Workflows

Calculating frequencies of gene expression... (1)

This workflow retrieves data from the MaxD microarray database and calculates the frequencies of gene expression levels using an R script

Created: 2010-03-15

Credits: Peter Li

Kegg pathway diagrams (1)

• Download

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

caArray data retrieving (1)

• Download

Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They ca be later used as training and test data set in many classification algorithms.Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They can be later used as training and test data set in many classification algorithms.

Created: 2009-11-23

Credits: Wei Tan

chicken_ensembl_gene_id (1)

• Download

Accepts a chromosome eg. 1 and returns the ensembl gene ids for that chromosome

Created: 2009-09-07 | Last updated: 2009-09-09

Credits: Rory

Tab Parser (1)

This workflow takes in a tab separated file, and then parses specific rows and columns from the file into an Ondex Graph. Additional prarameters are provided, though these are optional: graphId Long the ID of the Graph (REQUIRED) input String the plugin input (REQUIRED) skip Integer How many rows to skip at begin of document (Optional). Default value is 22. fromCol Integer Index of concept parser id for from concept. Default value is 0. (REQUIRED) toCol Integer Index of concept par...

Created: 2009-08-19

Credits: Paul Fisher

GWAS to biomedical concept (3)

• Download

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)

• Download

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)

• Download

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

UnigeneID to KEGG Pathways (3)

• Download

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)

• Download

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