Workflows

Triplify KEGG database list [myexperiments... (2)

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TAG: knowledgescope, kegg, bio2rdf, banff_manifesto, rdf

Created: 2009-11-28 | Last updated: 2009-11-30

Credits: Francois Belleau

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

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

Kegg_DrugID (1)

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 This workflow accepts looks up drug identifiers from KEGG given a pathway identifier. You can enter a pathway ID in the form path:map07026

Created: 2009-03-18 | Last updated: 2009-03-18

Credits: Rory

get_elements_by_pathway (1)

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Retrieve all objects on specified pathway get_elements_by_pathway Input example: path:bsu00010

Created: 2008-10-08

Credits: Franck Tanoh

get_element_relations_by_pathway (1)

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Retrieve all objects and relations on specified pathway Input example: path:bsu00010

Created: 2008-10-08

Credits: Franck Tanoh

get_drugs_by_pathways (1)

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Retrieves all drugs on the specified pathway. input example: path:map07025 ; path:eco00020

Created: 2008-10-07

Credits: Franck Tanoh

color_pathway_by_elements (2)

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Color the objects (rectangles and circles on a pathway map) corresponding to the given 'element_id_list' with the specified colors and return the URL of the colored image. Example of inputs: pathway_id: path:bsu00010 element_list: (to add as list) 78 79 fg_color_list:(to add as list) red blue bg_color_list: (to add as list) green yellow

Created: 2008-09-30 | Last updated: 2008-10-01

Credits: Franck Tanoh

KEGG pathway analysis (1)

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The KEGG pathway analysis of the workflow takes a list of UniProt accession numbers in any of the following formats with the following prefixes: External database Database prefix ----------------- --------------- NCBI GI ncbi-gi: NCBI GeneID ncbi-geneid: GenBank genbank: UniGene unigene: UniProt uniprot: It performs this using the web service bconv, provided by the KEGG database (Kanehisa et al., 2010), described in the KEGG API available at: http://www.genome.jp/kegg/docs/keggapi...

Created: 2010-03-19

Credits: Baywatch Solutions

Kegg pathway diagrams (missing part 3) (2)

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Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram. Colour all enzyme boxes with colours specified. This workflow still has one problem. The list of colours have to be specified. I would like ideally to only except one background and one foreground colour and expand that to a list with length equivalent to the number of enzymes found - just duplicating the specified colours. However with almost no Taverna documentation to speak of, none of...

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Gregg Iceton