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02. Data manipulation

Data Access, property calculation and visualisation 2. Use the Row Filternode to filter for rowsthat have"CHEMBL214" astarget_chembl_id 4. Use the Joinernode to perform aninner join based onthe molregno 5. As we don't needthe molregnocolumn anymore,use the ColumnFilter to exclude it 7. Use the RDKit From Molecule node to make it an RDKitmolecule column and then the Renderer to Image node torender the molecules and create png images 8. Use the RDKitDescriptorCalculation node tocalculate molecularproperties 9. Use the Rule Enginenode to create theactivity target column(set all values lowerthan 10 nM in thestandard value to'active' and all others to'inactive') 10. Create a component for an interactive view and data visualisation 1. Use the File Reader(Complex Format)node to importcompound_data.csv.Read the SMILESdirectly in the correctdata type 3. Use the picoting node with molregno as group,the target_chmebl_id as pivot and the followingaggregations: * pref_name->Minimum* standard_value->Minimum* pchembl_value->Maximum* standard_type->Minimum* standard_relation->Minimum* published_units->Minimum* assay_chembl_id->Minimum 6. Use the Column Rename(Regex) node to replace"CHEMBL214+" using thefollowing expression ^CHEMBL214\+* Molecular PropertiesMolecule Overviewassay_data.xlsxParallelCoordinates Plot Tile View Color Manager Interactive RangeSlider Filter Widget Filter Apply Excel Reader Excel Writer Data Access, property calculation and visualisation 2. Use the Row Filternode to filter for rowsthat have"CHEMBL214" astarget_chembl_id 4. Use the Joinernode to perform aninner join based onthe molregno 5. As we don't needthe molregnocolumn anymore,use the ColumnFilter to exclude it 7. Use the RDKit From Molecule node to make it an RDKitmolecule column and then the Renderer to Image node torender the molecules and create png images 8. Use the RDKitDescriptorCalculation node tocalculate molecularproperties 9. Use the Rule Enginenode to create theactivity target column(set all values lowerthan 10 nM in thestandard value to'active' and all others to'inactive') 10. Create a component for an interactive view and data visualisation 1. Use the File Reader(Complex Format)node to importcompound_data.csv.Read the SMILESdirectly in the correctdata type 3. Use the picoting node with molregno as group,the target_chmebl_id as pivot and the followingaggregations: * pref_name->Minimum* standard_value->Minimum* pchembl_value->Maximum* standard_type->Minimum* standard_relation->Minimum* published_units->Minimum* assay_chembl_id->Minimum 6. Use the Column Rename(Regex) node to replace"CHEMBL214+" using thefollowing expression ^CHEMBL214\+* Molecular PropertiesMolecule Overviewassay_data.xlsxParallelCoordinates Plot Tile View Color Manager Interactive RangeSlider Filter Widget Filter Apply Excel Reader Excel Writer

Nodes

Extensions

Links

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

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Created by: glandrum
Created at: 2019-09-23
On NodePit since: 2023-09-08
Last update: 2024-11-21
Created with KNIME version: v4.7.7

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