{
  "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=126569974",
  "ord_data_issue": null,
  "title": "Deconvoluting Low Yield from Weak Potency in Direct-to-Biology Workflows with Machine Learning",
  "doi": "10.26434/chemrxiv-2023-b8wmh",
  "journal": "ChremRxiv",
  "publication_date": "2023-12-18",
  "authors": [
    "William McCorkindale",
    "Mihajlo Filep",
    "Nir London",
    "Alpha A. Lee",
    "Emma King‐Smith"
  ],
  "article_open_access": {
    "status": "green",
    "license": "cc-by"
  },
  "dataset_size_estimate": 300,
  "experiment_type": "HTE D2B",
  "ord_priority": null,
  "ord_difficulty": null,
  "source_data_kind": "open_repository_machine_readable",
  "smiles_in_source": "partial",
  "needs_author_contact": false,
  "data_locations": [
    {
      "url": "https://gitlab.com/wjm41/noisyamides",
      "what": "Project repo. data/amine_coupling_yield_updated/yield.csv (about 299 wells) has columns Well, HOAt, Acid, P, 'random stuff', comment, yield, Plate Well, SMILES (product). The same folder has raw.csv, grid.csv and activity.csv. Older versions sit in data/amine_coupling_yield/ and data/amide_yields.csv. Also holds xlsx/numbers originals, CDD activity exports and an enumerated amine list with SMILES. There is also an unrelated-looking 'Chan Lam yield.xlsx'.",
      "license": "none stated (no LICENSE in repo)"
    },
    {
      "url": "https://doi.org/10.1039/d3md00719g",
      "what": "Journal version (RSC Medicinal Chemistry 2024). Needed for coupling conditions, reagents, scale and the LC analysis method. The landing page returned a bot challenge, so its ESI was not inspected.",
      "license": "CC-BY-3.0 (per Crossref)"
    },
    {
      "url": "https://doi.org/10.26434/chemrxiv-2023-b8wmh",
      "what": "ChemRxiv preprint (v1 and v2)",
      "license": "CC-BY-4.0 (per Crossref)"
    }
  ],
  "notes": "Data are in the public GitLab repository gitlab.com/wjm41/noisyamides, which has no license file. Use data/amine_coupling_yield_updated/yield.csv (about 300 wells, one plate). It gives LC peak-area fractions for HOAt, acid, product (P) and other species, a derived 'yield' in percent, and product SMILES. Earlier versions of the same data exist (data/amine_coupling_yield/, data/amide_yields.csv). The repo README notes the source spreadsheet was corrected, including annotations on 0% yields (side reaction vs no reaction), so confirm which version matches the published paper. Reactant SMILES are not given per row. The carboxylic acid is a common core, and each amine must be derived from the product SMILES (amide disconnection) or matched against data/enamine_primary_and_secondary_amines.csv. The notebook fix_acid_smiles.ipynb documents a correction to acid SMILES. Coupling conditions, stoichiometry, scale and the LC-MS method come from the paper (RSC Med Chem 2024, 10.1039/d3md00719g, CC BY 3.0; preprint 10.26434/chemrxiv-2023-b8wmh, CC BY 4.0). 'Chan Lam yield.xlsx' and the bioactivity/prediction files are outside the reaction dataset unless the paper reports them as reactions. Cite the journal DOI.",
  "verification_caveats": "Outcomes are crude LC peak-area percentages from direct-to-biology plates, not isolated yields. Encode them as area-percent measurements with the analysis method. Multiple spreadsheet versions exist. Some 0% wells carry comments distinguishing side reactions from no reaction. Amine reactant SMILES must be derived, and stereochemistry and salt forms need checking. Wells map to plate positions (Well vs Plate Well columns differ)."
}