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R4A_​AnnotationTool_​v1

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This workflow reads chemical information given as InChIKeys, e.g. coming from R4A_StructureHarmonisation_IDgenerator workflow(https://hub.knime.com/-/spaces/-/~9qa2Cmp7a47KU5GR/current-state/) and generates two tables.
1 - The Assay Information table contains the compound annotated with Chembl assay results. The user can alter constrains for pChembl, Assay Type and Confidence score range in the table creator node. The standard type is set to retrieve only AC50, EC50, IC50, Ki, MIC, GI50, TGI, Km, Kd, CC50, LC50.
2 - The ClinicalTrial Information table containds the compounds annotated with information of clinical trials, e.g. max phase, year of approval, indication.
Both files also contain CIDs, ChemblIDs, SChemblID. Synonyms and Chembl preferred molecule name.
This workflow is part of the data harmonisation pipeline developed in the Remedi4all project.
The REMEDi4ALL project has received funding from the European Union’s Horizon Europe Research & Innovation programme under grant agreement No 101057442.

Set constrains for Chembl Assay DatapChembl: integer valueassayType: string, comma separated (F, B, A, T, P)Confidence score: range, integer, comma separatedNote: standard type is set to: AC50, EC50, IC50, Ki, MIC, GI50, TGI, Km, Kd, CC50, LC50 Input file:Must contain column withCompound InChI Key Input CompoundsAssayInfo filter(pChembl, AssayType,ConfidenceScore)Node 181Node 196Node 197top: Assay databottom: Clinical trial information Node 281AssayInformation Table Node 295ClinicalTrialInformationClinicalTrialInformation Table Node 298 CSV Reader Table Creator Table RowTo Variable Get CID from InChIKey (PubChemIdentifier Exchange Service) Chembl ID andSChembl ID Chembl Annotation Table Writer Excel Writer ExcelCompatibility Table Writer Excel Writer ExcelCompatibility Set constrains for Chembl Assay DatapChembl: integer valueassayType: string, comma separated (F, B, A, T, P)Confidence score: range, integer, comma separatedNote: standard type is set to: AC50, EC50, IC50, Ki, MIC, GI50, TGI, Km, Kd, CC50, LC50 Input file:Must contain column withCompound InChI Key Input CompoundsAssayInfo filter(pChembl, AssayType,ConfidenceScore)Node 181Node 196Node 197top: Assay databottom: Clinical trial information Node 281AssayInformation Table Node 295ClinicalTrialInformationClinicalTrialInformation Table Node 298CSV Reader Table Creator Table RowTo Variable Get CID from InChIKey (PubChemIdentifier Exchange Service) Chembl ID andSChembl ID Chembl Annotation Table Writer Excel Writer ExcelCompatibility Table Writer Excel Writer ExcelCompatibility

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Created by: Jeanette.Reinshagen
Created at: 2024-02-10
On NodePit since: 2024-02-13
Last update: 2024-04-28
Created with KNIME version: v5.1.2

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