# Curate this paper into an ORD dataset

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

- **Paper:** Nanoscale synthesis and affinity ranking
- **Authors:** Nathan J. Gesmundo, Bérengère Sauvagnat, Patrick J. Curran et al.
- **Published:** Nature, 2018-04-19
- **DOI:** [10.1038/s41586-018-0056-8](https://doi.org/10.1038/s41586-018-0056-8)
- **ORD wishlist card:** [open on GitHub](https://github.com/orgs/open-reaction-database/projects/11?pane=issue&itemId=126570092)

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

Nanomole-scale (1536-well) Pd-catalysed coupling screens (Suzuki, C-N amination, amide/diverse nucleophile couplings) and library syntheses from Gesmundo et al., Nature 2018 (doi:10.1038/s41586-018-0056-8). Reaction data is in the article's Source Data Excel files (Fig. 2-4 and Extended Data Figs. 2-6, 8-10) on nature.com. Rows give reactant and product SMILES, plate position, catalyst (trade names such as XPhos Pd G3), base (e.g. P2-Et, BTMG, BTTP), solvent, LC-UV areas and a calculated percent yield from a product-to-internal-standard ratio. Reagent volumes are in the plate-map sheets. Concentrations, stoichiometry, temperature and time must be taken from the Supplementary Information PDF. Pitfalls: (1) some sheets identify building blocks only by MFCD number, so resolve SMILES from other sheets; (2) the 'Compiled Yield Data' sheet repeats rows from the individual screen sheets, so do not double-count; (3) some sheets have two yield columns (e.g. 'Calc. Percent Yield' and 'Calc'd % Yield Updated'), so state which one is used; (4) affinity-selection mass spectrometry (ASMS) binding data is not reaction data and is out of scope; (5) catalyst and base names need structures. The ORD Dataset must cite the paper DOI.

Known locations:

- [https://www.nature.com/articles/s41586-018-0056-8](https://www.nature.com/articles/s41586-018-0056-8): Article landing page; lists the Supplementary Information PDF (MOESM1) and 11 Source Data files (Fig. 2, 3, 4; ED Fig. 2-6, 8-10) as XLS/XLSX (license: Springer Nature, closed-access article (Crossref: springer.com/tdm only))
- [https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-018-0056-8/MediaObjects/41586_2018_56_MOESM9_ESM.xlsx](https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-018-0056-8/MediaObjects/41586_2018_56_MOESM9_ESM.xlsx): Source Data for ED Fig. 6 (catalyst/base survey, 0.78 MB). Sheets: Suzuki Coupling Screen 1 (687 rows), Suzuki 2 Optimization (162), C-N Coupling Screen 1 (384), C-N Coupling Screen 2 (364), Diverse Coupling Screen (1,536), Compiled Yield Data (2,110), plus plate maps. Columns include Core SMILES… (license: Springer Nature source data; no CC license stated)
- [https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-018-0056-8/MediaObjects/41586_2018_56_MOESM2_ESM.xls](https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-018-0056-8/MediaObjects/41586_2018_56_MOESM2_ESM.xls): Source Data for Fig. 2 (library synthesis; 1.3 MB per HEAD); MOESM3-8 and MOESM10-12 are the other figure source data files (HEAD checked only on MOESM2/3/9/12) (license: Springer Nature source data; no CC license stated)
- [https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-018-0056-8/MediaObjects/41586_2018_56_MOESM1_ESM.pdf](https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-018-0056-8/MediaObjects/41586_2018_56_MOESM1_ESM.pdf): Supplementary Information PDF (procedures, concentrations and amounts, compound data) (license: Springer Nature; closed)

## Pitfalls

Yields are LC-UV estimates against an internal standard, not isolated yields; conversion and yield columns coexist. Screens are spread across many sheets and files with overlap (compiled vs per-screen), so reviewers must check for deduplication. Many reactions give 0% yield (valid negative data). Precatalysts are named by trade name. Reaction conditions such as temperature, time and concentrations live in the SI PDF, not in the spreadsheets. It may need 2 datasets if library synthesis and condition screens are kept separate.

## 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.