Pack: Phenotypic screening annotation protocols

Description:

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 workflow).

Description:

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 targets for a list of compound URIs (retrieved in the Protocol 0 metanode) and joins the data with interaction data from IUPHAR/BPS. For each target the highest affinity antagonist and agonist is retained.

Description:

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 compounds,  as well as targets for the compounds. These targets are further annotated with target classifications/GO terms, pathways and diseases.