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Solution with JSON

Data Manipulation

Solution to "Manipulation Data" exercise for basic Life Science User Training
- Concatenate data from two different sources
- Modify String values
- Join data from multiple tables
- Remove duplicates in the data

URL: Advaced ETL Functionalities and Machine Learning based Pre-Processing https://youtu.be/IEAsUTN8q68
URL: Joining Data Tables https://youtu.be/6BigLM6vbhs
URL: Joining Data Tables - Inner Join https://youtu.be/9uV99ByH-TA
URL: Concatenate https://youtu.be/VzH2lHbDAg0
URL: Concatenate Node https://youtu.be/ku6SyEZ1Pv8
URL: Data Manipulation: Numbers, Strings, and Rules https://youtu.be/mJrBXmLQ4ko
URL: Slides for KNIME Analytics Platform Course (L1-LS) https://www.knime.com/form/material-download-registration

Compounds REOS rules-- "MW" if AMW is smaller than 100 or greater than 700-- "Complexity" if NumHeavyAtoms is smaller than 5 or greater than 50 or NumRotatableBonds is greater or equal to 12-- "HBond" if NumHBD is greater than 5 or NumHBA is greater than 10-- "logP" if SlogP is smaller -5 or greater than 7.5-- "Pass" for all other cases Assay data Data manipulation Data exploration Data export Get ChEMBL ID of compound Get activity data from ChEMBL Get activity data from ChEMBL for thr first 20 compounds Always get best performing compound, independent of input data molecules_properties.tableKNIME-native formatassay datacorrect sample IDsmalariahts_molecules.sdfmalariahts_experiment_no-hits.xlsxmalariahts_experiment_hits.csvchange data typesrename columnjoin two tablesfilter out missing valuescreateREOS rulesexclude duplicatescorrect column typecombine all datafilter missing pEC50filter out NumSaturatedRingsINTERACTION REQUIREDexclude "selected" columnsort for highest pEC50convert to InChI Keyconstruct request URLbase URLChEMBLextract ChEMBL IDactivity URLChEMBLconstruct activity URLconstruct request URLconvert to InChI Keyextract ChEMBL IDconstruct activity URLexclude compounds without ChEMBL IDexclude compounds without ChEMBL IDconstruct activity URL Table Reader Table Writer Concatenate String Manipulation SDF Reader Excel Reader CSV Reader Table Manipulator Joiner Missing Value Rule Engine Data Explorer DuplicateRow Filter Column Expressions Joiner Row Splitter Column Filter RDKit From Molecule RDKit Moleculeto SVG Interactive datavisualization SDF Writer Excel Writer Column Filter Sorter RDKit To InChI Table Rowto Variable String Manipulation Table Creator GET Request JSON Path Table Creator Table Rowto Variable String Manipulation GET Request XPath String Manipulation RDKit To InChI GET Request JSON Path String Manipulation GET Request XPath Row Filter JSON Path GET Request Row Filter String Manipulation Row Filter Compounds REOS rules-- "MW" if AMW is smaller than 100 or greater than 700-- "Complexity" if NumHeavyAtoms is smaller than 5 or greater than 50 or NumRotatableBonds is greater or equal to 12-- "HBond" if NumHBD is greater than 5 or NumHBA is greater than 10-- "logP" if SlogP is smaller -5 or greater than 7.5-- "Pass" for all other cases Assay data Data manipulation Data exploration Data export Get ChEMBL ID of compound Get activity data from ChEMBL Get activity data from ChEMBL for thr first 20 compounds Always get best performing compound, independent of input data molecules_properties.tableKNIME-native formatassay datacorrect sample IDsmalariahts_molecules.sdfmalariahts_experiment_no-hits.xlsxmalariahts_experiment_hits.csvchange data typesrename columnjoin two tablesfilter out missing valuescreateREOS rulesexclude duplicatescorrect column typecombine all datafilter missing pEC50filter out NumSaturatedRingsINTERACTION REQUIREDexclude "selected" columnsort for highest pEC50convert to InChI Keyconstruct request URLbase URLChEMBLextract ChEMBL IDactivity URLChEMBLconstruct activity URLconstruct request URLconvert to InChI Keyextract ChEMBL IDconstruct activity URLexclude compounds without ChEMBL IDexclude compounds without ChEMBL IDconstruct activity URL Table Reader Table Writer Concatenate String Manipulation SDF Reader Excel Reader CSV Reader Table Manipulator Joiner Missing Value Rule Engine Data Explorer DuplicateRow Filter Column Expressions Joiner Row Splitter Column Filter RDKit From Molecule RDKit Moleculeto SVG Interactive datavisualization SDF Writer Excel Writer Column Filter Sorter RDKit To InChI Table Rowto Variable String Manipulation Table Creator GET Request JSON Path Table Creator Table Rowto Variable String Manipulation GET Request XPath String Manipulation RDKit To InChI GET Request JSON Path String Manipulation GET Request XPath Row Filter JSON Path GET Request Row Filter String Manipulation Row Filter

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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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On NodePit since: 2024-12-04
Last update: 2024-12-17
Created with KNIME version: v5.2.3
Tags: ETLconcatenatejoinpreprocessingremove duplicatestransformreplaceeducationfilterlife science

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