Build an Open Reaction Database (ORD) dataset of the reactions reported in:
The reference input card holds these facts, the source-data locations and the notes below in machine-readable form.
Every reaction the paper reports with its data (the wishlist estimates about 384 reactions; D2B HTE): inputs with amounts and roles, conditions, workups, outcomes and provenance, following the ord-curation Skill. Submit one ORD Dataset for the paper; if its data come from several screens or methods, keep them together and say so in the dataset description.
Paper: Wang et al., Nat. Commun. 2023, 14, doi:10.1038/s41467-023-43614-3, CC BY 4.0. It describes a 384-well nanoscale plate built around a pomalidomide-derived isocyanide. Wells A1-F8 are Ugi-4CR (amine, aldehyde/ketone, carboxylic acid, isocyanide). Wells F9-K16 are Ugi with aqueous formaldehyde as the oxo component. Wells K17-P24 are Ugi-tetrazole (amine, oxo component, isocyanide, TMSN3, 2.4 equiv). Building blocks were dispensed by I.DOT as 0.5 M TFE stocks (isocyanide 0.25 M, TMSN3 0.6 M). Each well was analysed by direct-injection MS and classified as major product (the [M+H], [M+Na] or [M+K] peak is the highest), no product (peak absent), or medium product (otherwise). The Fig. 4A heatmap source data should be in 'source data in manuscript.xlsx' inside the Source Data zip (MOESM3; the zip is about 377 MB, so download selectively). Raw Waters MassLynx .raw folders are provided for every well. Building-block identities are in the SI PDF (MOESM1, including Supplementary Table 1 for the isocyanide) and need converting to SMILES. The biology data (proteomics, viability, western blots) is out of scope.
Known locations:
Outcomes are qualitative (three classes) with no yields, so they must be encoded carefully, for example as product identity plus a custom or qualitative measurement. Three reaction templates share one plate. This is direct-to-biology synthesis with no purification. Products are implied rather than characterized, apart from a few resynthesized hits. The well-to-building-block mapping must be reconstructed from the SI plate layout.
dataset: the ORD Dataset, compressed (.binpb.gz, .pb.gz, .txtpb.gz, .pbtxt.gz or .parquet), citing the DOI above in every reaction's provenance, with no dataset or reaction IDs.sources: a .zip with a README.md (which tables or files each part came from, how structures were checked), the template and spreadsheet or the script or notebook that rebuild the dataset, and validation.txt, the output of ORD's validator (ord-schema 0.8.3) on the dataset file.Open the wishlist card. If it is no longer Available, someone has reserved or started it: coordinate with them or choose another paper. Get the source data only through legitimate channels (the publisher's Supporting Information, the repositories above, or the authors). Submitting the finished dataset to ORD, and ORD's separate Dataset Rewards program, follow ORD's own rules.