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 1,100 reactions; 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.
Amide couplings for PROTAC synthesis in 1536-well plates, including reproducibility data. The data is in SI Tables S1-S9 of the SI PDF (ACS, mirrored on figshare, CC BY-NC 4.0; the article itself is CC-BY 4.0). Values are LCMS product peak-area %, calculated with the PyParse software, plus conversion (product/(product + amine)). Batch-scale comparisons (310-fold scale-up) include isolated yields after HPLC purification. Each table supports a specific paper figure (Figures 2A/2B, 3, 4A/4B, 5A, 6A/6B, Table 1). Some tables are processed data and others unprocessed (e.g. S2 vs S3); decide which to record and avoid double counting. The tables are text-extractable but the page layout interleaves table columns with captions, so extract carefully and cross-check against figure values. No SMILES are provided. The number of unique chemicals is small but they are large PROTAC fragments; structures must come from the paper and SI schemes and names. Cite DOI 10.1021/acs.joc.4c02456.
Known locations:
Outcomes are LCMS area %/conversion rather than isolated yields (except batch-scale runs). Processed and unprocessed duplicates of the same experiments exist. Repeated wells for reproducibility must be modeled as separate reactions or replicates. Salt form (free amine vs TFA salt) and solvent variables must be captured.
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.