Pack: Open PHACTS Drug Discovery FAQ Workflows

Description:

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 Compound Pharmacology with filter activity_type=IC50|EC50|AC50|Ki|Kd|Potency to answer scientific competency question Q10: For a given compound, summarize all similar compounds and their activities.

Description:

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 followed by Compound Classifications with filter tree=chebi to answer scientific competency question Q11: Retrieve all data for a given list of compounds depicted by their chemical structure (SMILES) with options to match stereochemistry.

Description:

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 scientific competency question Q15: a) Which chemical series have been shown to be active against target X? b) Which new targets have been associated with disease Y? 

Description:

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:Targets in Parkinson's disease or Alzheimer's disease are activated by which compounds? and Q20: For a given disease, retrieve all targets in the pathway and all active compounds hitting them.

Description:

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, activity_unit=nanomolar to answer scientific competency question Q18: For pathway X, find compounds that agonize targets assayed in only functional assays with potency <1 µM

Description:

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 question Q19: For the targets in a given pathway, retrieve the compounds that are active with more than one target.

Description:

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.

Description:

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 competency question Q3; Given a target find me all actives against that target. Find/predict polypharmacology of actives.

Description:

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 searchOptions.Threshold=0.85 followed by Compound Information to answer scientific competency question Q4: For a given interaction profile, give me similar compounds.

Description:

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 Discovery Platform. 

Description:

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 specific assays.

Description:

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 compounds with the relevant assay data, and Q17: For my specific target, which active compounds have been reported in the literature? 

Description:

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 all known protein-protein interaction inhibitors.

Description:

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 given compound, give me the interaction profile with targets.