Integrative data mining of chemical compounds from public domain

Created: 2018-07-26 12:37:09      Last updated: 2018-07-27 11:50:16

This workflow downloads ligand data  for hepatic Organic Anion Transporting Polypeptides (OATPs) from five different open sources (CHEMBL, Metrabase, USFC-FDA Transportal, IUPHAR, and Drugbank) in an automatized fashion. This workflow can be adopted to any other ligand data linked to a particular membrane transporter. If missing, structural file format is  mapped via PubChem webservices. Pre-curated data are further unified, activity threshold is set up based on pre-selected cutoff, and data are combined and grouped by in order to reveal their pharmacological profiles across hepatic OATPs. Further, an effort has been made to treat OATP substrates and inhibitors separately based on different activity end-points and annotations for substrates versus inhibitors. Finally, pre-curated ligands are subjected to standardization procedure (Atkinson standardization script has been used, for further details see


- Knime v3.4

- KNIME ‘Trusted Community Contributions (3.4)’:

1) EMBL-EBI Nodes for KNIME


3) Marvin Chemistry

4) KNIME Core Chemisry



- Download the workflow (*.knwf file)

- Start your KNIME environment

- Import workflow

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