Curate this paper into an ORD dataset

Build an Open Reaction Database (ORD) dataset of the reactions reported in:

• Paper: Developing Pharmaceutically Relevant Pd-Catalyzed C–N Coupling Reactivity Models Leveraging High-Throughput Experimentation
• Authors: Seung Kyun Ha, Dipannita Kalyani, Michael S. West et al.
• Published: JACS, 2025-05-29
• DOI: 10.1021/jacs.5c00933
• ORD wishlist card: open on GitHub

The reference input card holds these facts, the source-data locations and the notes below in machine-readable form.

Scope

Every reaction the paper reports with its data (the wishlist estimates about 2,000 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.

Source data

Pd-catalyzed C–N coupling HTE dataset (MIT / Merck collaboration), JACS 2025, DOI 10.1021/jacs.5c00933. The published reaction outcomes are only grid images in the SI PDF (ja5c00933_si_001.pdf on ACS figshare). There is no machine-readable SI file, and no public code or data repository was found. Many reactants and catalysts would need SMILES. The card lists about 2000 reactions, but the SI description mentions 4204 unique products, so the full dataset may be larger. Curating from the images alone is not practical, so an author-supplied tabular dataset (ideally with SMILES) is needed before this can be worked.

Known locations:

• https://doi.org/10.1021/jacs.5c00933: Article landing page (ACS) (license: ACS standard terms per Crossref (TDM policy links only); OpenAlex reports green OA via PubMed (article license, not data))
• https://acs.figshare.com/articles/journal_contribution/Developing_Pharmaceutically_Relevant_Pd-Catalyzed_C_N_Coupling_Reactivity_Models_Leveraging_High-Throughput_Experimentation/29182375: Only SI file: ja5c00933_si_001.pdf (14.7 MB). Per curator notes it holds the grid-image data. Checked by figshare API listing only, not downloaded. (license: CC BY-NC 4.0 (figshare label on the ACS SI record))
• https://europepmc.org/article/PMC/PMC13047508: PMC copy (PMID 40439243). The Europe PMC full-text XML is not available, so no data-availability statement or repository link was found. (license: unknown)

Pitfalls

Outcomes would come from images unless tabular data appears. The size is unclear (2000 on the card vs 4204 unique products in the SI description). Pharma HTE components may use internal identifiers. Checking many generated SMILES against drawn structures needs expert review.

Deliver

• 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.

Before you start

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.