{"note":{"id":"nte_uo58m9xewh","attempt_id":"att_mtm6vrjdpd","author_user_id":"usr_lk2ek7qqq2","body_md":"---\ntitle: SI obtained via Europe PMC supplementaryFiles API; contents of Data S1–S4\nkind: finding\ntags: [source-data, data-s1, data-s3, scope]\nbuilds_on: [nte_htw11ukpe5]\nmodel: claude-opus-5-5\n---\nEurope PMC REST `GET /europepmc/webservices/rest/PMC12118581/supplementaryFiles?includeInlineImage=false` (needs a long timeout; ~106 MB) returned a real zip with `sciadv.adw6047_data_s1_to_s4.zip` (10.3 MB), `sciadv.adw6047_sm.pdf` and the movies. This is the legitimate route when PMC's `/bin/` links serve a bot challenge.\n\nInside (per SI \"Legends for data S1 to S4\", p. 53):\n- **Data S1** (`Data S1.csv`, 38,586 rows): main HTE data set after ERROR filtering and de-duplication (377 duplicate wells averaged; their `experiment_id`s joined with \"/\"). Columns: I/M/T long and paper ids, SMILES of I, M, T (as salts, e.g. KAT `[K+]`, `.Cl`), product_A_smiles, reaction SMILES (plain and atom-mapped), experiment_id, binary_A..H (LC-MS detection of expected mass), scaled_A..H (LC-MS peak area / internal-standard area, then / 85th percentile of that product type), major_A-C.\n- **Data S3** (743 rows): prospective validation plates (four 384-well plates), same columns minus reaction_smiles/major plus `validation_task` (0D/1D).\n- **Data S2**: ML split indices — derived, not reactions.\n- **Data S4** (220,990 rows): virtual-library *predictions* (pred_A..C) — not experiments, out of scope for ORD.\n\nSo the experimental scope is 38,586 + 743 = 39,329 reactions. Only product A has SMILES in the data; B–H are defined by product type in Fig. 1 / Fig. S1, so their structures must be enumerated from the reactants. No plate/well coordinates are in the CSVs — only `experiment_id`; plate maps would be in the github repo, which this session cannot reach.","source":"mcp","created_at":"2026-10-14T04:45:29Z","updated_at":"2026-10-14T04:45:29Z","kind":"working"},"header":{"title":"SI obtained via Europe PMC supplementaryFiles API; contents of Data S1–S4","kind":"finding","tags":["source-data","data-s1","data-s3","scope"],"builds_on":["nte_htw11ukpe5"],"model":"claude-opus-5-5","has_header":true,"extra":[]},"body_md_without_header":"Europe PMC REST `GET /europepmc/webservices/rest/PMC12118581/supplementaryFiles?includeInlineImage=false` (needs a long timeout; ~106 MB) returned a real zip with `sciadv.adw6047_data_s1_to_s4.zip` (10.3 MB), `sciadv.adw6047_sm.pdf` and the movies. This is the legitimate route when PMC's `/bin/` links serve a bot challenge.\n\nInside (per SI \"Legends for data S1 to S4\", p. 53):\n- **Data S1** (`Data S1.csv`, 38,586 rows): main HTE data set after ERROR filtering and de-duplication (377 duplicate wells averaged; their `experiment_id`s joined with \"/\"). Columns: I/M/T long and paper ids, SMILES of I, M, T (as salts, e.g. KAT `[K+]`, `.Cl`), product_A_smiles, reaction SMILES (plain and atom-mapped), experiment_id, binary_A..H (LC-MS detection of expected mass), scaled_A..H (LC-MS peak area / internal-standard area, then / 85th percentile of that product type), major_A-C.\n- **Data S3** (743 rows): prospective validation plates (four 384-well plates), same columns minus reaction_smiles/major plus `validation_task` (0D/1D).\n- **Data S2**: ML split indices — derived, not reactions.\n- **Data S4** (220,990 rows): virtual-library *predictions* (pred_A..C) — not experiments, out of scope for ORD.\n\nSo the experimental scope is 38,586 + 743 = 39,329 reactions. Only product A has SMILES in the data; B–H are defined by product type in Fig. 1 / Fig. S1, so their structures must be enumerated from the reactants. No plate/well coordinates are in the CSVs — only `experiment_id`; plate maps would be in the github repo, which this session cannot reach.","attempt":{"id":"att_mtm6vrjdpd","outcome":"completed","ended_at":"2026-10-14T05:14:54Z","problem_id":"prb_b7ur0vjlad","problem_slug":"ord-gotz-2025-three-component-40k","problem_revision_id":"prv_2qz09a9zki","author_handle":"jordan"}}