Workflows

Pathways and Gene annotations for QTL region (7)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path...

Created: 2009-11-19 | Last updated: 2012-09-07

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

SNPs to Concept Set through Concept Profil... (6)

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Purpose: Currently, this workflow takes one SNP and a concept set as input, calculates the matching score between these, finds co-occuring documents between the query concept and the match concept, finds the concept that contributes the most to the match, and the documents that support this finding. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www...

Created: 2012-06-26 | Last updated: 2013-02-05

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

Attributions: Find Supporting Documents SNP_ID2EntrezGene_ID DatabaseID to ConceptID Match gene lists based on information in literature Match concept profiles Explain concept scores

DatabaseID to ConceptID (7)

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Purpose: This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology. Result: Concept Identifiers from the EMC ontology. Comments: Database: one of CAS, DRUG, etc. The supported databases are listed below (database, description, example). CAS, Chemical Abstracts Service registry number, 64-17-5. DRUG, Drug Bank, DB00316. AF, Affymetrix, 200007_at. CHEB, ChEBI, 16236. CHID, ChemIDplus, 0000050000. EG, Entrez-Gene, 3064. GO, Gene Ontol...

Created: 2012-06-25 | Last updated: 2014-07-14

Credits: Marco Roos Martijn Schuemie Reinout van Schouwen BioSemantics

entreztoKeggImage (1)

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This workflow accepts a list of Entrez Gene IDs. It dentifies which KEGG pathway each gene is involved with and displays the pathway diagrams

Created: 2014-09-05

Credits: Katy Wolstencroft

Map genes to chromosomal location for T2WEB (1)

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This workflow maps a gene list on the genome using the biomart service. IMPORTANT NOTE: Keep in mind that for uploading files on t2web, you need to wait few minutes before executing the workflow. That's essential because the file needs first to be uploaded on the server.

Created: 2013-11-04

Credits: Eleni

Map genes to chromosomal location (1)

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This workflow maps a gene list to the genome using the biomart service, and afterwards computes a promoter region for each gene. The user needs to define the promoter region to be computed. The direction that a gene is transcribed is being taken into account in the "compute_promoter_region_with_strand" component. The variable "strand" is responsible for that. NOTE: The library(biomaRt) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

Annotate a gene list with disease concepts (1)

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Purpose: Currently, this workflow takes a list of genes and a concept set as input, calculates the matching score between these and finds the concept that contributes the most to the match. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/368 for functional gene annotation and knowledge discovery.

Created: 2013-02-06

Credits: Kristina Hettne Reinout van Schouwen Marco Roos BioSemantics

Attributions: SNPs to Concept Set through Concept Profile Matching v2

Get Pathway-Genes and gene description by ... (2)

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Given a specific entrez gene id, returns the pathways that this gene participates in and for each of those pathways which genes (including their description) are associated with.

Created: 2012-03-27 | Last updated: 2012-04-03

Credits: Eleni

Get Pathway-Genes by Entrez gene id (4)

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Given a specific entrez gene id, returns the pathways that this gene participates in and for each of those pathways which genes are associated with. The workflow outputs also a KEGG pathway map and the objects are colored according to the input color values.

Created: 2012-03-08 | Last updated: 2012-04-14

Credits: Eleni