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Pack Phenotypic screening annotation protocols


Created: 2016-05-06 12:02:23 | Last updated: 2016-05-06 12:03:03

This is a collection of all protocols published in Digles et al., Open PHACTS Computational Protocols for in silico Target validation of Cellular Phenotypic Screens: Knowing the Knowns, MedChemComm, submitted.The workflows require the Open PHACTS KNIME nodes (org.openphacts.utils.json_1.1.0.zip) available from https://github.com/openphacts/OPS-Knime.

3 items in this pack

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Workflow 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: User Daniela Digles Network-member Open PHACTS

Workflow 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: User Daniela Digles Network-member Open PHACTS

Workflow Phenotypic screening annotation: protocols... (1)

This workflow contains protocols 1-4 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.Starting with a list of compound URIs (here retrieved in the metanode Protocol 0), the workflow returns ChEBI classifications for the compound...

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

Credits: User Daniela Digles Network-member Open PHACTS

Workflow Chemical2URIs (1)

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This workflow will map a chemical name or identifier to uniform resource identifiers (URIs). First the ChemSpider web service is used to map the chemical name to a ChemSpider identifier, then the ChemSpider identifier is mapped to URIs via the Open PHACTS platform.

Created: 2015-08-18

Credits: User Kristina Hettne User Eelke van der Horst Network-member BioSemantics

Pack Open PHACTS Drug Discovery FAQ Workflows


Created: 2014-11-05 11:12:18 | Last updated: 2014-11-05 11:15:59

Computational drug discovery using the KNIME workflow engine and the integrated resources of Open PHACTS for answering a number of important frequently asked pharmacology questions. 14 workflows for answering 16 different questions.

14 items in this pack

Comments: 0 | Viewed: 156 times | Downloaded: 31 times

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

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

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

Workflow Q16:Targets in Parkinson's disease or Alzh... (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 for Disease followed by Target Pharmacology with filter minEx-pChembl=5 to answer scientific competency question Q16:Target...

Created: 2014-10-22

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

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