Workflows

Use Case B, KNIME workflow (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’, PLoS One. 2014 Dec 18; 9(12):e115460. PMID: 25522365; authored by Joseline Ratnam, Barbara Zdrazil, Daniela Digles, Cuadrado-Rodriguez E, et al. This workflow can be used to retrieve data and perform the analysis described in use case BRequirements:- Knime v2.9- Open PHACTS Knime nodes version 1.0.0 (DON'...

Created: 2014-11-20 | Last updated: 2015-11-03

Credits: Barbara Zdrazil Emiliano Cuadrado Daniela Digles Lars Richter Open PHACTS

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

Q4: For a given interaction profile, give ... (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 Information followed by Compound Information (Batch) followed by Chemical Structure Search: Similarity with filter search...

Created: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS

Q19: For the targets in a given pathway, r... (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 Pathway Information: Get Targets followed by Target Pharmacology with filter minEx-pChembl=5 to answer scientific competency quest...

Created: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS

Q18:For pathway X, find compounds that ago... (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 Pathway Information: Get Targets followed byTarget Pharmacology with filters activity_type=Potency, max-activity_value=1000, activ...

Created: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS

Q15: a) Which chemical series have been sh... (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 a) Classification of Compounds for Target with filter minEx-pChembl=5 and b) Associations for Disease to answer scientif...

Created: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS

Q11: Retrieve all data for a given list of... (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 Chemical Structure Search: Exact with filter searchOptions.MatchType=2 followed by Compound Pharmacology and Compound Information ...

Created: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS

Q10:For a given compound, summarize all si... (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 Chemical Structure Search: Similarity with filters searchOptions.SimilarityType=0 and searchOptions.Threshold=0.80, followe by Com...

Created: 2014-10-22

Credits: Christine Chichester Daniela Digles Open PHACTS