Icon

W1_​Data_​acquisition_​from_​ChEMBL

W1_Data_acquisition_from_ChEMBL
1. Data acquisition from ChEMBLInformation on compound structure, bioactivity, and associated targetsare organized in databases such as ChEMBL, PubChem, orDrugBank. The following steps show how to obtain data for a querytarget (default target: EGFR). Step 1Download ChEMBL bioactivity data Note that the database query can be slow.*Alternatively, the query results can be loaded from file with the "Table Reader" node which needs to beconnected to the "Column Resorter" node instead of the "Get activities" - "Column Resorter" connection.This workflow adapts the KNIME workflow example 50_Applications/30_RESTful_ChEMBL/03_ChEMBL_Bioactivity_Search (KNIME EXAMPLES Server, accessed: 2019-05-18). Step 2Get bioactivity (IC50) &compound (SMILES) data fromChEMBL ID This workflow is part of the TeachOpenCADD pipeline: https://hub.knime.com/volkamerlab/space/TeachOpenCADDRead more on the theoretical background of this workflow on our TeachOpenCADD platform: https://projects.volkamerlab.org/teachopencadd/talktorials/T001_query_chembl.html Step 3Filter out entries with missingvalues & duplicates Step 4Filter for entries with IC50 inmolar units with exactmeasurements Step 5Convert all molar units to nM Step 6Convert bioactivityto pIC50 Ca. 10s per 1000 molsOnly IC50Only binding assay dataNo duplicatesOnly molar unitsOnly exactmeasurementsAdd pIC50Only SMILES presentConvert all molar units to nMOnly nMSave compound listNode 275Node 276Node 277Load results* Input targetChEMBL ID Table View Get activitiescount Get activities Row Filter Row Filter GroupBy Row Filter Row Filter Column Resorter Column Filter Column Rename Column Resorter Math Formula Row Filter Java Snippet Row Filter CSV Writer String To Number WorkflowService Input WorkflowService Output Table Reader 1. Data acquisition from ChEMBLInformation on compound structure, bioactivity, and associated targetsare organized in databases such as ChEMBL, PubChem, orDrugBank. The following steps show how to obtain data for a querytarget (default target: EGFR). Step 1Download ChEMBL bioactivity data Note that the database query can be slow.*Alternatively, the query results can be loaded from file with the "Table Reader" node which needs to beconnected to the "Column Resorter" node instead of the "Get activities" - "Column Resorter" connection.This workflow adapts the KNIME workflow example 50_Applications/30_RESTful_ChEMBL/03_ChEMBL_Bioactivity_Search (KNIME EXAMPLES Server, accessed: 2019-05-18). Step 2Get bioactivity (IC50) &compound (SMILES) data fromChEMBL ID This workflow is part of the TeachOpenCADD pipeline: https://hub.knime.com/volkamerlab/space/TeachOpenCADDRead more on the theoretical background of this workflow on our TeachOpenCADD platform: https://projects.volkamerlab.org/teachopencadd/talktorials/T001_query_chembl.html Step 3Filter out entries with missingvalues & duplicates Step 4Filter for entries with IC50 inmolar units with exactmeasurements Step 5Convert all molar units to nM Step 6Convert bioactivityto pIC50 Ca. 10s per 1000 molsOnly IC50Only binding assay dataNo duplicatesOnly molar unitsOnly exactmeasurementsAdd pIC50Only SMILES presentConvert all molar units to nMOnly nMSave compound listNode 275Node 276Node 277Load results* Input targetChEMBL ID Table View Get activitiescount Get activities Row Filter Row Filter GroupBy Row Filter Row Filter Column Resorter Column Filter Column Rename Column Resorter Math Formula Row Filter Java Snippet Row Filter CSV Writer String To Number WorkflowService Input WorkflowService Output Table Reader

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: tymsk
Created at: 2022-01-22
On NodePit since: 2022-01-28
Last update: 2024-04-27
Created with KNIME version: v4.5.1
Tags: ChEMBLWeb service queryData filtering & formattingTeachOpenCADD

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!