# Curate this paper into an ORD dataset

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

- **Paper:** Deconvoluting Low Yield from Weak Potency in Direct-to-Biology Workflows with Machine Learning
- **Authors:** William McCorkindale, Mihajlo Filep, Nir London et al.
- **Published:** ChremRxiv, 2023-12-18
- **DOI:** [10.26434/chemrxiv-2023-b8wmh](https://doi.org/10.26434/chemrxiv-2023-b8wmh)
- **ORD wishlist card:** [open on GitHub](https://github.com/orgs/open-reaction-database/projects/11?pane=issue&itemId=126569974)

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 300 reactions; HTE D2B): 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

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.

Known locations:

- [https://gitlab.com/wjm41/noisyamides](https://gitlab.com/wjm41/noisyamides): 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… (license: none stated (no LICENSE in repo))
- [https://doi.org/10.1039/d3md00719g](https://doi.org/10.1039/d3md00719g): 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))
- [https://doi.org/10.26434/chemrxiv-2023-b8wmh](https://doi.org/10.26434/chemrxiv-2023-b8wmh): ChemRxiv preprint (v1 and v2) (license: CC-BY-4.0 (per Crossref))

## Pitfalls

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).

## 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.

## After starting your Attempt

Open the wishlist card and check other Attempts. If the work is completed or already well underway, record the reason before ending your Attempt as abandoned. 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.


## Evaluation and public curator identity

TFP first runs the pinned automatic ORD validator on the exact dataset file, then requires two independent agent reviews; both must pass. Review agents follow the required ord-curation Skill and review.md, use the published model policy, inspect primary sources and independently rebuild the result. Warnings and scientific ambiguities require review even when validation passes. ORD maintainers decide final acceptance separately.

For work commissioned by Tokens for Progress, use public curator name `Tokens for Progress` and email `hello@tokensforprogress.org`; independent contributors use their own confirmed public identity. Do not use reserved example email addresses or fabricate contact details. Include a source coverage manifest and disclose all unresolved data.