Workflows

Use Case C, Worflow 4 (1)

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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

Use Case C, Worflow 3 (1)

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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

Use Case C, Worflow 2 (1)

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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 version 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- D...

Created: 2014-05-26 | Last updated: 2014-11-25

Credits: Emiliano Cuadrado Joseline Ratnam Daniela Digles Open PHACTS

Use Case C, Worflow 1 (1)

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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.  This workflow can be used to get approved drugs from a pathway of interest using the Open PHACTS APIRequirements:- 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...

Created: 2014-05-26 | Last updated: 2014-11-25

Credits: Emiliano Cuadrado Joseline Ratnam Daniela Digles Open PHACTS

Visualize PAV provenance as SVG (1)

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VoID descriptions are fetched as Turtle, cleaned up to be valid OWL ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance. Note that this workflow downloads CWM, Pellet and ProvToolbox on demand, and uses UNIX command line tools like wget and md5 which are unlikely to work in Windows. This workflow has been tested on Ubuntu 12.10 wit...

Created: 2014-05-08

Credits: Katy Wolstencroft Aleksandra Pawlik

Find master regulators in networks (GeneWays) (1)

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This workflow is designed to find master regulatory molecules upstream of an input list of genes. Input file is any gene or protein table.At the first step, the input table is converted into a table with Entrez Gene IDs.At the next step the Entrez genes are annotated with additional information, gene description and gene symbols.The annotated gene table is subjected to master regulator search in the GeneWays network. For each potential master regulator, FDR, Score, and Z-score are calculated....

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

Credits: geneXplain

Analyze promoters (GTRD) (1)

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This workflow is designed to search for putative transcription factor binding sites, TFBS, on the promoters of an input gene set.As input, any gene or protein table can be submitted. The input table contains genes under study, and it is called “Yes” set.At the first step, the input table is converted into a table with Ensembl Gene IDs.At the next step, promoters are analyzed for potential cis-regulatory sites. Promoters in this workflow are defined as sequences from -1000 to +100 ...

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

Credits: geneXplain

Analyze any DNA sequence for site enrichment (1)

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This workflow is designed to reveal TFBS  enrichment in any DNA sequence.  As input, any sequence collection in FASTA, EMBL or GeneBank format can be used. Yes and No sequence sets can be specified in the corresponding input fields.  As input, DNA sequences of any organisms and from any genome regions can be taken.At the first step Yes and No sequences are subjected to Site search on track analysis using the profile of positional weight matrices specified in the input form. The...

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

Credits: geneXplain

Mapping to ontologies (Gene table) (1)

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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