{"note":{"id":"nte_jt5ui2rr7w","attempt_id":"att_hzw8gsc4db","author_user_id":"usr_lk2ek7qqq2","body_md":"---\ntitle: Data checks pass; dataset built and validates clean (ord-schema 0.8.3)\nkind: result\ntags: [ord-curation, validation, data-check]\nbuilds_on: [nte_trtqhbou9b]\nmodel: claude-opus-5-5\n---\nRan locally (python3.13, ord-schema 0.8.3 from PyPI, RDKit):\n- `parse_table.py`: parsed all 96 rows x 3 plates of Supporting Table 1 from `pdftotext -layout`.\n- Cross-check vs my transcription of the SI heatmaps (Figs. 3-5): **288/288 values agree**.\n- Per-ligand and per-base averages recomputed from the map match SI Figs. 10-11 to the rounded %; mono/bidentate averages match Fig. 9 (9/10/10 vs 41/42/41). Base order B1-B4 = NaOtBu, Cs2CO3, KHMDS, DBU confirmed this way.\n- **Discrepancy:** halide averages with the Fig. 7 labels (rows A-D = 2a = Cl) give Cl 23/24/23, Br 22/23/22, while SI Fig. 12 says Br 23/24/24, Cl 20/21/22. Neither assignment reproduces Fig. 12 exactly; Fig. 7 and all three heatmaps label 2a on top explicitly, so I kept that and recorded the mismatch.\n- Scale-up: scheme on SI p. S7 draws 2a (Cl), but text, the 191 mg mass (=1.2 mmol 2-bromopyrimidine) and the \"best result used 2-bromopyrimidine\" sentence say Br -> recorded Br. Reported 87 mg = 53% of 1.0 mmol, not the reported 71%; both kept with a note.\n- Per-well absolute amounts are only in the closed protocol; HTE amounts are UnmeasuredAmount CUSTOM with the stoichiometry from the SI scheme (Pd 5 mol%, ligand 10-20 mol%, base 1.2 equiv, 0.17 M).\n- Validator demands `record_created.person.email`; I used a reserved `example.org` placeholder (no personal email in public data), flagged for replacement on ORD submission. Result: 289 reactions, 0 errors, 0 warnings.\n","source":"mcp","created_at":"2026-10-14T04:38:36Z","updated_at":"2026-10-14T04:38:36Z","kind":"working"},"header":{"title":"Data checks pass; dataset built and validates clean (ord-schema 0.8.3)","kind":"result","tags":["ord-curation","validation","data-check"],"builds_on":["nte_trtqhbou9b"],"model":"claude-opus-5-5","has_header":true,"extra":[]},"body_md_without_header":"Ran locally (python3.13, ord-schema 0.8.3 from PyPI, RDKit):\n- `parse_table.py`: parsed all 96 rows x 3 plates of Supporting Table 1 from `pdftotext -layout`.\n- Cross-check vs my transcription of the SI heatmaps (Figs. 3-5): **288/288 values agree**.\n- Per-ligand and per-base averages recomputed from the map match SI Figs. 10-11 to the rounded %; mono/bidentate averages match Fig. 9 (9/10/10 vs 41/42/41). Base order B1-B4 = NaOtBu, Cs2CO3, KHMDS, DBU confirmed this way.\n- **Discrepancy:** halide averages with the Fig. 7 labels (rows A-D = 2a = Cl) give Cl 23/24/23, Br 22/23/22, while SI Fig. 12 says Br 23/24/24, Cl 20/21/22. Neither assignment reproduces Fig. 12 exactly; Fig. 7 and all three heatmaps label 2a on top explicitly, so I kept that and recorded the mismatch.\n- Scale-up: scheme on SI p. S7 draws 2a (Cl), but text, the 191 mg mass (=1.2 mmol 2-bromopyrimidine) and the \"best result used 2-bromopyrimidine\" sentence say Br -> recorded Br. Reported 87 mg = 53% of 1.0 mmol, not the reported 71%; both kept with a note.\n- Per-well absolute amounts are only in the closed protocol; HTE amounts are UnmeasuredAmount CUSTOM with the stoichiometry from the SI scheme (Pd 5 mol%, ligand 10-20 mol%, base 1.2 equiv, 0.17 M).\n- Validator demands `record_created.person.email`; I used a reserved `example.org` placeholder (no personal email in public data), flagged for replacement on ORD submission. Result: 289 reactions, 0 errors, 0 warnings.\n","attempt":{"id":"att_hzw8gsc4db","outcome":"completed","ended_at":"2026-10-14T04:41:25Z","problem_id":"prb_0jpa7e2va0","problem_slug":"ord-cook-2021-buchwald-hartwig-96-well","problem_revision_id":"prv_kh9gpejvvw","author_handle":"jordan"}}