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GGP2113_​ChEMBLSMILES

Extract SMILES or other data from ChEMBL

Pull any data (SMILES, Activity, Assay, others from ChEMBL via API GET services)

Input: CSV or List of ChEMBL ID (Target or Molecule or Assay) and others.

Output: Table or SDF or other chemcial formats based on your string extraction from JSON

Options: Ref: https://www.ebi.ac.uk/chembl/api/data/docs for more string manipulation query from ChEMBL

Generate a issue query in GitHub if you have any queries.

Use any oneworkflow, Loopworks only forone end node.This workflowis better to filterif any missing databased on yourstring manipulationfrom ChEMBL API data Created by: Girinath PillaiKNIME ver: 4.3.2Download from : https://github.com/giribio/knimeNodes : Chunk, JSON, GET, CSV, KNIME ChemistryDescription: Pull any data (SMILES, Activity, Assay, others fromChEMBL via API GET services) Input: CSV or List of ChEMBL ID (Target or Molecule or Assay)and others.Output: Table or SDF or other chemcial formats based on yourstring extraction from JSONOptions: Ref: https://www.ebi.ac.uk/chembl/api/data/docs formore string manipulation query from ChEMBLGenerate a issue query in GitHub if you have any queries.Thanks @giribio www.nyroindia.org Optional:Alternate ChEMBL nodeas well asfor JSON path Iterationsas per rowsDefine IterationsExtracteddata tocolumnsDefine Mol TypegiribioExtract datapulled from ChEMBL WebgiribioExcludemissingChEMBLIDsMerge all datagiribioResource URLupdatedgiribioAPI lookupChEMBLData pulled fromChEMBL - giribioReport missing dataCSV file with ChEMBLIDFilter columnsConvert MolformatFilter columnsDefine Mol TypegiribioIterationsas per rowsConvert MolformatExtracteddata tocolumnsFilter columns ChEMBL Lookup Loop End Chunk Loop Start JSON to Table Molecule Type Cast JSON Path Rule-basedRow Splitter Concatenate String Manipulation String Manipulation GET Request Rule Engine CSV Reader Column Filter MolConverter Column Filter Molecule Type Cast Loop End MolConverter JSON to Table Column Filter Use any oneworkflow, Loopworks only forone end node.This workflowis better to filterif any missing databased on yourstring manipulationfrom ChEMBL API data Created by: Girinath PillaiKNIME ver: 4.3.2Download from : https://github.com/giribio/knimeNodes : Chunk, JSON, GET, CSV, KNIME ChemistryDescription: Pull any data (SMILES, Activity, Assay, others fromChEMBL via API GET services) Input: CSV or List of ChEMBL ID (Target or Molecule or Assay)and others.Output: Table or SDF or other chemcial formats based on yourstring extraction from JSONOptions: Ref: https://www.ebi.ac.uk/chembl/api/data/docs formore string manipulation query from ChEMBLGenerate a issue query in GitHub if you have any queries.Thanks @giribio www.nyroindia.org Optional:Alternate ChEMBL nodeas well asfor JSON path Iterationsas per rowsDefine IterationsExtracteddata tocolumnsDefine Mol TypegiribioExtract datapulled from ChEMBL WebgiribioExcludemissingChEMBLIDsMerge all datagiribioResource URLupdatedgiribioAPI lookupChEMBLData pulled fromChEMBL - giribioReport missing dataCSV file with ChEMBLIDFilter columnsConvert MolformatFilter columnsDefine Mol TypegiribioIterationsas per rowsConvert MolformatExtracteddata tocolumnsFilter columns ChEMBL Lookup Loop End Chunk Loop Start JSON to Table Molecule Type Cast JSON Path Rule-basedRow Splitter Concatenate String Manipulation String Manipulation GET Request Rule Engine CSV Reader Column Filter MolConverter Column Filter Molecule Type Cast Loop End MolConverter JSON to Table Column 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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Created by: gpillai
Created at: 2021-07-18
On NodePit since: 2021-10-01
Last update: 2024-05-02
Created with KNIME version: v4.3.4
Tags: giribionyroindiachemblsmilesdatadatabasechemical spacebioactivity

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