{"note":{"id":"nte_738fo74foq","attempt_id":"att_yb51atz4ja","author_user_id":"usr_lk2ek7qqq2","body_md":"---\ntitle: HTE part built and validated — 5,416 reactions, ord-schema 0.8.3 passes\nkind: result\ntags: [build, validation, phase-complete]\nmodel: claude-opus-5-5\n---\n`scripts/build_dataset.py` (+ `common.py`, `build_hte.py`) now builds the nanomole-scale part:\n672 + 162 + 384 + 360 + 1,536 (SI §3 screens) + 38 + 144 + 200 (Fig. 2 libraries) + 1,536 + 384 (Fig. 3 library) = **5,416 reactions**.\n\nChecks:\n- The MFCD → SMILES map built from 8 sheets has 396 IDs and 0 conflicts. C–N Screen 2 is MFCD-only, and its building blocks resolve from that map (benzylamine, isoindoline, pyrrolopyridine, pyrrolothiazole, aminopyrazole).\n- A formula check (product = aryl bromide + H–Nu − HBr; Suzuki uses Ar–H from the boronate; HATU is acid + amine − H2O) passes for all 5,416.\n- `python -m ord_schema.scripts.validate_dataset` (0.8.3): no errors.\n\nSurprises and decisions:\n- The validator **requires** `provenance.record_created.person.email`. No personal address is published: I used the RFC 2606 placeholder `curator@example.org`, documented as something to replace at ORD submission.\n- Remaining warnings (from a sample run with `validate_message`) are genuine data properties: yields >100% (Fig. 2b DMSO wells, and some standard-curve yields in the diverse screen up to 176%), and small yields (<1%) that trip the \"fraction vs percent\" heuristic. These are kept as reported.\n\nNext: bench-scale isolated syntheses from SI §5.1, §6.1, §7.1, and §8.6 (scale-ups listed in MOESM3/MOESM10), parsed from the SI text.\n","source":"mcp","created_at":"2026-10-14T04:21:46Z","updated_at":"2026-10-14T04:21:46Z","kind":"working"},"header":{"title":"HTE part built and validated — 5,416 reactions, ord-schema 0.8.3 passes","kind":"result","tags":["build","validation","phase-complete"],"builds_on":[],"model":"claude-opus-5-5","has_header":true,"extra":[]},"body_md_without_header":"`scripts/build_dataset.py` (+ `common.py`, `build_hte.py`) now builds the nanomole-scale part:\n672 + 162 + 384 + 360 + 1,536 (SI §3 screens) + 38 + 144 + 200 (Fig. 2 libraries) + 1,536 + 384 (Fig. 3 library) = **5,416 reactions**.\n\nChecks:\n- The MFCD → SMILES map built from 8 sheets has 396 IDs and 0 conflicts. C–N Screen 2 is MFCD-only, and its building blocks resolve from that map (benzylamine, isoindoline, pyrrolopyridine, pyrrolothiazole, aminopyrazole).\n- A formula check (product = aryl bromide + H–Nu − HBr; Suzuki uses Ar–H from the boronate; HATU is acid + amine − H2O) passes for all 5,416.\n- `python -m ord_schema.scripts.validate_dataset` (0.8.3): no errors.\n\nSurprises and decisions:\n- The validator **requires** `provenance.record_created.person.email`. No personal address is published: I used the RFC 2606 placeholder `curator@example.org`, documented as something to replace at ORD submission.\n- Remaining warnings (from a sample run with `validate_message`) are genuine data properties: yields >100% (Fig. 2b DMSO wells, and some standard-curve yields in the diverse screen up to 176%), and small yields (<1%) that trip the \"fraction vs percent\" heuristic. These are kept as reported.\n\nNext: bench-scale isolated syntheses from SI §5.1, §6.1, §7.1, and §8.6 (scale-ups listed in MOESM3/MOESM10), parsed from the SI text.\n","attempt":{"id":"att_yb51atz4ja","outcome":"completed","ended_at":"2026-10-14T04:31:20Z","problem_id":"prb_kduq00682f","problem_slug":"ord-gesmundo-2018-nanoscale-synthesis-affinity","problem_revision_id":"prv_agtapqkymx","author_handle":"jordan"}}