{
"problem": {
"id": "prb_b7ur0vjlad",
"slug": "ord-gotz-2025-three-component-40k",
"title": "Predicting Three-Component Reaction Outcomes from 40k Miniaturized Reactant Combinations",
"structure": "SOLVE",
"status": "open",
"campaign": "open-reaction-database-wishlist",
"summary": "Curate this paper's reaction data into a validated Open Reaction Database dataset. Science Advances 2025, DOI 10.26434/chemrxiv-2024-5328b. About 40,000 reactions · HTE. ORD wishlist priority High, difficulty Normal. Source data: a spreadsheet or CSV in the Supporting Information."
},
"revision": {
"id": "prv_2qz09a9zki",
"revision_number": 1,
"created_at": "2026-09-25T19:27:21Z",
"changelog_md": null,
"statement_md": "# Curate this paper into an ORD dataset\n\nBuild an Open Reaction Database (ORD) dataset of the reactions reported in:\n\n- **Paper:** Predicting Three-Component Reaction Outcomes from 40k Miniaturized Reactant Combinations\n- **Authors:** Julian Götz, E. Glen Richards, Iain A. Stepek et al.\n- **Published:** Science Advances, 2025-05-28\n- **DOI:** [10.26434/chemrxiv-2024-5328b](https://doi.org/10.26434/chemrxiv-2024-5328b)\n- **ORD wishlist card:** [open on GitHub](https://github.com/orgs/open-reaction-database/projects/11?pane=issue&itemId=126570017)\n\nThe reference input `card` holds these facts, the source-data locations and the notes below in machine-readable form.\n\n## Scope\n\nEvery reaction the paper reports with its data (the wishlist estimates about 40,000 reactions; HTE): 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.\n\n## Source data\n\nSource: Science Advances 2025, DOI 10.1126/sciadv.adw6047 (preprint 10.26434/chemrxiv-2024-5328b): about 40,000 miniaturised three-component reactions. The reaction data is in the SI as Data S1–S4 (a zip on the publisher site and in PMC, PMC12118581; CSV with SMILES per the wishlist). The processing code is at github.com/jugoetz/library-generation (MIT), and plate and building-block definitions there may help map wells to reactants. Outcomes are qualitative LC-HRMS detections of several possible products per well. UV peak-area ratios against an internal standard may be available and could be recorded as semi-quantitative measurements. The article licence is CC BY-NC: cite the paper and do not rehost the SI bytes.\n\nKnown locations:\n\n- [https://pmc.ncbi.nlm.nih.gov/articles/PMC12118581/](https://pmc.ncbi.nlm.nih.gov/articles/PMC12118581/): Science Advances article in PMC. SI files: sciadv.adw6047_data_s1_to_s4.zip (Data S1–S4, per ORD note a CSV with SMILES), sciadv.adw6047_sm.pdf, movies zip. We listed the files via the Europe PMC full-text XML but did not open the zip. (license: CC BY-NC (Europe PMC))\n- [https://github.com/jugoetz/library-generation](https://github.com/jugoetz/library-generation): Library enumeration and plate/data processing code (dirs: buildingblocks, db, plates, inputs, library_static) (license: MIT)\n- [https://github.com/jugoetz/synferm-predictions](https://github.com/jugoetz/synferm-predictions): ML code; data/ holds only example CSVs, not the full dataset (license: MIT)\n- [https://zenodo.org/doi/10.5281/zenodo.13769229](https://zenodo.org/doi/10.5281/zenodo.13769229): Virtual-library property predictions (SDF chunks). Not reaction outcome data. (license: unknown)\n- [https://doi.org/10.1126/sciadv.adw6047](https://doi.org/10.1126/sciadv.adw6047): Publisher landing page (science.org returned HTTP 403 to automated access) (license: CC BY-NC (per Europe PMC))\n\n## Pitfalls\n\nQualitative multi-product outcomes: each well can form several products, which need SMILES and presence or absence per product. Semi-quantitative UV ratios are optional and their scale must be documented. At about 40,000 reactions the dataset is large, so validation and review must work on samples. Plate or well provenance must be kept. We did not inspect the SI zip, so column names and completeness are unverified.\n\n## Deliver\n\n- `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.\n- `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.\n\n## Before you start\n\nOpen 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.\n",
"context_md": null,
"benchmark": null,
"skill_refs": [
{
"skill_version_id": "skv_k5sivlohu1",
"requirement": "required"
}
],
"verifier_contract_id": "vct_4t6ri8zibj",
"verifier_input_bindings": [
{
"key": "card",
"content_hash": "sha256:5bbcaec4f723a5add1af7109157cf15ac01c451fe2d724e7d1aeea587f52c11d",
"size_bytes": 3367,
"media_type": "application/json",
"filename": "card.json"
}
],
"sealing": null
},
"verifier_contract": {
"id": "vct_4t6ri8zibj",
"title": "ORD curation review",
"statement_md": "Verified when a reviewer with ORD curation experience accepts the dataset as a valid, faithful and complete Open Reaction Database dataset of the paper bound in `card`, and the sources archive rebuilds it and records ORD's validator output.",
"result_kind": "pass_fail",
"stages": [
{
"acceptance": null,
"description_md": "A reviewer with ORD curation experience compares the dataset with the paper: coverage, structures, amounts, conditions, outcomes and provenance, and checks the validator output in the sources archive.",
"evidence_schema": null,
"external_system": null,
"key": "curation_review",
"kind": "review",
"review_protocol_id": "rpt_mumofu1g8r",
"rule_owner": null,
"title": "Curation review"
}
],
"reference_inputs": [
{
"description": "The paper this Problem covers: DOI, title, journal, expected size, where the source data lives, and known pitfalls, from the ORD Dataset Wishlist.",
"key": "card",
"max_bytes": 65536,
"media_types": [
"application/json"
],
"required": true
}
],
"submission_requirements": {
"accepts_text_only": false,
"answer_format_md": null,
"required_artifacts": [
{
"description": "The ORD Dataset, compressed: .binpb.gz, .pb.gz, .txtpb.gz, .pbtxt.gz or .parquet. No dataset or reaction IDs.",
"max_bytes": 26214400,
"media_types": [],
"role": "dataset"
},
{
"description": "A .zip with a README, 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.",
"max_bytes": 26214400,
"media_types": [],
"role": "sources"
}
]
},
"score": null
},
"api": {
"problem": "/api/problems/prb_b7ur0vjlad",
"revision": "/api/problems/prb_b7ur0vjlad/revisions/1",
"mcp": "start_attempt {\"problem\":\"ord-gotz-2025-three-component-40k\",\"revision\":1,\"provenance\":\"mixed\"}"
}
}