | Last updated: 2011-12-16

getFirstElementDFS (2)

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Returns the first element of a nested list using depth first search. The maximum depth of the input is set to 2. You can savely increase this by increasing the depth of the workflow input port and the beanshell input port. Taverna will wrap the input into a list with correct depth. However this will create a little overhead.

Created: 2012-01-13 | Last updated: 2012-02-13

Render gene via BioGPS (2)

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This workflow uses the REST API of BioGPS to list the plugins and then allow the user to select which plugin to use to display the input gene id

Created: 2012-02-10 | Last updated: 2012-02-15

Credits: Alan Williams

Get image mimetype (1)

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Returns the mimetype of an image.

Created: 2012-02-21 | Last updated: 2012-02-21

Credits: Markus Plangg

RAWverna Image evaluation - Read images (R... (1)

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Reads images for evaluation by RAWverna. The read parameters depend on the type of the images.

Created: 2012-02-21 | Last updated: 2012-02-21

Credits: Markus Plangg

RAWverna Image evaluation - Read Image (RAW) (1)

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Reads an image from the given path using dcraw for image comparison.

Created: 2012-02-21 | Last updated: 2012-02-21

Credits: Markus Plangg

RAWverna image evaluation - Read images (RAW) (1)

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Reads RAW images for evaluation by RAWverna.

Created: 2012-02-21

Credits: Markus Plangg

RAWverna Image Evaluator - Evaluate Equals (1)

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Takes two images as byte array and compares them for equality using the RAWverna Image Evaluator.

Created: 2012-02-21 | Last updated: 2012-02-21

Credits: Markus Plangg

RAWverna Image Evaluator - Evaluate relative (1)

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Takes two images as byte array and compares them using the RAWverna Image Evaluator.

Created: 2012-02-21 | Last updated: 2012-02-21

Credits: Markus Plangg

Image QA (RAW/NonRAW, Ssim, Equals) (1)

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Reads images either by reading the file directly or using dcraw depending on the image mimetype. Then runs QA algorithms to compare the images.

Created: 2012-02-27 | Last updated: 2012-02-27

Credits: Markus Plangg

Render gene via BioGPS (3)

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This workflow uses the REST API of BioGPS to list the plugins and then allow the user to select which plugin to use to display the input gene id

Created: 2012-04-05 | Last updated: 2012-05-23

Credits: Alan Williams

ICDAR 2011 End-to-End Applications contest... (1)

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Full workflow for use with the DAE platform and as used for the ICDAR 2011 "Document Analysis Algorithm Contributions in End-to-End Applications" contest, including contributed algorithms.

Created: 2012-04-14 | Last updated: 2012-04-14

Credits: Bart Lamiroy

Convert table to CDS format (1)

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It converts a csv file (comma separated values) to the CDS format. It also provides relevant information to create the ReadMe file. The first row in the input file must be the column names. If you want to run this workflow, you have to install astrotaverna plugin. You can easyly cusomize the workflow to provide a votable or fits table as input.

Created: 2012-05-28 | Last updated: 2012-05-28

Credits: Julian Garrido

List Concept Sets (3)

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Pupose: The workflow returns a list of all Concept Set IDs currently available in the database. The Concept Sets have an hierarchical structure that can be inferred by referring to the parent Concept Set ID.

Created: 2012-07-06 | Last updated: 2014-07-14

Credits: Kristina Hettne Marco Roos Reinout van Schouwen Martijn Schuemie BioSemantics