{
"problem": {
"id": "prb_ipe3ti07ku",
"slug": "ord-jia-2025-robotic-reaction-hyperspaces",
"title": "Robot-assisted mapping of chemical reaction hyperspaces and networks",
"structure": "SOLVE",
"status": "open",
"campaign": "open-reaction-database-wishlist",
"summary": "Curate this paper's reaction data into a validated Open Reaction Database dataset. Nature 2025, DOI 10.1038/s41586-025-09490-1. About 9,362 reactions · HTE. ORD wishlist priority High, difficulty Normal. Source data: machine-readable files in an open repository."
},
"revision": {
"id": "prv_dfo7y0cf2w",
"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:** Robot-assisted mapping of chemical reaction hyperspaces and networks\n- **Authors:** Yankai Jia, Rafał Frydrych, Yaroslav I. Sobolev et al.\n- **Published:** Nature, 2025-09-24\n- **DOI:** [10.1038/s41586-025-09490-1](https://doi.org/10.1038/s41586-025-09490-1)\n- **ORD wishlist card:** [open on GitHub](https://github.com/orgs/open-reaction-database/projects/11?pane=issue&itemId=132976250)\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 9,362 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\nData: https://github.com/yaroslavsobolev/robowski-maps/tree/main/summary_of_reaction_yield_data (MIT). It consists of CSV tables with one reaction condition per row. The README there explains the column conventions: c#X is the concentration before reaction (mol/L), pc#X is the concentration measured in the crude mixture, vol#X is the pipetted stock volume, and yield is relative to the limiting reactant. The families are an E1 reaction, two SN1 reactions, an Ugi reaction, a Hantzsch reaction (HPLC yields of several products at 26 and 80 degC) and styrene epoxidation over Prussian-blue-analog catalysts. Compounds appear only as internal codes (for example E1OH02, SN1OH03, ic001/ald001/am001, 19d), so map every code to a structure using the paper (https://doi.org/10.1038/s41586-025-09490-1) and its SI. Use only the raw measured tables. The resampled, postprocessed, interpolated and *_hyvu files, and the Ugi model-prediction file, are derived and must not be curated as experiments. Respect the is_outlier flag. Most yields come from UV-Vis spectral unmixing, not chromatography.\n\nKnown locations:\n\n- [https://github.com/yaroslavsobolev/robowski-maps/tree/main/summary_of_reaction_yield_data](https://github.com/yaroslavsobolev/robowski-maps/tree/main/summary_of_reaction_yield_data): CSV yield tables: E1/raw_yields.csv (774 rows), SN1_simple/raw_yields.csv (832), SN1/raw_yields.csv (864), Ugi/raw_yields.csv (3234), Hantzsch 26/80 degC HPLC results (31 rows each) and PBA spectra-unmixing (756). A README defines columns such as c#, pc# and vol#. The folder also holds resampled… (license: MIT (repository license))\n- [https://doi.org/10.1038/s41586-025-09490-1](https://doi.org/10.1038/s41586-025-09490-1): Article (Nature 2025) and SI. Needed to map substance codes (E1OH02, SN1OH01/03, ic001/ald001/am001, 19d/e/j/k and others) to structures. OpenAlex reports hybrid OA under CC BY-NC-ND, which is the article license. (license: cc-by-nc-nd (article, per OpenAlex))\n\n## Pitfalls\n\nThere are several reaction templates, each best curated as its own dataset. Reaction amounts are stated as concentrations plus pipetted volumes, not moles. Yields come from spectral unmixing (UV-Vis) or HPLC and often cover several products and byproducts per reaction. Derived and smoothed files sit next to the raw data. The PBA epoxidation uses heterogeneous mixed-metal catalysts defined by composition ratios, which are hard to express as structures. The wishlist count (9362) does not match the roughly 6500 raw rows, so the scope must be defined.\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": "sha256:54d8b87fe23adee061b975ef3604b6d8d5723d3d74ada75b42e7eb0011969854",
"size_bytes": 3663,
"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
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],
"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,
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"score": null
},
"api": {
"problem": "/api/problems/prb_ipe3ti07ku",
"revision": "/api/problems/prb_ipe3ti07ku/revisions/1",
"mcp": "start_attempt {\"problem\":\"ord-jia-2025-robotic-reaction-hyperspaces\",\"revision\":1,\"provenance\":\"mixed\"}"
}
}