After the individual datasets were processed and aggregated into the Papyrus dataset, molecular structures were standardised. This last standardisation ensured normalisation across different sources that each applied different prior standardisation. For instance, tautomerization tools can alter a compound's stereochemistry by removing or introducing a chiral centre. To limit the effects of having bioactivity values relating to the same molecular compound having different stereochemistry across sources, a set with removed stereochemistry was created and deemed of higher quality than the set with conserved stereochemistry. Molecular structures in the latter, after having removed stereochemistry, were first neutralized with the RDKit by adding or removing hydrogen atoms. Subsequently they were standardised with the ChEMBL structure pipeline after which parent structures were obtained. OpenBabel was then used to recreate dative bonds and to neutralize molecules that were not during the previous step. Tetravalent negatively charged boron atoms were overlooked in the latter stage, making them erroneously pentavalent. This was corrected by detecting these pentavalent boron atoms, removing the newly introduced implicit hydrogen atom and reassigning them a negative formal charge. SMILES of molecules with the same connectivity differing by overall charge were converted to InChi with OpenBabel, a step that consists in incorporating the normalisations after the InChI canonicalization process. For these molecules the canonicalization process removed the dative bonds, these were then recreated using OpenBabel. Then Dimorphite-DL was used to deprotonate molecules by setting minimum pH to 14.0. This ensured that after the last standardisation step, equivalent to that applied to individual datasets, in which molecules are neutralised, only one charge state of the same molecular species was present in the set.