Workflows

Phenotypic screening annotation: protocol 6 (1)

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This workflow contains protocol 6 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 and the IUPHAR/BPS Guide to Pharmacology data file available from http://guidetopharmacology.org/DATA/interactions.csv.The workflow returns targe...

Created: 2016-05-06

Credits: Daniela Digles Open PHACTS

Phenotypic screening annotation: protocol 5 (1)

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This workflow contains protocol 5 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.This workflow shows compounds which are found both in an assay of interest (upper part of the workflow) and in kinase assays (lower part of the w...

Created: 2016-05-06

Credits: Daniela Digles Open PHACTS

Phenotypic screening annotation: protocols... (1)

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

Credits: Daniela Digles Open PHACTS

Q7: For a target, give me all active compo... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Target Pharmacology and filter minEx-pChembl=5 to answer scientific competency question Q7; For a target, give me all active compo...

Created: 2014-10-22 | Last updated: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS

Q6:For a specific target family, retrieve ... (1)

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In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Target Class Pharmacology to answer scientific competency question Q6; For a specific target family, retrieve all compounds in spe...

Created: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS

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

Find compounds pharmacology targets in Ope... (2)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTS API https://dev.openphacts.org/docs/1.5. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this means this workflow would be propagating 404 Not Found errors. Until there is a Local worker to filter out...

Created: 2013-10-16 | Last updated: 2015-11-19

Credits: Stian Soiland-Reyes

Attributions: Find compounds pharmacology and align against target sequences