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1. Q4: For a given interaction profile, give me similar compounds.
2. Q19: For the targets in a given pathway, retrieve the compounds that are active with more than one target.
3. Q18:For pathway X, find compounds that agonize targets assayed in only functional assays with potency <1 µM.
4. 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.
5. Q15: a) Which chemical series have been shown to be active against target X? b) Which new targets have been associated with disease Y?
6. Q11: Retrieve all data for a given list of compounds depicted by their chemical structure (SMILES) with options to match stereochemistry.
7. Q10:For a given compound, summarize all similar compounds and their activities.
8. Q9:For a given compound, give me the interaction profile with targets.
9. Q8:Identify all known protein-protein interaction inhibitors
10. 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?
11. Q6:For a specific target family, retrieve all compounds in specific assays
12. Q3: Given a target find me all actives against that target. Find/predict polypharmacology of actives
13. Q1: Give me all oxidoreductase inhibitors active <100 nM in human and mouse
14. Q5: For molecules that contain substructure X, retrieve all bioactivity data in serine protease assays.
Q4: For a given interaction profile, give ...
(1)
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)
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)
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
Q16:Targets in Parkinson's disease or Alzh...
(1)
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:
Christine Chichester
Daniela Digles
Open PHACTS
Q15: a) Which chemical series have been sh...
(1)
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)
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)
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
Q9:For a given compound, give me the inter...
(1)
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:
Christine Chichester
Daniela Digles
Open PHACTS
Q8:Identify all known protein-protein inte...
(1)
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:
Christine Chichester
Daniela Digles
Open PHACTS
Q7: For a target, give me all active compo...
(1)
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)
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
Q3: Given a target find me all actives aga...
(1)
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:
Christine Chichester
Daniela Digles
Open PHACTS
Q1: Give me all oxidoreductase inhibitors ...
(2)
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:
Christine Chichester
Daniela Digles
Open PHACTS
Q5: For molecules that contain substructur...
(1)
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:
Christine Chichester
Daniela Digles
Open PHACTS
User: Christine Chichester
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