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

Triplify search results from KEGG bfind SO... (3)

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This workflow use KEGG's SOAP service provided to do a BFIND serch within one of the KEGG's official database. The results are returned in RDF ntriples format. 

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

Credits: Francois Belleau

Triplify search results from all KEGG data... (3)

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Search all KEGG databases using bfind SOAP service and merge results into a bmuri list and a ntriples string. 

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

Credits: Francois Belleau

Triplify namespace list from global search... (1)

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

Credits: Francois Belleau

Get Kegg Pathway information (1)

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This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. Example input: path:mmu04010 path:mmu05014

Created: 2010-03-10 | Last updated: 2010-03-10

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

Compare genome, extract proteins which are... (1)

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  Takes GI number for source (non-pathogenic) and target (pathogneic) genomes, extracts list of all proteins from each genome using GenBank database. Outputs prtoeins in FastA format. Creates database from source proteins using formatdb (locally installed) and blasts (local installed) proteins from target against this database. Extracts protens which are unique (no blast hits) to the target (pathogenic) genome based on eValue set by user. Takes unique proteins from target and blasts aga...

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

Credits: Ian Laycock nclteamc

Attributions: fetchEnsemblSeqsAndBlast NCBI Gi to Kegg Pathways color_pathway_by_objects

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

NCBI Gi to Kegg Pathways (1)

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User inputs background and foreground colour to be used to highlight proteins in KEGG pathway image. User provides NCBI GI numbers. Worflow calculates KEGG ID and pathway ID and sends value to colour service, which adds colour to that KEGG id on pathway image. Also outputs kegg description, pathway description and url of image.

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

Credits: Ian Laycock nclteamc

Attributions: color_pathway_by_objects NCBI Gi to Kegg Pathways

Entrez Gene to KEGG Pathway (2)

This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

Created: 2010-04-15 | Last updated: 2010-04-15

Credits: Paul Fisher