Curate this paper into an ORD dataset

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

• Paper: Pharmaceutical diversification via palladium oxidative addition complexes
• Authors: Mycah R. Uehling, Ryan P. King, Shane W. Krska et al.
• Published: Science, 2019-01-25
• DOI: 10.1126/science.aac6153
• 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: 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

Late-stage diversification of drug molecules via isolated Pd(II) oxidative addition complexes (Science 2019, academic-industrial collaboration). Data source: the supplementary materials PDF on science.org, which must be downloaded manually. Its format (numeric tables vs heatmap figures) has not been confirmed. Scope first whether the coupling results are quantitative yields or qualitative (e.g. MS-detected) outcomes.

Known locations:

• https://www.science.org/doi/10.1126/science.aac6153: Science 2019 article and supplementary materials (returned HTTP 403 to automated fetch). (license: closed article (AAAS); SI licence unknown)

Pitfalls

Pd oxidative addition complexes used as reactants are organometallic species that are hard to encode as SMILES (dative bonds, ligand-bound Pd). Outcomes may be qualitative or relative (MS detection, heatmap colours). The work may span several coupling types (C-N, C-O, C-S, C-C), i.e. multiple templates.

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.