Workflows

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

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 a...

Created: 2010-03-19

Credits: Baywatch Solutions

Kegg pathway diagrams (1)

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Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.for each protein draw a diagram of the Kegg pathway that its protein is involved in and where available visualise the structures

Created: 2010-03-13

Credits: Jannetta

get_enzymes_by_compound (1)

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Retrieve all enzymes which have a link to a given compound id Input example: cpd:C00345

Created: 2008-10-08

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

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_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

btit (1)

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Retrieve definitions of given database entries available on GenomeNet database. Example of input: hsa:1798 mmu:13478

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

Credits: Franck Tanoh

binfo (1)

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Show the version information of a specificied database.  Example of input: "gb"  for Genbank database "sp" for swissprot database "emb" for embl database

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

Credits: Franck Tanoh