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Tag: annotation Licence: by-sa
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Taverna 2
Uploader
4399?size=60x60 Gb Paul Fisher

Workflow 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: User Paul Fisher

Taverna 1
Uploader
4399?size=60x60 Gb Paul Fisher

Workflow Pathways and Gene annotations for QTL region (2)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the Pig, Sus scrofa. 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 pathway ...

Created: 2009-11-20 | Last updated: 2009-11-20

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

Taverna 1
Uploader
4399?size=60x60 Gb Paul Fisher

Workflow Pfam Based Ortholog Filter (1)

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This workflow filters an Ondex graph based on the occurrence of Pfam orthologs within the graph. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ConfidenceThreshold - Threshold value for inparanoid confidence. Default value is 100. AnnotationScoreThreshold - Threshold...

Created: 2009-08-19

Credits: User Paul Fisher

Taverna 2
Uploader
3772?size=60x60 Nl Kristina Hettne

Workflow 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: User Kristina Hettne User Eleni User Harish Dharuri User Reinout van Schouwen User Marco Roos User Martijn Schuemie Network-member BioSemantics

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

KNIME
Uploader
Avatar Daniela Digles

Workflow Phenotypic screening annotation: protocols... (1)

This workflow contains protocols 1-4 as published in Digles et al., Open PHACTS Computational Protocols for in silico Target validation of Cellular Phenotypic Screens: Knowing the Knowns, MedChemComm, submitted.This workflow requires the Open PHACTS KNIME nodes (org.openphacts.utils.json_1.1.0.zip) available from https://github.com/openphacts/OPS-Knime.Starting with a list of compound URIs (here retrieved in the metanode Protocol 0), the workflow returns ChEBI classifications for the compound...

Created: 2016-05-06 | Last updated: 2016-05-06

Credits: User Daniela Digles Network-member Open PHACTS

Taverna 2
Uploader
3772?size=60x60 Nl Kristina Hettne

Workflow Chemical2URIs (1)

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This workflow will map a chemical name or identifier to uniform resource identifiers (URIs). First the ChemSpider web service is used to map the chemical name to a ChemSpider identifier, then the ChemSpider identifier is mapped to URIs via the Open PHACTS platform.

Created: 2015-08-18

Credits: User Kristina Hettne User Eelke van der Horst Network-member BioSemantics

Bioinformatics
Uploader
Avatar Nikolaos Bismpikos

Workflow SNP identification and evaluation for Diab... (1)

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This workflow gathers SNP information for a gene set of Diabetes Type II phenotype using BioMart queries. Furthermore, GO Terms and functional annotation clustering are defined for this gene set using FunctionalClusterDavid workflow. 

Created: 2015-06-23

Credits: User Nikolaos Bismpikos User Katy Wolstencroft

Attributions: Workflow FunctionalClusterDavid

Taverna 2
Uploader
3772?size=60x60 Nl Kristina Hettne

Workflow 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: User Kristina Hettne User Reinout van Schouwen User Marco Roos Network-member BioSemantics

Attributions: Workflow SNPs to Concept Set through Concept Profile Matching v2

Taverna 2
Uploader
3772?size=60x60 Nl Kristina Hettne

Workflow Match concept profiles with predefined set (2)

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Purpose of workflow: The workflow can be used to match a set of concept profiles with predefined set of concept profiles. Result: A list of concepts ordered by their match to the query concept profiles.

Created: 2013-02-05 | Last updated: 2014-07-14

Credits: User Kristina Hettne User Marco Roos User Reinout van Schouwen Network-member BioSemantics

Taverna 2
Uploader
30?size=60x60 Nl Marco Roos

Workflow Match concept profiles (6)

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Purpose of workflow: The workflow can be used to match a set of concept profiles with another set of concept profiles. Result: A list of concepts ordered by their match to the query concept profiles.

Created: 2011-12-02 | Last updated: 2014-07-14

Credits: User Marco Roos User Kristina Hettne User Martijn Schuemie User Reinout van Schouwen

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Funded by: BioVeL, EPSRC, JISC, Microsoft

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