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Category: Workflow Type: KNIME Group: Open PHACTS

Workflow Q9:For a given compound, give me the inter... (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 Compound Pharmacology with filter activity_type=IC50|EC50|AC50|Ki|Kd|Potency to answer scientific competency question Q9: For a gi...

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

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Workflow Q8:Identify all known protein-protein inte... (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 and filters target_type=ppi and minEx-pChembl=5 to answer scientific competency question Q8: Identify al...

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

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Workflow 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: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Workflow 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: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Workflow Q3: Given a target find me all actives aga... (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 with filter minEx-pChembl=5 followed by Compound Pharmacology with minEx-pChembl=0. to answer scientific compe...

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

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Workflow Q1: Give me all oxidoreductase inhibitors ... (2)

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A new version of the Open PHACTS drug discovery question 1 workflow (answers the question: Give me all oxidoreductase inhibitors active <100nM in human and mouse) with improvements contributed by Ellert van Koperen.  To run workflow the parameters for Human and Mouse in the OPS_Swagger node must be re-entered. They become corrupted upon on export to zip file.

Created: 2014-10-22 | Last updated: 2015-06-02

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Workflow Q5: For molecules that contain substructur... (1)

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This workflow requires the input of a substructure of a chemical as represented as a SMILES string and a class of targets from either the ENZYME or Chembl target classification. It answers one of the scientific use cases (Question 5 see K. Azzaoui et al. Scientific competency questions as the basis for semantically enriched open pharmacological space development. Drug Discov. Today 18 (2013), p. 843-852) that was used as the basis for the development of the Open PHACTS Dis...

Created: 2014-09-29 | Last updated: 2014-09-29

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Workflow 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: User Emiliano Cuadrado User Joseline Ratnam User Daniela Digles Network-member Open PHACTS

Workflow 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: User Emiliano Cuadrado User Joseline Ratnam User Daniela Digles Network-member Open PHACTS

Workflow 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: User Emiliano Cuadrado User Joseline Ratnam User Daniela Digles Network-member Open PHACTS

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