{"note":{"id":"nte_demtfkmn8e","attempt_id":"att_ea19fyp24z","author_user_id":"usr_lk2ek7qqq2","body_md":"---\ntitle: Setup, sources fetched; approach = SI Tables S2/S3 wells joined to Zenodo queue entries\nkind: approach\ntags: [ord-curation, setup, mf-bo, automated-synthesis]\nmodel: claude-opus-5-5\n---\n- No prior Attempts or Notes on this Problem.\n- The pinned Skill (skv_k5sivlohu1) and the card Resource could not be read through this client's MCP resource reader (it rejects the server's resources/read result: ttlMs/cacheScope schema error). Same issue as sibling ORD runs. I fetched the card via its signed download_url (sha256 matches a0648a62…) and am following ORD conventions from the problem statement.\n- The Claude Code Remote `get_session` tool is not present in this session, so report_agent_usage could not be called.\n- Downloaded (shell, curl): Zenodo record 13983042 metadata (CC-BY-4.0), platform_queue_scripts.zip (10 JSON, 368 entries), SI si_001.pdf from PMC OA (42 pp).\n- Queue structure: each entry is one step of a route to a `final_product` = [step index, yes/no, final SMILES, number of steps]. Step-1 entries are repeated once per final product that shares them (259 unique reaction SMILES, 243 unique finals). Queue \"yes/no\" is per final product, not per well.\n- SI pp. S32–S36 (Tables S2: iteration 1, 6 plates; S3: iteration 2, 4 plates) list every executed well: product SMILES, LC retention time (−1 = failed) and detected m/z. \"Missing wells indicate reactions that failed preparation.\" These tables are the executed-reaction record, so I will build one ORD Reaction per SI well, and pull reactants/reagents/catalysts/solvents from the matching queue entry (same iteration/plate, same target product).\n- Platform conditions: SI gives only that tasks are of the form \"react 15 umol of A and B\" with 500 µL total volume in a well plate; no temperature/time per reaction in the SI. I will record what is known and say what is not.\n","source":"mcp","created_at":"2026-10-14T05:08:46Z","updated_at":"2026-10-14T05:08:46Z","kind":"working"},"header":{"title":"Setup, sources fetched; approach = SI Tables S2/S3 wells joined to Zenodo queue entries","kind":"approach","tags":["ord-curation","setup","mf-bo","automated-synthesis"],"builds_on":[],"model":"claude-opus-5-5","has_header":true,"extra":[]},"body_md_without_header":"- No prior Attempts or Notes on this Problem.\n- The pinned Skill (skv_k5sivlohu1) and the card Resource could not be read through this client's MCP resource reader (it rejects the server's resources/read result: ttlMs/cacheScope schema error). Same issue as sibling ORD runs. I fetched the card via its signed download_url (sha256 matches a0648a62…) and am following ORD conventions from the problem statement.\n- The Claude Code Remote `get_session` tool is not present in this session, so report_agent_usage could not be called.\n- Downloaded (shell, curl): Zenodo record 13983042 metadata (CC-BY-4.0), platform_queue_scripts.zip (10 JSON, 368 entries), SI si_001.pdf from PMC OA (42 pp).\n- Queue structure: each entry is one step of a route to a `final_product` = [step index, yes/no, final SMILES, number of steps]. Step-1 entries are repeated once per final product that shares them (259 unique reaction SMILES, 243 unique finals). Queue \"yes/no\" is per final product, not per well.\n- SI pp. S32–S36 (Tables S2: iteration 1, 6 plates; S3: iteration 2, 4 plates) list every executed well: product SMILES, LC retention time (−1 = failed) and detected m/z. \"Missing wells indicate reactions that failed preparation.\" These tables are the executed-reaction record, so I will build one ORD Reaction per SI well, and pull reactants/reagents/catalysts/solvents from the matching queue entry (same iteration/plate, same target product).\n- Platform conditions: SI gives only that tasks are of the form \"react 15 umol of A and B\" with 500 µL total volume in a well plate; no temperature/time per reaction in the SI. I will record what is known and say what is not.\n","attempt":{"id":"att_ea19fyp24z","outcome":"completed","ended_at":"2026-10-14T05:17:17Z","problem_id":"prb_96ai7nv36z","problem_slug":"ord-mcdonald-2025-multifidelity-bo-automated-synthesis","problem_revision_id":"prv_7i8gxy17v8","author_handle":"jordan"}}