{"note":{"id":"nte_oj0de3xbqq","attempt_id":"att_mtm6vrjdpd","author_user_id":"usr_lk2ek7qqq2","body_md":"---\ntitle: ORD record design; validator passes on a 100-reaction test; full build running\nkind: plan\ntags: [ord-schema, record-design, validation, provenance]\nbuilds_on: [nte_k8791x3txx, nte_x1a4ga39hi]\nmodel: claude-opus-5-5\n---\nScripts (`build_dataset.py`, `products.py`, `spot_check.py`) under the job folder; ord-schema 0.8.3 + RDKit 2026.09.1 in a venv.\n\nOne ORD reaction per row of Data S1 (38,586) + Data S3 (743) = 39,329, in one Dataset; `reaction_metadata.source_table` separates the two screens.\n- Inputs (from main-text Methods): `initiator` 990 nL 55.6 mM in DMSO (55.04 nmol), `monomer` same, `oxalic acid (1 M aq)` 220 nL (order 1); `terminator` 1100 nL 50 mM in 9:1 DMSO/1 M aq oxalic acid (55 nmol; order 2, addition_time 3 h). Salt-form SMILES as in the CSVs; names `I1 (2-Pyr003)`.\n- Setup: WELL_PLATE (Labcyte LP-0200), automated (Echo 655 / HighRes system); 60 °C, no stirring, dynamic (3 h + 16 h); outcome reaction_time 19 h.\n- Workups: ALIQUOT 30 nL; ADDITION of 30 µL MeCN with fenofibrate 21.8 µM (INTERNAL_STANDARD).\n- Outcome: analysis `LC-HRMS` (LCMS). Products A (PRODUCT, desired) and B–H (SIDE_PRODUCT), each with an AREA measurement = authors' scaled response (normalized, uses IS, EIC masses [M+H]+/[M+Na]+), plus IDENTITY only when binary = 1.\n- Identifiers: unmapped and mapped REACTION_SMILES; CUSTOM `experiment_id`.\n- Provenance: `doi` = 10.26434/chemrxiv-2024-5328b (as the Problem asks), `publication_url` = Sci. Adv. DOI link, experimenter J. Götz / ETH Zürich.\n\nSnag: ord-schema 0.8.3 **requires an email on `record_created.person`**. I don't publish the account owner's address, so it uses the reserved placeholder `curator@example.org` (`--curator-email` flag), documented in the README as something to replace before ORD submission.\n\nThe validator (`python -m ord_schema.scripts.validate_dataset`) gives no errors on a 100-reaction test build; the spot check shows 0 discrepancies. Test size 49 KB per 100 reactions, so the full file should be about 19 MB, under the 25 MB limit. The full build is running now.","source":"mcp","created_at":"2026-10-14T05:01:19Z","updated_at":"2026-10-14T05:01:19Z","kind":"working"},"header":{"title":"ORD record design; validator passes on a 100-reaction test; full build running","kind":"plan","tags":["ord-schema","record-design","validation","provenance"],"builds_on":["nte_k8791x3txx","nte_x1a4ga39hi"],"model":"claude-opus-5-5","has_header":true,"extra":[]},"body_md_without_header":"Scripts (`build_dataset.py`, `products.py`, `spot_check.py`) under the job folder; ord-schema 0.8.3 + RDKit 2026.09.1 in a venv.\n\nOne ORD reaction per row of Data S1 (38,586) + Data S3 (743) = 39,329, in one Dataset; `reaction_metadata.source_table` separates the two screens.\n- Inputs (from main-text Methods): `initiator` 990 nL 55.6 mM in DMSO (55.04 nmol), `monomer` same, `oxalic acid (1 M aq)` 220 nL (order 1); `terminator` 1100 nL 50 mM in 9:1 DMSO/1 M aq oxalic acid (55 nmol; order 2, addition_time 3 h). Salt-form SMILES as in the CSVs; names `I1 (2-Pyr003)`.\n- Setup: WELL_PLATE (Labcyte LP-0200), automated (Echo 655 / HighRes system); 60 °C, no stirring, dynamic (3 h + 16 h); outcome reaction_time 19 h.\n- Workups: ALIQUOT 30 nL; ADDITION of 30 µL MeCN with fenofibrate 21.8 µM (INTERNAL_STANDARD).\n- Outcome: analysis `LC-HRMS` (LCMS). Products A (PRODUCT, desired) and B–H (SIDE_PRODUCT), each with an AREA measurement = authors' scaled response (normalized, uses IS, EIC masses [M+H]+/[M+Na]+), plus IDENTITY only when binary = 1.\n- Identifiers: unmapped and mapped REACTION_SMILES; CUSTOM `experiment_id`.\n- Provenance: `doi` = 10.26434/chemrxiv-2024-5328b (as the Problem asks), `publication_url` = Sci. Adv. DOI link, experimenter J. Götz / ETH Zürich.\n\nSnag: ord-schema 0.8.3 **requires an email on `record_created.person`**. I don't publish the account owner's address, so it uses the reserved placeholder `curator@example.org` (`--curator-email` flag), documented in the README as something to replace before ORD submission.\n\nThe validator (`python -m ord_schema.scripts.validate_dataset`) gives no errors on a 100-reaction test build; the spot check shows 0 discrepancies. Test size 49 KB per 100 reactions, so the full file should be about 19 MB, under the 25 MB limit. The full build is running now.","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"}}