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{
"source": "ORD Dataset Wishlist",
"snapshot_date": "2026-09-25",
"ord_wishlist_status_at_snapshot": "Available",
"ord_wishlist_card": "https://github.com/orgs/open-reaction-database/projects/11?pane=issue&itemId=126570038",
"ord_data_issue": null,
"title": "Automated stopped-flow library synthesis for rapid optimisation and machine learning directed experimentation",
"doi": "10.1039/D2SC03016K",
"journal": "Chemical Science",
"publication_date": "2022-09-13",
"authors": [
"Claudio Ávila",
"Carlo Cassani",
"Thierry Kogej",
"Javier Mazuela",
"Sunil Sarda",
"Adam D. Clayton",
"Michael Kossenjans",
"Clive P. Green",
"Richard A. Bourne"
],
"article_open_access": {
"status": "diamond",
"license": "cc-by"
},
"dataset_size_estimate": 900,
"experiment_type": "optimisation in flow",
"ord_priority": "Medium",
"ord_difficulty": "Normal",
"source_data_kind": "si_spreadsheet_or_csv",
"smiles_in_source": "yes",
"needs_author_contact": false,
"data_locations": [
{
"url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9601405.1/SC-013-D2SC03016K-s001.txt",
"what": "ESI data file s001 (verified). Whitespace/tab-delimited, 836 rows. Columns: Set (Train 661 / Test 175), Exp_name, RXN (reaction SMILES with agents), CA (coupling agent SMILES), Time (120-600), Temperature (50-200), Success (0-86.07). It covers 24 amide products, 96 reactant/agent combinations and 4 coupling agents.",
"license": "CC BY (PMC OA subset license_code; article CC BY 3.0 per Crossref)"
},
{
"url": "https://pmc-oa-opendata.s3.amazonaws.com/metadata/PMC9601405.1.json",
"what": "PMC OA metadata listing every ESI file: s001-s007 .txt (~150-200 KB each), s008 .ipynb, s009 .py, s010 .yml, s011 .h5 (9.3 MB model), s012/s013 .txt, and s014 SI PDF.",
"license": "CC BY"
},
{
"url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9601405.1/SC-013-D2SC03016K-s014.pdf",
"what": "SI PDF: stopped-flow platform, concentrations and stoichiometry, analytical method (listed, not downloaded).",
"license": "CC BY"
},
{
"url": "https://pubs.rsc.org/en/content/articlelanding/2022/sc/d2sc03016k",
"what": "Publisher landing page with the ESI. It returned a Cloudflare bot challenge.",
"license": "CC BY 3.0 (article)"
},
{
"url": "https://github.com/MolecularAI/HTE_Publication_Avila_et_al",
"what": "Code repository cited in the paper. The GitHub API returns 404, so it is not publicly available.",
"license": "unknown"
}
],
"notes": "Chemical Science 2022, 13, 12087 (DOI 10.1039/D2SC03016K). Diamond open access, article CC BY 3.0. The PMC OA copy (PMC9601405), including its supplementary files, is licensed CC BY. The ESI data is plain-text tables that can be fetched from the PMC open-data mirror (pmc-oa-opendata S3); the publisher site blocks automated clients. File s001 has columns Set, Exp_name, RXN, CA, Time, Temperature and Success. RXN is a reaction SMILES with agents between the '>' separators, so split it into reactants, agents and product. s001 holds 836 experiments: 24 amide products and 96 reactant/coupling-agent combinations with 4 coupling agents, over a 5x5 time-temperature grid. The Set column marks a Train/Test split. s002-s005 are almost the same size and are probably alternative splits of the same experiments, so deduplicate by Exp_name/RXN/conditions before building the dataset. s006, s007, s012 and s013 need checking for additional experiments (the board estimates ~900 reactions in total). Take units (Time is probably seconds), the meaning of Success (probably HPLC yield or conversion in %), concentrations, stoichiometry, solvent and the analytical method from the SI PDF (s014). The code repository cited in the paper is no longer publicly reachable.",
"verification_caveats": "The same experiments probably appear in several split files, so a merged dataset could contain duplicate reactions unless deduplicated. The meaning and units of Success and Time must be confirmed from the SI PDF. Stopped-flow reactions must be represented as flow or batch-like conditions consistently. Solvent, base and concentrations are not in the TSV and must be added from the SI methods."
}