All content

FunctionalClusterDavid (1)

• Download

This workflow takes a list of Entrez Gene IDs as input and submits them to the DAVID REST API for functional clustering using OG annotaiton, biological pathways and disease associations. Used for analysing a set of genes (i.e. those differentially expressed for a particular disease condition).

Created: 2014-09-05

Credits: Katy Wolstencroft

Use Case C, Worflow 4 (1)

• Download

Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, currently submitted to PLOS ONE.  Requirements:- Knime v2.9- Open PHACTS Knime nodes 1.0.0 (DON'T use any later version!): https://github.com/openphacts/OPS-KnimeInstallation:- Download "org.openphacts.utils.json_1.0.0.zip" and unzip it in the plugins folder of your KNIME installation- Download ...

Created: 2014-05-27 | Last updated: 2014-11-25

Credits: Emiliano Cuadrado Joseline Ratnam Daniela Digles Open PHACTS

Mapping to ontologies (Gene table) (1)

• Download

This workflow is designed to classify an input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set. The input file can be any gene or protein table.At the first step, the input table is converted into a table with Ensembl Gene IDs.This table with Ensembl Gene Ids is subjected to functional classification, which is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions, Reactome...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Match concept profiles with predefined set (2)

• Download

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: Kristina Hettne Marco Roos Reinout van Schouwen BioSemantics

Get a list of proteins annotated with an O... (3)

• Download

A service to look for models in BioModels using an Ontology Id as input. First the workflow will look in QuickGO for UniProt accessions annotated with the provided Ontology Id. Then it will look for models using the list of proteins. If one of the input protein is found in one model the workflow will provide the BioModels Id, the SBML and a link to the BioModels database. Please use taverna 2.4 or above.

Created: 2012-08-22 | Last updated: 2013-07-10

Credits: Rafael C. Jimenez

Get a list of proteins from a Gene Ontolog... (1)

• Download

Get a list of UniProt proteins that have been annotated with the same Gene Ontology (GO) term. This workflow uses the the QuickGO service

Created: 2012-02-20 | Last updated: 2012-02-22

Credits: Rafael C. Jimenez

Get names of proteins similar to RNA bindi... (1)

• Download

A very simple demo workflow using some existing SADI services. It finds UniProt proteins of GO function "RNA Binding", it then runs a BLAST service to find similar UniProt proteins and then outputs their names.

Created: 2011-05-18 | Last updated: 2011-05-18

Credits: hindlem

[untitled] (1)

• Download

This workflow allows the user to search for processes that are involved with a certain gene. Using microarray-files (CEL-files), consisting of wild type and KO mice to which a stimulant is induced, the user can get an idea of the processes involved. (This is done using the global test and the literature weighted global test.) The results are then given as a text-file. Warning: workflow is not working (needs some revisions), all input is currently hardcoded! (You will have to change the file...

Created: 2011-04-26 | Last updated: 2011-04-26

Credits: Dennis Leenheer

Gene expression interpretation by the Glob... (1)

This workflow adds meaning to gene expresion values by performing a standard and a literature weighted Global Test. Gene expression is expected to be from Affymetrix microarrays, for which an RMA normalization and entrez Gene ID mapping/summation is performed. Original workflow is by Dennis Leenheer, edits by Marco Roos. Scripts by Kristina Hettne, acknowledging Rob Jellier, Jelle Goeman, and Peter-Bram 't Hoen. The workflow was created for the LUMC BioSemantics group, part of the Human Gen...

Created: 2011-04-26 | Last updated: 2011-04-26

Credits: Marco Roos

KEGG Pathways and Additional Information f... (2)

• Download

Takes in a tab-delimited BLAST file and finds additional information about the target proteins from KEGG, Gene Ontology, Interpro and PubMed.

Created: 2011-03-29 | Last updated: 2011-03-30

Credits: Morgan Taschuk

Attributions: extract_uniprot_embl_gi.xml