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 300 reactions; HTE D2B): 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.
Data are in the public GitLab repository gitlab.com/wjm41/noisyamides, which has no license file. Use data/amine_coupling_yield_updated/yield.csv (about 300 wells, one plate). It gives LC peak-area fractions for HOAt, acid, product (P) and other species, a derived 'yield' in percent, and product SMILES. Earlier versions of the same data exist (data/amine_coupling_yield/, data/amide_yields.csv). The repo README notes the source spreadsheet was corrected, including annotations on 0% yields (side reaction vs no reaction), so confirm which version matches the published paper. Reactant SMILES are not given per row. The carboxylic acid is a common core, and each amine must be derived from the product SMILES (amide disconnection) or matched against data/enamine_primary_and_secondary_amines.csv. The notebook fix_acid_smiles.ipynb documents a correction to acid SMILES. Coupling conditions, stoichiometry, scale and the LC-MS method come from the paper (RSC Med Chem 2024, 10.1039/d3md00719g, CC BY 3.0; preprint 10.26434/chemrxiv-2023-b8wmh, CC BY 4.0). 'Chan Lam yield.xlsx' and the bioactivity/prediction files are outside the reaction dataset unless the paper reports them as reactions. Cite the journal DOI.
Known locations:
Outcomes are crude LC peak-area percentages from direct-to-biology plates, not isolated yields. Encode them as area-percent measurements with the analysis method. Multiple spreadsheet versions exist. Some 0% wells carry comments distinguishing side reactions from no reaction. Amine reactant SMILES must be derived, and stereochemistry and salt forms need checking. Wells map to plate positions (Well vs Plate Well columns differ).
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.