{
"problem": {
"id": "prb_7xp5lid1mo",
"slug": "ord-clarke-2024-pd-cross-coupling-complexity",
"title": "Deciphering complexity in Pd–catalyzed cross-couplings",
"structure": "SOLVE",
"status": "open",
"campaign": "open-reaction-database-wishlist",
"summary": "Curate this paper's reaction data into a validated Open Reaction Database dataset. Nature Communications 2024, DOI 10.1038/s41467-024-47939-5. About 700 reactions · HTE. ORD wishlist priority High, difficulty Hard. Source data: machine-readable files in an open repository."
},
"revision": {
"id": "prv_ynps3bpk17",
"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:** Deciphering complexity in Pd–catalyzed cross-couplings\n- **Authors:** George E. Clarke, James D. Firth, Lyndsay A. Ledingham et al.\n- **Published:** Nature Communications, 2024-05-10\n- **DOI:** [10.1038/s41467-024-47939-5](https://doi.org/10.1038/s41467-024-47939-5)\n- **ORD wishlist card:** [open on GitHub](https://github.com/orgs/open-reaction-database/projects/11?pane=issue&itemId=126570018)\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 700 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: Nature Communications 10.1038/s41467-024-47939-5 (Universities of York and Leeds; CC BY 4.0), about 700 HTE Pd-catalysed cross-coupling reactions with complex side-product and by-product distributions. The HTE data are in Research Data York (DOI 10.15124/37869e97-c94a-41a7-9f69-fe3ed1c10984, CC BY). It contains an experimental-information CSV, processed LC-MS extract CSVs (EXTRAC_1/2) and PCA input tables (2-hour and 110 °C sets), plus about 10 GB of raw LC-MS zips, which are not needed for curation. The article's Source Data CSV holds IR reaction-monitoring time courses, not the screening outcomes. Data are spread over several spreadsheets whose structure is not fully documented, so work out the mapping between conditions and outcomes first and flag any ambiguity. Author clarification may be needed. Crystal structures are in the CCDC (numbers listed in the article).\n\nKnown locations:\n\n- [https://doi.org/10.15124/37869e97-c94a-41a7-9f69-fe3ed1c10984](https://doi.org/10.15124/37869e97-c94a-41a7-9f69-fe3ed1c10984): Research Data York dataset: basic_experimental_information_to_accompany_raw_data_Fairlamb.csv (27.9 KB), 2HourDataForPCA.csv, 110DegCDataForPCA.csv, EXTRAC_1.CSV, EXTRAC_2.CSV, highMediumLowRanges.csv, readme.txt, and six LC-MS raw-data zips of 1.4-1.9 GB each. The landing page lists every file as… (license: CC BY)\n- [https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41467-024-47939-5/MediaObjects/41467_2024_47939_MOESM3_ESM.csv](https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41467-024-47939-5/MediaObjects/41467_2024_47939_MOESM3_ESM.csv): Nature Communications Source Data CSV (9.9 KB): IR in operando reaction-monitoring time courses, not the HTE outcome table (license: CC BY 4.0 (article license))\n- [https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41467-024-47939-5/MediaObjects/41467_2024_47939_MOESM1_ESM.pdf](https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41467-024-47939-5/MediaObjects/41467_2024_47939_MOESM1_ESM.pdf): Supplementary Information PDF (10.5 MB): experimental details and representative NMR data (license: CC BY 4.0 (article license))\n\n## Pitfalls\n\nOutcomes are product distributions, with many products and side products per reaction, quantified as LC-MS peak areas or normalised responses rather than yields. Each reaction needs multiple product entries with a clear analysis type. The PCA tables may be processed or normalised values. SMILES must be built from the SI. Raw LC-MS archives are too large to use as review evidence. The IR Source Data is kinetic monitoring (time-course), which is different from the endpoint HTE data.\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:b1fb254ef92515eb24b3fa1933c2b406ad7f295265c3cd352d70d985adc687d5",
"size_bytes": 3706,
"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": [],
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"score": null
},
"api": {
"problem": "/api/problems/prb_7xp5lid1mo",
"revision": "/api/problems/prb_7xp5lid1mo/revisions/1",
"mcp": "start_attempt {\"problem\":\"ord-clarke-2024-pd-cross-coupling-complexity\",\"revision\":1,\"provenance\":\"mixed\"}"
}
}