Workflows

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 list of yeast enzymes ORF numbers

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

Credits: Peter Li

Kegg pathway diagrams (3)

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Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.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 - ...

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

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

Rank Phenotype Terms (1)

This workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated. The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ...

Created: 2009-08-10

Credits: Paul Fisher

GWAS to biomedical concept (3)

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Genome-Wide Association studies (GWAS) with metabolomic phenotypes yield several statistically significant SNP-metabolite associations. To understand the biological basis of the association, scientists typically dwell on identifying genes in the vicinity of the SNP and the possible pathways that the gene participates in. The information needed to arrive at an understanding of the mechanistic basis of the association requires integration of disparate data sources. The purpose of this workflow ...

Created: 2013-04-15 | Last updated: 2014-07-14

Credits: Kristina Hettne Harish Dharuri Marco Roos Reinout van Schouwen

UnigeneID to KEGG Pathways (3)

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This workflow accepts a list of Unigene gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in (plus pathway image) from the KEGG database. This workflow replaces the earlier SOAP version with the new KEGG REST services

Created: 2012-01-16 | Last updated: 2012-12-17

Credits: Katy Wolstencroft Paul Fisher

Attributions: NCBI Gi to Kegg Pathways

NCBI Gi to Kegg Pathway Descriptions (5)

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This workflow accepts a list of NCBI gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in (plus pathway image) from the KEGG database. This workflow replaces the earlier SOAP version with the new KEGG REST services

Created: 2012-01-12 | Last updated: 2013-01-30

Credits: Katy Wolstencroft

Attributions: NCBI Gi to Kegg Pathways

omim and pathways (2)

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This workflow searches OMIM for entries associated with a particular disease in OMIM, returns the IDs and maps them to Kegg Gene IDs. For each gene, it then gets the description and any corresponding pathways those genes are involved with

Created: 2009-03-03 | Last updated: 2009-11-02

Credits: Katy Wolstencroft Paul Fisher

Attributions: Get Kegg Gene information

KEGG:Get PW for met (1)

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The purpose of the workflow is to retrieve all the pathways that the input metabolite(s) participates in.

Created: 2016-06-21

Credits: Kristina Hettne Harish Dharuri

Attributions: KEGG:Pathway Scheme

AllPW2CHEBI (2)

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This workflow uses the WikiPathways Webservice/API to query to retrieve all Chemical Entities of Biological Interest (ChEBI) identifers for all pathways and merge them to one, unique list.

Created: 2015-09-01 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni